Package org.rcsb.cif.model
Class BaseBlock
- java.lang.Object
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- org.rcsb.cif.model.BaseBlock
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description AtomSitegetAtomSite()Data items in the ATOM_SITE category record details about the atom sites in a macromolecular crystal structure, such as the positional coordinates, atomic displacement parameters, magnetic moments and directions.AtomSiteAnisotropgetAtomSiteAnisotrop()Data items in the ATOM_SITE_ANISOTROP category record details about anisotropic displacement parameters.AtomSitesgetAtomSites()Data items in the ATOM_SITES category record details about the crystallographic cell and cell transformations, which are common to all atom sites.AtomSitesAltgetAtomSitesAlt()Data items in the ATOM_SITES_ALT category record details about the structural ensembles that should be generated from atom sites or groups of atom sites that are modelled in alternative conformations in this data block.AtomSitesAltEnsgetAtomSitesAltEns()Data items in the ATOM_SITES_ALT_ENS category record details about the ensemble structure generated from atoms with various alternative conformation IDs.AtomSitesAltGengetAtomSitesAltGen()Data items in the ATOM_SITES_ALT_GEN category record details about the interpretation of multiple conformations in the structure.AtomSitesFootnotegetAtomSitesFootnote()Data items in the ATOM_SITES_FOOTNOTE category record detailed comments about an atom site or a group of atom sites.AtomTypegetAtomType()Data items in the ATOM_TYPE category record details about the properties of the atoms that occupy the atom sites, such as the atomic scattering factors.AuditgetAudit()Data items in the AUDIT category record details about the creation and subsequent updating of the data block.AuditAuthorgetAuditAuthor()Data items in the AUDIT_AUTHOR category record details about the author(s) of the data block.AuditConformgetAuditConform()Data items in the AUDIT_CONFORM category describe the dictionary versions against which the data names appearing in the current data block are conformant.AuditContactAuthorgetAuditContactAuthor()Data items in the AUDIT_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the content of this data block.AuditLinkgetAuditLink()Data items in the AUDIT_LINK category record details about the relationships between data blocks in the current CIF.StringgetBlockHeader()The header of thisBlock.CategorygetCategory(String name)Retrieve a particularCategoryby name.List<String>getCategoryNames()CellgetCell()Data items in the CELL category record details about the crystallographic cell parameters.CellMeasurementgetCellMeasurement()Data items in the CELL_MEASUREMENT category record details about the measurement of the crystallographic cell parameters.CellMeasurementReflngetCellMeasurementRefln()Data items in the CELL_MEASUREMENT_REFLN category record details about the reflections used to determine the crystallographic cell parameters.ChemCompgetChemComp()Data items in the CHEM_COMP category give details about each of the chemical components from which the relevant chemical structures can be constructed, such as name, mass or charge.ChemCompAnglegetChemCompAngle()Data items in the CHEM_COMP_ANGLE category record details about angles in a chemical component.ChemCompAtomgetChemCompAtom()Data items in the CHEM_COMP_ATOM category record details about the atoms in a chemical component.ChemCompBondgetChemCompBond()Data items in the CHEM_COMP_BOND category record details about the bonds between atoms in a chemical component.ChemCompChirgetChemCompChir()Data items in the CHEM_COMP_CHIR category provide details about the chiral centres in a chemical component.ChemCompChirAtomgetChemCompChirAtom()Data items in the CHEM_COMP_CHIR_ATOM category enumerate the atoms bonded to a chiral atom within a chemical component.ChemCompLinkgetChemCompLink()Data items in the CHEM_COMP_LINK category give details about the links between chemical components.ChemCompPlanegetChemCompPlane()Data items in the CHEM_COMP_PLANE category provide identifiers for the planes in a chemical component.ChemCompPlaneAtomgetChemCompPlaneAtom()Data items in the CHEM_COMP_PLANE_ATOM category enumerate the atoms in a plane within a chemical component.ChemCompTorgetChemCompTor()Data items in the CHEM_COMP_TOR category record details about the torsion angles in a chemical component.ChemCompTorValuegetChemCompTorValue()Data items in the CHEM_COMP_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_COMP_TOR list.ChemicalgetChemical()Data items in the CHEMICAL category would not in general be used in a macromolecular CIF.ChemicalConnAtomgetChemicalConnAtom()Data items in the CHEMICAL_CONN_ATOM category would not, in general, be used in a macromolecular CIF.ChemicalConnBondgetChemicalConnBond()Data items in the CHEMICAL_CONN_BOND category would not, in general, be used in a macromolecular CIF.ChemicalFormulagetChemicalFormula()Data items in the CHEMICAL_FORMULA category would not, in general, be used in a macromolecular CIF.ChemLinkgetChemLink()Data items in the CHEM_LINK category give details about the links between chemical components.ChemLinkAnglegetChemLinkAngle()Data items in the CHEM_LINK_ANGLE category record details about angles in a link between chemical components.ChemLinkBondgetChemLinkBond()Data items in the CHEM_LINK_BOND category record details about bonds in a link between components in the chemical structure.ChemLinkChirgetChemLinkChir()Data items in the CHEM_LINK_CHIR category provide details about the chiral centres in a link between two chemical components.ChemLinkChirAtomgetChemLinkChirAtom()Data items in the CHEM_LINK_CHIR_ATOM category enumerate the atoms bonded to a chiral atom in a link between two chemical components.ChemLinkPlanegetChemLinkPlane()Data items in the CHEM_LINK_PLANE category provide identifiers for the planes in a link between two chemical components.ChemLinkPlaneAtomgetChemLinkPlaneAtom()Data items in the CHEM_LINK_PLANE_ATOM category enumerate the atoms in a plane in a link between two chemical components.ChemLinkTorgetChemLinkTor()Data items in the CHEM_LINK_TOR category record details about the torsion angles in a link between two chemical components.ChemLinkTorValuegetChemLinkTorValue()Data items in the CHEM_LINK_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_LINK_TOR list.CitationgetCitation()Data items in the CITATION category record details about the literature cited as being relevant to the contents of the data block.CitationAuthorgetCitationAuthor()Data items in the CITATION_AUTHOR category record details about the authors associated with the citations in the CITATION list.CitationEditorgetCitationEditor()Data items in the CITATION_EDITOR category record details about the editors associated with the books or book chapters cited in the CITATION list.ColumngetColumn(String name)Retrieve aColumnby name.ComputinggetComputing()Data items in the COMPUTING category record details about the computer programs used in the crystal structure analysis.DatabasegetDatabase()Data items in the DATABASE category have been superseded by data items in the DATABASE_2 category.Database2getDatabase2()Data items in the DATABASE_2 category record details about the database identifiers of the data block.DatabasePDBCaveatgetDatabasePDBCaveat()Data items in the DATABASE_PDB_CAVEAT category record details about features of the data block flagged as 'caveats' by the Protein Data Bank (PDB).DatabasePDBMatrixgetDatabasePDBMatrix()The DATABASE_PDB_MATRIX category provides placeholders for transformation matrices and vectors used by the Protein Data Bank (PDB).DatabasePDBRemarkgetDatabasePDBRemark()Data items in the DATABASE_PDB_REMARK category record details about the data block as archived by the Protein Data Bank (PDB).DatabasePDBRevgetDatabasePDBRev()Data items in the DATABASE_PDB_REV category record details about the history of the data block as archived by the Protein Data Bank (PDB).DatabasePDBRevRecordgetDatabasePDBRevRecord()Data items in the DATABASE_PDB_REV_RECORD category record details about specific record types that were changed in a given revision of a PDB entry.DatabasePDBTvectgetDatabasePDBTvect()The DATABASE_PDB_TVECT category provides placeholders for the TVECT matrices and vectors used by the Protein Data Bank (PDB).DiffrngetDiffrn()Data items in the DIFFRN category record details about the diffraction data and their measurement.DiffrnAttenuatorgetDiffrnAttenuator()Data items in the DIFFRN_ATTENUATOR category record details about the diffraction attenuator scales employed.DiffrnDetectorgetDiffrnDetector()Data items in the DIFFRN_DETECTOR category describe the detector used to measure the scattered radiation, including any analyser and post-sample collimation.DiffrnMeasurementgetDiffrnMeasurement()Data items in the DIFFRN_MEASUREMENT category record details about the device used to orient and/or position the crystal during data measurement and the manner in which the diffraction data were measured.DiffrnOrientMatrixgetDiffrnOrientMatrix()Data items in the DIFFRN_ORIENT_MATRIX category record details about the orientation matrix used in the measurement of the diffraction data.DiffrnOrientReflngetDiffrnOrientRefln()Data items in the DIFFRN_ORIENT_REFLN category record details about the reflections that define the orientation matrix used in the measurement of the diffraction intensities.DiffrnRadiationgetDiffrnRadiation()Data items in the DIFFRN_RADIATION category describe the radiation used in measuring the diffraction intensities, its collimation and monochromatization before the sample.DiffrnRadiationWavelengthgetDiffrnRadiationWavelength()Data items in the DIFFRN_RADIATION_WAVELENGTH category describe the wavelength of the radiation used to measure the diffraction intensities.DiffrnReflngetDiffrnRefln()Data items in the DIFFRN_REFLN category record details about the intensities in the diffraction data set identified by _diffrn_refln.diffrn_id.DiffrnReflnsgetDiffrnReflns()Data items in the DIFFRN_REFLNS category record details about the set of intensities measured in the diffraction experiment.DiffrnReflnsClassgetDiffrnReflnsClass()Data items in the DIFFRN_REFLNS_CLASS category record details about the classes of reflections measured in the diffraction experiment.DiffrnScaleGroupgetDiffrnScaleGroup()Data items in the DIFFRN_SCALE_GROUP category record details of the scaling factors applied to place all intensities in the reflection lists on a common scale.DiffrnSourcegetDiffrnSource()Data items in the DIFFRN_SOURCE category record details of the source of radiation used in the diffraction experiment.DiffrnStandardReflngetDiffrnStandardRefln()Data items in the DIFFRN_STANDARD_REFLN category record details about the reflections treated as standards during the measurement of a set of diffraction intensities.DiffrnStandardsgetDiffrnStandards()Data items in the DIFFRN_STANDARDS category record details about the set of standard reflections used to monitor intensity stability during the measurement of diffraction intensities.Em2dCrystalEntitygetEm2dCrystalEntity()Data items in the EM_SYMMETRY_2DX category record 2D crystal symmetry parameters utilized in a 3DEM reconstruction.Em2dProjectionSelectiongetEm2dProjectionSelection()Data items in the EM_2D_PROJECTION_SELECTION category record details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs.Em3dCrystalEntitygetEm3dCrystalEntity()Data items in the EM_SYMMETRY_3DX category record 3D crystal symmetry parameters utilized in 3DEM reconstruction averaging.Em3dFittinggetEm3dFitting()Data items in the 3D_FITTING category record details of the method of fitting atomic coordinates from a PDB file into a 3d-em volume map fileEm3dFittingListgetEm3dFittingList()Data items in the 3D_FITTING_LIST category lists the methods of fitting atomic coordinates from a PDB file into a 3d-em volume map fileEm3dReconstructiongetEm3dReconstruction()Data items in the EM_3D_RECONSTRUCTION category record details of the 3D reconstruction procedure from 2D projections.EmAdmingetEmAdmin()Administration-related data itemsEmAssemblygetEmAssembly()Data items in the EM_ASSEMBLY category record details about the imaged EM sample.EmAuthorListgetEmAuthorList()Category to collect the authors of this entryEmBuffergetEmBuffer()Data items in the BUFFER category record details of the sample buffer.EmBufferComponentgetEmBufferComponent()Buffer categoryEmCrystalFormationgetEmCrystalFormation()Description of growth of a 2D, 3D, or helical crystal array.EmCtfCorrectiongetEmCtfCorrection()Description of the Contrast Transfer Function (CTF) correctionEmDbReferencegetEmDbReference()Category holds links to raw data sources for the entry, e.g., held by a remote server.EmDbReferenceAuxiliarygetEmDbReferenceAuxiliary()Category holds links to raw data sources for the entry, e.g., held by a remote server.EmDepositorInfogetEmDepositorInfo()Data items in the EM_DEPOSITOR INFO category record parameters for EM depositions that are provided by the depositorEmDepuigetEmDepui()Some internal items to power the deposition interfaceEmDetectorgetEmDetector()Data items in the EM_DETECTOR category record details of the image detector type.EmDiffractiongetEmDiffraction()Microscopy parameters relevant only for crystallographyEmDiffractionShellgetEmDiffractionShell()Statistical parameters for electron diffraction measurements within a resolution shellEmDiffractionStatsgetEmDiffractionStats()Statistical parameters for electron diffraction measurementsEmEmbeddinggetEmEmbedding()Sugar embedding categoryEmEntityAssemblygetEmEntityAssembly()Data items in the EM_ENTITY_ASSEMBLY category record details about each component of the complex.EmEntityAssemblyMolwtgetEmEntityAssemblyMolwt()Data items in this category record details about the molecular weight of an assembly component of the sample.EmEntityAssemblyNaturalsourcegetEmEntityAssemblyNaturalsource()Data items in this category record taxonomic details about the natural source for EM assemblies and assembly components.EmEntityAssemblyRecombinantgetEmEntityAssemblyRecombinant()Data items in this category record details about recombinant expression of the assembly or assembly component.EmEulerAngleAssignmentgetEmEulerAngleAssignment()Category to describe the euler angle assignementEmExperimentgetEmExperiment()Data items in the EM_EXPERIMENT category provide high-level classification of the EM experiment.EmFiducialMarkersgetEmFiducialMarkers()Description of fiducial markers.EmFigureDepositorInfogetEmFigureDepositorInfo()Listing of image files (figures) associated with an EMDB entryEmFinalClassificationgetEmFinalClassification()Information about the final image classificationEmFocusedIonBeamgetEmFocusedIonBeam()Description of sectioning by focused_ion_beamEmFscCurvegetEmFscCurve()Data items in the EMD_VALIDATION_FSC_CURVE category record details of the Fourier Shell Correlation (FSC) curve file.EmGridPretreatmentgetEmGridPretreatment()Data items describing glow discharge pretreatment for an EM gridEmHelicalEntitygetEmHelicalEntity()Data items in the EM_HELICAL_ENTITY category record details for a helical or filament type of assembly component.EmHighPressureFreezinggetEmHighPressureFreezing()Description of high pressure freezingEmImageProcessinggetEmImageProcessing()Data items in the EM_IMAGE_PROCESSING category record details of the EM image processing procedure.EmImageRecordinggetEmImageRecording()Data items in the EM_IMAGE_RECORDING category record details of the image recording (either film/microdensitometer or electronic detector) and parameters for image digitization.EmImageScansgetEmImageScans()Data items in the EM_IMAGE_SCANS category record details of the image scanning device (microdensitometer) and parameters for digitization of the image.EmImaginggetEmImaging()Data items in the EM_IMAGING category record details about the parameters used in imaging the sample in the electron microscope.EmImagingOpticsgetEmImagingOptics()Description of a few specialist optics apparatusEmInterpretFiguregetEmInterpretFigure()Listing of all layer line files associated with the EM entryEmLayerLinesgetEmLayerLines()Listing of all layer line files associated with the EM entryEmLayerLinesDepositorInfogetEmLayerLinesDepositorInfo()Listing of layer line files associated with the EM entryEmMapgetEmMap()Data items in the EMD_MAP category record parameters of the CCP4 binary-format map file header (see ftp://ftp.wwpdb.org/pub/emdb/doc/map_format/EMDB_mapFormat_v1.0.pdf), parameters derived from the map header, pixel size, contour level, and annotation details from the depositor.EmMapDepositorInfogetEmMapDepositorInfo()Data items in the EM_MAP_DEPOSITOR INFO category record map parameters that are provided by the depositorEmMaskDepositorInfogetEmMaskDepositorInfo()Data items in the EM_MASK_DEPOSITOR_INFO category record mask parameters that are provided by the depositorEmObsoletegetEmObsolete()List of EMD entries made obsolete by this entry.EmParticleSelectiongetEmParticleSelection()Data items in this category record details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs.EmSamplePreparationgetEmSamplePreparation()Data items in the EM_SAMPLE_PREPARATION category record details of sample conditions prior to and upon loading onto grid support.EmSampleSupportgetEmSampleSupport()Data items in the EM_SAMPLE_SUPPORT category record details of the electron microscope grid type, grid support film and pretreatment of whole before sample is appliedEmShadowinggetEmShadowing()Data items related to shadowing of an EM specimenEmSingleParticleEntitygetEmSingleParticleEntity()Data items in the EM_SINGLE_PARTICLE_ENTITY category provide the details of the symmetry for a single particle entity type.EmSoftwaregetEmSoftware()Description of the software that was used for data collection, data processing, data analysis, structure calculations and refinement.EmSpecimengetEmSpecimen()Data items in the EMD_SPECIMEN category record details about specimens prepared for imaging by electron microscopy.EmStaininggetEmStaining()Staining categoryEmStartModelgetEmStartModel()The startup model employed to begin refinement of the parameters for a 3DEM reconstructionEmStructureFactorsgetEmStructureFactors()Listing of all structure factor files associated with the EM entryEmStructureFactorsDepositorInfogetEmStructureFactorsDepositorInfo()Structure factor files associated with the EM entryEmSupersedegetEmSupersede()List of newer entries that replace this entry.EmSupportFilmgetEmSupportFilm()Data items to describe films supporting the specimenEmTomographygetEmTomography()Microscopy parameters only relevant for tomographyEmTomographySpecimengetEmTomographySpecimen()Description specimen preparation for imaging using tomography.EmUltramicrotomygetEmUltramicrotomy()Description of sectioning by ultramicrotomyEmVirusEntitygetEmVirusEntity()Data items in the EM_VIRUS_ENTITY category record details of the icosahedral virus.EmVirusNaturalHostgetEmVirusNaturalHost()Data items in this category record details of a virus entity.EmVirusShellgetEmVirusShell()Data items in the EMD_VIRUS_SHELL category record details of the viral shell number, shell diameter, and icosahedral triangulation number.EmVitrificationgetEmVitrification()Data items in the EM_VITRIFICATION category record details about the method and cryogen used in rapid freezing of the sample on the grid prior to its insertion in the electron microscopeEmVolumeSelectiongetEmVolumeSelection()Volume selection in image processingEntitygetEntity()Data items in the ENTITY category record details (such as chemical composition, name and source) about the molecular entities that are present in the crystallographic structure.EntityKeywordsgetEntityKeywords()Data items in the ENTITY_KEYWORDS category specify keywords relevant to the molecular entities.EntityLinkgetEntityLink()Data items in the ENTITY_LINK category give details about the links between entities.EntityNameComgetEntityNameCom()Data items in the ENTITY_NAME_COM category record the common name or names associated with the entity.EntityNameSysgetEntityNameSys()Data items in the ENTITY_NAME_SYS category record the systematic name or names associated with the entity and the system that was used to construct the systematic name.EntityPolygetEntityPoly()Data items in the ENTITY_POLY category record details about the polymer, such as the type of the polymer, the number of monomers and whether it has nonstandard features.EntityPolySeqgetEntityPolySeq()Data items in the ENTITY_POLY_SEQ category specify the sequence of monomers in a polymer.EntitySrcGengetEntitySrcGen()Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated.EntitySrcNatgetEntitySrcNat()Data items in the ENTITY_SRC_NAT category record details of the source from which the entity was obtained in cases where the entity was isolated directly from a natural tissue.EntrygetEntry()There is only one item in the ENTRY category, _entry.id.EntryLinkgetEntryLink()Data items in the ENTRY_LINK category record the relationships between the current data block identified by _entry.id and other data blocks within the current file which may be referenced in the current data block.ExptlgetExptl()Data items in the EXPTL category record details about the experimental work prior to the intensity measurements and details about the absorption-correction technique employed.ExptlCrystalgetExptlCrystal()Data items in the EXPTL_CRYSTAL category record the results of experimental measurements on the crystal or crystals used, such as shape, size or density.ExptlCrystalFacegetExptlCrystalFace()Data items in the EXPTL_CRYSTAL_FACE category record details of the crystal faces.ExptlCrystalGrowgetExptlCrystalGrow()Data items in the EXPTL_CRYSTAL_GROW category record details about the conditions and methods used to grow the crystal.ExptlCrystalGrowCompgetExptlCrystalGrowComp()Data items in the EXPTL_CRYSTAL_GROW_COMP category record details about the components of the solutions that were 'mixed' (by whatever means) to produce the crystal.GeomgetGeom()Data items in the GEOM and related (GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_HBOND and GEOM_TORSION) categories record details about the molecular geometry as calculated from the contents of the ATOM, CELL and SYMMETRY data.GeomAnglegetGeomAngle()Data items in the GEOM_ANGLE category record details about the bond angles as calculated from the contents of the ATOM, CELL and SYMMETRY data.GeomBondgetGeomBond()Data items in the GEOM_BOND category record details about the bond lengths as calculated from the contents of the ATOM, CELL and SYMMETRY data.GeomContactgetGeomContact()Data items in the GEOM_CONTACT category record details about interatomic contacts as calculated from the contents of the ATOM, CELL and SYMMETRY data.GeomHbondgetGeomHbond()Data items in the GEOM_HBOND category record details about hydrogen bonds as calculated from the contents of the ATOM, CELL and SYMMETRY data.GeomTorsiongetGeomTorsion()Data items in the GEOM_TORSION category record details about torsion angles as calculated from the contents of the ATOM, CELL and SYMMETRY data.Ihm2demClassAverageFittinggetIhm2demClassAverageFitting()Data items in the IHM_2DEM_CLASS_AVERAGE_FITTING category records the details of the fitting of the model to the 2DEM class averages used in the IHM modeling.Ihm2demClassAverageRestraintgetIhm2demClassAverageRestraint()Data items in the IHM_2DEM_CLASS_AVERAGE_RESTRAINT category records the details of the 2DEM class averages used in the IHM modeling.Ihm3demRestraintgetIhm3demRestraint()Data items in the IHM_3DEM_RESTRAINT category records the details of the 3DEM maps used as restraints in the IHM modeling.IhmCrossLinkListgetIhmCrossLinkList()Data items in the IHM_CROSS_LINK_LIST category records the list of spatial restraints derived from chemical crosslinking experiment.IhmCrossLinkRestraintgetIhmCrossLinkRestraint()Data items in the IHM_CROSS_LINK_RESTRAINT category enumerates the implementation details of the chemical crosslinking restraints in the integrative modeling.IhmCrossLinkResultgetIhmCrossLinkResult()Data items in the IHM_CROSS_LINK_RESULT category records the results of the crosslinking restraints in the IHM modeling.IhmCrossLinkResultParametersgetIhmCrossLinkResultParameters()Data items in the IHM_CROSS_LINK_RESULT_PARAMETERS category records the results of the crosslinking restraint parameters in the IHM modeling.IhmDatasetExternalReferencegetIhmDatasetExternalReference()Category provides additional details regarding input data hosted externally at other resources.IhmDatasetGroupgetIhmDatasetGroup()Category provides a mechanism to group datasets.IhmDatasetListgetIhmDatasetList()Category holds the list of all datasets used in the IHM modeling.IhmDatasetRelatedDbReferencegetIhmDatasetRelatedDbReference()Category holds information related to data sources for the entry.IhmDerivedDistanceRestraintgetIhmDerivedDistanceRestraint()Data items in the IHM_DERIVED_DISTANCE_RESTRAINT category records the list of distance restraints used in the integrative modeling experiment.IhmEnsembleInfogetIhmEnsembleInfo()Data items in the IHM_ENSEMBLE_INFO category records the details of the model clusters or ensembles obtained after sampling.IhmExternalFilesgetIhmExternalFiles()Category provides details regarding external files.IhmExternalReferenceInfogetIhmExternalReferenceInfo()Category holds links to other external data sources for the I/H model entry.IhmFeatureListgetIhmFeatureList()IHM_FEATURE_LIST is the high level category that provides defintions to select atoms/residues from polymeric and non-polymeric entities.IhmGaussianObjEnsemblegetIhmGaussianObjEnsemble()Data items in the IHM_GAUSSIAN_OBJ_ENSEMBLE category records the details of the gaussian objects representing an ensemble or cluster of models.IhmGaussianObjSitegetIhmGaussianObjSite()Data items in the IHM_GAUSSIAN_OBJ_SITE category records the details of the gaussian objects modeled in the integrative structural model.IhmGeometricObjectAxisgetIhmGeometricObjectAxis()Data items in the IHM_GEOMETRIC_OBJECT_AXIS category records the details of an axis used in a spatial restraint.IhmGeometricObjectCentergetIhmGeometricObjectCenter()Data items in the IHM_GEOMETRIC_OBJECT_CENTER category records the center of geometric objects used as restraints in the integrative modeling study.IhmGeometricObjectDistanceRestraintgetIhmGeometricObjectDistanceRestraint()Data items in the IHM_GEOMETRIC_OBJECT_DISTANCE_RESTRAINT category records the details of distance restraints involving geometric objects.IhmGeometricObjectHalfTorusgetIhmGeometricObjectHalfTorus()Data items in the IHM_GEOMETRIC_OBJECT_HALF_TORUS category records the parameters of half-torus that represents a membrane.IhmGeometricObjectListgetIhmGeometricObjectList()Data items in the IHM_GEOMETRIC_OBJECT_LIST category records the list of geometric objects used as restraints in the integrative modeling study.IhmGeometricObjectPlanegetIhmGeometricObjectPlane()Data items in the IHM_GEOMETRIC_OBJECT_PLANE category records the details of a plane used in a spatial restraint.IhmGeometricObjectSpheregetIhmGeometricObjectSphere()Data items in the IHM_GEOMETRIC_OBJECT_SPHERE category records the parameters of a sphere.IhmGeometricObjectTorusgetIhmGeometricObjectTorus()Data items in the IHM_GEOMETRIC_OBJECT_TORUS category records the parameters of a torus.IhmGeometricObjectTransformationgetIhmGeometricObjectTransformation()Data items in the IHM_GEOMETRIC_OBJECT_TRANSFORMATION category records the details of the rotation matrix and translation vector applied for transforming the geometric object.IhmHydroxylRadicalFpRestraintgetIhmHydroxylRadicalFpRestraint()Data items in the IHM_HYDROXYL_RADICAL_FP_RESTRAINT category records the restraints derived from hydroxyl radical footprinting experiment.IhmInterfaceResidueFeaturegetIhmInterfaceResidueFeature()Data items in the IHM_INTERFACE_RESIDUE_FEATURE category captures the details of residues that are identified to be at the binding interface from experiments.IhmLocalizationDensityFilesgetIhmLocalizationDensityFiles()Data items in the IHM_LOCALIZATION_DENSITY_FILES category records the details of files that provide information regarding localization densities of ensembles.IhmModelingPostProcessgetIhmModelingPostProcess()Data items in the IHM_MODELING_POST_PROCESS category records the details of the post processing of the models/results of the modeling protocol.IhmModelingProtocolgetIhmModelingProtocol()Data items in the IHM_MODELING_PROTOCOL category records the step-wise details of the integrative modeling workflow.IhmModelListgetIhmModelList()Data items in the IHM_MODEL_LIST category record the details of the models being deposited.IhmModelRepresentationgetIhmModelRepresentation()Data items in the IHM_MODEL_REPRESENTATION category records the details about the architecture and representation of structural models created by the integrative model building tasks.IhmModelRepresentativegetIhmModelRepresentative()Data items in the IHM_MODEL_REPRESENTATIVE category record the details of the representative model in an ensemble or cluster.IhmMultiStateModelinggetIhmMultiStateModeling()Data items in the IHM_MULTI_STATE_MODELING category records the details of the multi-state modeling protocol, if applicable.IhmNonPolyFeaturegetIhmNonPolyFeature()Data items in the IHM_NON_POLY_FEATURE category provides the defintions required to select a non-polymeric (ligand) feature.IhmOrderedEnsemblegetIhmOrderedEnsemble()Data items in the IHM_ORDERED_ENSEMBLE category records the details of the ensembles ordered by time or other order.IhmPolyAtomFeaturegetIhmPolyAtomFeature()Data items in the IHM_POLY_ATOM_FEATURE category provides the defintions required to select specific atoms.IhmPolyResidueFeaturegetIhmPolyResidueFeature()Data items in the IHM_POLY_RESIDUE_FEATURE category provides the defintions required to select a specific residue or a set of residues that may or may not be in a contiguous range.IhmPredictedContactRestraintgetIhmPredictedContactRestraint()Data items in the IHM_PREDICTED_CONTACT_RESTRAINT category records the list of predicted contacts used in the integrative modeling experiment.IhmPseudoSiteFeaturegetIhmPseudoSiteFeature()Data items in the IHM_PSEUDO_SITE_FEATURE category records the details of pseudo positions for the features listed in IHM_FEATURE_LIST.IhmRelatedDatasetsgetIhmRelatedDatasets()Category holds information about related datasets, where one is derived from the other.IhmResiduesNotModeledgetIhmResiduesNotModeled()Data items in the IHM_RESIDUES_NOT_MODELED category record the details of the residues that are defined in the IHM_STRUCT_ASSEMBLY category but are missing in the three-dimensional model (ATOM_SITE, IHM_SPHERE_OBJ_SITE, IHM_GAUSSIAN_OBJ_SITE categories) i.e., residues in the assembly that are not modeled.IhmSasRestraintgetIhmSasRestraint()Data items in the IHM_SAS_RESTRAINT category records the details of the SAS data used as restraints in the IHM modeling.IhmSphereObjSitegetIhmSphereObjSite()Data items in the IHM_SPHERE_OBJ_SITE category records the details of the spherical objects modeled in the integrative structural model.IhmStartingComparativeModelsgetIhmStartingComparativeModels()Data items in the IHM_STARTING_COMPARATIVE_MODELS category records additional details about comparative models used as starting inputs in the integrative model building process.IhmStartingComputationalModelsgetIhmStartingComputationalModels()Data items in the IHM_STARTING_COMPUTATIONAL_MODELS category records additional details about computational models used as starting inputs in the integrative model building process.IhmStartingModelCoordgetIhmStartingModelCoord()Data items in the IHM_STARTING_MODEL_COORD category records the coordinates for structural templates used as starting inputs in the integrative model building tasks.IhmStartingModelDetailsgetIhmStartingModelDetails()Data items in the IHM_STARTING_MODEL_DETAILS category records the details about structural models used as starting inputs in the integrative model building process.IhmStartingModelSeqDifgetIhmStartingModelSeqDif()Data items in the IHM_STARTING_MODEL_SEQ_DIF category provide a mechanism for indicating and annotating point differences between the sequence of the entity or biological unit described in the data block and the sequence of the starting model used in the integrative modeling referenced from a database.IhmStructAssemblygetIhmStructAssembly()Data items in the IHM_STRUCT_ASSEMBLY category records the details of the structural assemblies and used in the IHM modeling.IhmStructAssemblyClassgetIhmStructAssemblyClass()Data items in the IHM_STRUCT_ASSEMBLY_CLASS category provides details regarding the structural assembly classes.IhmStructAssemblyClassListgetIhmStructAssemblyClassList()Data items in the IHM_STRUCT_ASSEMBLY_CLASS_LIST category lists all the structural assembly classes relevant to the entry.IhmStructAssemblyDetailsgetIhmStructAssemblyDetails()Data items in the IHM_STRUCT_ASSEMBLY_DETAILS category provides additional details regarding the structure assembly.JournalgetJournal()Data items in the JOURNAL category record details about the book-keeping by the journal staff when processing a data block submitted for publication.JournalIndexgetJournalIndex()Data items in the JOURNAL_INDEX category are used to list terms used to generate the journal indexes.NdbOriginalNdbCoordinatesgetNdbOriginalNdbCoordinates()Placeholder category for PDB coordinate data.NdbStructConfNagetNdbStructConfNa()Data items in the NDB_STRUCT_CONF_NA category describes secondary structure features in this entry.NdbStructFeatureNagetNdbStructFeatureNa()Data items in the NDB_STRUCT_FEATURE_NA category describes tertiary and other special structural features in this entry.NdbStructNaBasePairgetNdbStructNaBasePair()Data items in the NDB_STRUCT_NA_BASE_PAIR category record details of base pairing interactions.NdbStructNaBasePairStepgetNdbStructNaBasePairStep()Data items in the NDB_STRUCT_NA_BASE_PAIR_STEP category record details of base pair step interactions.PdbxAtlasgetPdbxAtlas()Gives information about the organization of the NDB Structural Atlas.PdbxAtomSiteAnisoTlsgetPdbxAtomSiteAnisoTls()Data items in the PDBX_ATOM_SITE_ANISO_TLS category record details about the TLS contribution to anisotropic displacement parameters.PdbxAuditgetPdbxAudit()The PDBX_AUDIT holds current version information.PdbxAuditAuthorgetPdbxAuditAuthor()Data items in the PDBX_AUDIT_AUTHOR category record details about the author(s) of the data block.PdbxAuditConformExtensiongetPdbxAuditConformExtension()Data items in the PDBX_AUDIT_CONFORM_EXTENSION category describe extension dictionary versions against which the data names appearing the current data block are conformant.PdbxAuditRevisionCategorygetPdbxAuditRevisionCategory()Data items in the PDBX_AUDIT_REVISION_CATEGORY category report the data categories associated with a PDBX_AUDIT_REVISION_HISTORY record.PdbxAuditRevisionDetailsgetPdbxAuditRevisionDetails()Data items in the PDBX_audit_revision_details category record descriptions of changes associated with PDBX_AUDIT_REVISION_HISTORY records.PdbxAuditRevisionGroupgetPdbxAuditRevisionGroup()Data items in the PDBX_AUDIT_revision_group category report the content groups associated with a PDBX_AUDIT_REVISION_HISTORY record.PdbxAuditRevisionHistorygetPdbxAuditRevisionHistory()Data items in the PDBX_AUDIT_REVISION_HISTORY category record the revision history for a data entry.PdbxAuditRevisionItemgetPdbxAuditRevisionItem()Data items in the PDBX_AUDIT_REVISION_ITEM category report the data items associated with a PDBX_AUDIT_REVISION_HISTORY record.PdbxAuditSupportgetPdbxAuditSupport()Data items in the PDBX_AUDIT_SUPPORT category record details about funding support for the entry.PdbxBondDistanceLimitsgetPdbxBondDistanceLimits()This category provides a table of upper and lower distance limits used as criteria in determining covalent bonds.PdbxBranchSchemegetPdbxBranchScheme()The PDBX_BRANCH_SCHEME category provides residue level nomenclature mapping for branch chain entities.PdbxBuffergetPdbxBuffer()Data items in the PDBX_BUFFER category record details of the sample buffer.PdbxBufferComponentsgetPdbxBufferComponents()Constituents of buffer in samplePdbxChemCompAtomEditgetPdbxChemCompAtomEdit()Data items in the PDBX_CHEM_COMP_ATOM_EDIT category provide atom level editing instructions to be applied to imported chemical components.PdbxChemCompAtomFeaturegetPdbxChemCompAtomFeature()Data items in the PDBX_CHEM_COMP_ATOM_FEATURE category provide a selected list of atom level features for the chemical component.PdbxChemCompAtomRelatedgetPdbxChemCompAtomRelated()PDBX_CHEM_COMP_ATOM_RELATED provides atom level nomenclature mapping between two related chemical components.PdbxChemCompAuditgetPdbxChemCompAudit()Data items in the PDBX_CHEM_COMP_AUDIT category records the status and tracking information for this component.PdbxChemCompBondEditgetPdbxChemCompBondEdit()Data items in the PDBX_CHEM_COMP_BOND_EDIT category provide bond level editing instructions to be applied to imported chemical components.PdbxChemCompDepositorInfogetPdbxChemCompDepositorInfo()Data items in the PDBX_CHEM_COMP_DEPOSITOR_INFO category record additional details provided by depositors about deposited chemical components.PdbxChemCompDescriptorgetPdbxChemCompDescriptor()Data items in the CHEM_COMP_DESCRIPTOR category provide string descriptors of component chemical structure.PdbxChemCompFeaturegetPdbxChemCompFeature()Additional features associated with the chemical component.PdbxChemCompIdentifiergetPdbxChemCompIdentifier()Data items in the CHEM_COMP_IDENTIFIER category provide identifiers for chemical components.PdbxChemCompImportgetPdbxChemCompImport()Data items in the PDBX_CHEM_COMP_IMPORT category identify existing chemical components to be imported into the current component definition.PdbxChemCompInstanceDepositorInfogetPdbxChemCompInstanceDepositorInfo()Data items in the PDBX_CHEM_COMP_INSTANCE_DEPOSITOR_INFO category records depositor provided information about the chemical context of component instances.PdbxChemCompModelgetPdbxChemCompModel()Data items in the PDBX_CHEM_COMP_MODEL category give details about each of the chemical component model instances.PdbxChemCompModelAtomgetPdbxChemCompModelAtom()Data items in the PDBX_CHEM_COMP_MODEL_ATOM category record coordinates for the chemical component model instance.PdbxChemCompModelAuditgetPdbxChemCompModelAudit()Data items in the PDBX_CHEM_COMP_MODEL_AUDIT category records the status and tracking information for this component model instance.PdbxChemCompModelBondgetPdbxChemCompModelBond()Data items in the PDBX_CHEM_COMP_MODEL_BOND category record details about the bonds between atoms in a chemical component model instance.PdbxChemCompModelDescriptorgetPdbxChemCompModelDescriptor()Data items in the CHEM_COMP_MODEL_DESCRIPTOR category provide string descriptors for component model structures.PdbxChemCompModelFeaturegetPdbxChemCompModelFeature()Additional features associated with the chemical component.PdbxChemCompModelReferencegetPdbxChemCompModelReference()Additional features associated with the chemical component.PdbxChemCompNonstandardgetPdbxChemCompNonstandard()Data items in the PDBX_CHEM_COMP_NONSTANDARD category describes common nucleotide modifications and nonstandard features.PdbxChemCompRelatedgetPdbxChemCompRelated()PDBX_CHEM_COMP_RELATED describes the relationship between two chemical components.PdbxChemCompSubcomponentEntityListgetPdbxChemCompSubcomponentEntityList()Data items in the pdbx_chem_comp_subcomponent_entity_list category list the constituent chemical entities and entity features in this chemical component.PdbxChemCompSubcomponentStructConngetPdbxChemCompSubcomponentStructConn()Data items in the pdbx_chem_comp_subcomponent_struct_conn list the chemical interactions among the subcomponents in the chemical component.PdbxChemCompSynonymsgetPdbxChemCompSynonyms()PDBX_CHEM_COMP_SYNONYMS holds chemical name and synonym correspondences.PdbxChemCompUploadDepositorInfogetPdbxChemCompUploadDepositorInfo()Data items in the PDBX_CHEM_COMP_UPLOAD_DEPOSITOR_INFO category record details of the uploaded files related to depositor provided chemical assignments.PdbxColumninfogetPdbxColumninfo()PdbxConnectgetPdbxConnect()Local data items describing ligand and monomer chemical features.PdbxConnectAtomgetPdbxConnectAtom()Local data items describing ligand and monomer atom names and connectivity.PdbxConnectModificationgetPdbxConnectModification()Local data items describing ligand and monomer modifications.PdbxConnectTypegetPdbxConnectType()Local data items describing ligand and monomer type information.PdbxConstructgetPdbxConstruct()Data items in the PDBX_CONSTRUCT category specify a sequence of nucleic acids or amino acids.PdbxConstructFeaturegetPdbxConstructFeature()Data items in the PDBX_CONSTRUCT_FEATURE category may be used to specify various properties of a nucleic acid sequence used during protein production.PdbxContactAuthorgetPdbxContactAuthor()Data items in the PDBX_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the contents of this data block.PdbxCoordgetPdbxCoord()Gives information about what kind of coordinates are available.PdbxCoordinateModelgetPdbxCoordinateModel()The details of the composition of the coordinate model.PdbxCrystalAlignmentgetPdbxCrystalAlignment()Data in the PDBX_CRYSTAL_ALIGNMENT are produced by log files from programs during indexingPdbxDatabaseMessagegetPdbxDatabaseMessage()The PDBX_DATABASE_MESSAGE category provides information about correspondance related to a structure deposition.PdbxDatabasePDBMastergetPdbxDatabasePDBMaster()The PDBX_DATABASE_PDB_MASTER category provides placeholders for the count of various PDB record types.PdbxDatabasePDBObsSprgetPdbxDatabasePDBObsSpr()The PDBX_DATABASE_PDB_OBS_SPR category provides placeholders for information on obsolete/superseded PDB entriesPdbxDatabasePdbOmitgetPdbxDatabasePdbOmit()Data items in the PDBX_DATABASE_PDB_OMIT category record list PDB record names that should be omitted in the PDB format file.PdbxDatabaseProcgetPdbxDatabaseProc()Internal records to track the data processing cycle.PdbxDatabaseRelatedgetPdbxDatabaseRelated()Data items in PDBX_DATABASE_RELATED contain references to entries that are related to the this entry.PdbxDatabaseRemarkgetPdbxDatabaseRemark()Data items in the PDBX_DATABASE_REMARK category record keep additional information about the entry.PdbxDatabaseStatusgetPdbxDatabaseStatus()These are internal RCSB records to keep track of data processing and status of the entry.PdbxDatabaseStatusHistorygetPdbxDatabaseStatusHistory()The pdbx_database_status_history category records the time evolution of entry processing status.PdbxDataProcessingCellgetPdbxDataProcessingCell()Crystallographic cell specifications used in data processing.PdbxDataProcessingDetectorgetPdbxDataProcessingDetector()Details of the detector used at data collection site.PdbxDataProcessingReflnsgetPdbxDataProcessingReflns()Details of reflections used in data processing.PdbxDataProcessingStatusgetPdbxDataProcessingStatus()Data items in the PDBX_DATA_PROCESSING_STATUS category record data processing instructions for workflow processing tasks.PdbxDbrefgetPdbxDbref()These records are used in the DBREF record of a PDB file and are used as place holders for NDB ID's in PDB files.PdbxDccDensitygetPdbxDccDensity()Data items in the category record various overall metrics calculated by DCC and various wrapped programs (such as Xtriage, pointless, REFMAC ...).PdbxDccDensityCorrgetPdbxDccDensityCorr()Data items in the category record calculated metrics from various programs (such as phenix, refmac, cns, sfcheck).PdbxDccGeometrygetPdbxDccGeometry()Data items in the category record the overall deviations about geometry (such as bond length, angle, dihedral, chirality, planarity).PdbxDccMapgetPdbxDccMap()Data items in the category record residual map properties such as Real Space electron density Correlation Coefficient (RSCC), real space R factors (RSR) and the Zscores for each residue, the main/side chains.PdbxDccMapmangetPdbxDccMapman()Data items in the category record details from the output of mapman used by the DCC program.PdbxDccRsccMapmangetPdbxDccRsccMapman()Data items in this category record residual map properties such as correlation, real space Rfactors and the Zscore calculated from refmac and mapman.PdbxDccRsccMapmanOverallgetPdbxDccRsccMapmanOverall()Data items in the category record overall map properties such as correlation, real space Rfactors and the Zscore calculated from refmac and mapman.PdbxDepositGroupgetPdbxDepositGroup()Data items in the pdbx_deposit_group category provide identifiers and related information for groups of entries deposited in a collection.PdbxDepositGroupIndexgetPdbxDepositGroupIndex()Data items in the pdbx_deposit_group_index category provides details about the individual data files in the collection of deposited entries.PdbxDepositionMessageFileReferencegetPdbxDepositionMessageFileReference()Data items in the PDBX_DEPOSITION_MESSAGE_FILE_REFERENCE category record details of files references associated with messages defined in the PDBX_DEPOSITION_MESSAGE_INFO data category.PdbxDepositionMessageInfogetPdbxDepositionMessageInfo()Data items in the PDBX_DEPOSITION_MESSAGE_INFO category record internal messages within the depositon and annotation system.PdbxDepuiEntityFeaturesgetPdbxDepuiEntityFeatures()Data items in the PDBX_DEPUI_ENTITY_FEATURES category record status details related to the features of individual entities.PdbxDepuiEntityStatusFlagsgetPdbxDepuiEntityStatusFlags()Data items in the PDBX_DEPUI_ENTITY_STATUS_FLAGS category record status details related to individual entities.PdbxDepuiEntryDetailsgetPdbxDepuiEntryDetails()Data items in the PDBX_DEPUI_ENTRY_DETAILS category record information required to identify the depositor and route deposition to an appropriate processing site.PdbxDepuiStatusFlagsgetPdbxDepuiStatusFlags()Data items in the PDBX_DEPUI_STATUS_FLAGS category record status details used to maintain state within the wwPDB deposition system.PdbxDepuiUploadgetPdbxDepuiUpload()Data items in the PDBX_DEPUI_UPLOAD category record the details of uploaded data files.PdbxDepuiValidationStatusFlagsgetPdbxDepuiValidationStatusFlags()Data items in the PDBX_DEPUI_VALIDATION_STATUS_FLAGS category record status details that assess the status of selected validation diagnostics.PdbxDiffrnReflnsShellgetPdbxDiffrnReflnsShell()Data items in the DIFFRN_REFLNS_SHELL category record details about the reflection data set within shells of resolution.PdbxDistantSolventAtomsgetPdbxDistantSolventAtoms()Data items in the PDBX_DISTANT_SOLVENT_ATOMS category list the solvent atoms remote from any macromolecule.PdbxDomaingetPdbxDomain()Data items in the PDBX_DOMAIN category record information about domain definitions.PdbxDomainRangegetPdbxDomainRange()Data items in the PDBX_DOMAIN_RANGE category identify the beginning and ending points of polypeptide chain segments that form all or part of a domain.PdbxDrugInfogetPdbxDrugInfo()Data items in the PDBX_DRUG_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated.PdbxEntityAssemblygetPdbxEntityAssembly()The PDBX_ENTITY_ASSEMBLY category provides a chemical description of the biological assembly studied in terms of its constituent entities.PdbxEntityBranchgetPdbxEntityBranch()Data items in the PDBX_ENTITY_BRANCH category specify the list of branched entities and the type.PdbxEntityBranchLinkgetPdbxEntityBranchLink()Data items in the PDBX_ENTITY_BRANCH_LINK category give details about the linkages between components within a branched entity.PdbxEntityBranchListgetPdbxEntityBranchList()Data items in the PDBX_ENTITY_BRANCH_LIST category specify the list of monomers in a branched entity.PdbxEntityDescriptorgetPdbxEntityDescriptor()Data items in the PDBX_ENTITY_DESCRIPTOR category provide string descriptors of entity chemical structure.PdbxEntityFuncBindModegetPdbxEntityFuncBindMode()Data items in the PDBX_ENTITY_FUNC_BIND_MODE category describe characteristics of protein oligonucleotide binding.PdbxEntityFuncEnzymegetPdbxEntityFuncEnzyme()Data items in the PDBX_ENTITY_FUNC_ENZYME category describe characteristics of protein oligonucleotide binding in which the binding mode is enzymatic.PdbxEntityFuncOthergetPdbxEntityFuncOther()Data items in the PDBX_ENTITY_FUNC_OTHER category describe characteristics of protein oligonucleotide binding in which the binding mode is not classified.PdbxEntityFuncRegulatorygetPdbxEntityFuncRegulatory()Data items in the PDBX_ENTITY_FUNC_REGULATORY category describe characteristics of protein oligonucleotide binding in which the binding mode is regulatory.PdbxEntityFuncStructuralgetPdbxEntityFuncStructural()Data items in the PDBX_ENTITY_FUNC_STRUCTURAL category describe characteristics of protein oligonucleotide binding in which the binding mode is structural.PdbxEntityInstanceFeaturegetPdbxEntityInstanceFeature()Data items in the pdbx_entity_instance_feature category records special features of selected entity instances.PdbxEntityNamegetPdbxEntityName()The PDBX_ENTITY_NAME records additional name information for each entity.PdbxEntityNameInstancegetPdbxEntityNameInstance()Data items in the PDBX_ENTITY_NAME_INSTANCE category list names used to define entities with their associated database, entity, chain, and molecule identifiers.PdbxEntityNameTaxonomygetPdbxEntityNameTaxonomy()Data items in the PDBX_ENTITY_NAME_TAXONOMY category define the names and synonyms of the entity name taxonomy.PdbxEntityNameTaxonomyTreegetPdbxEntityNameTaxonomyTree()Data items in the PDBX_ENTITY_NAME_TAXONOMY_TREE category define the tree structure of the entity name taxonomy.PdbxEntityNonpolygetPdbxEntityNonpoly()PdbxEntityPolyCompLinkListgetPdbxEntityPolyCompLinkList()Data items in the PDBX_ENTITY_POLY_COMP_LINK_LIST category enumerate the the linkages between components within the polymer entity.PdbxEntityPolyDomaingetPdbxEntityPolyDomain()Data items in the PDBX_ENTITY_POLY_DOMAIN category specify domains of monomers within a polymer.PdbxEntityPolyNaNonstandardgetPdbxEntityPolyNaNonstandard()Data items in the PDBX_ENTITY_POLY_NA_NONSTANDARD category describe the nonstandard features of the nucleic acid polymer entities.PdbxEntityPolyNaTypegetPdbxEntityPolyNaType()Data items in the PDBX_ENTITY_POLY_NA_TYPE category describe type of nucleic acid polymer entities.PdbxEntityPolyProteinClassgetPdbxEntityPolyProteinClass()Data items in the PDBX_ENTITY_POLY_PROTEIN_CLASS category provides a top-level protein classification.PdbxEntityProdProtocolgetPdbxEntityProdProtocol()This category contains descriptive protocols for the production of this entity.PdbxEntitySrcGenCharactergetPdbxEntitySrcGenCharacter()This category contains details of protein characterisation.PdbxEntitySrcGenChromgetPdbxEntitySrcGenChrom()This category contains details for the chromatographic steps used in the purification of the protein.PdbxEntitySrcGenClonegetPdbxEntitySrcGenClone()This category contains details for the cloning steps used in the overall protein production process.PdbxEntitySrcGenCloneLigationgetPdbxEntitySrcGenCloneLigation()This category contains details for the ligation-based cloning steps used in the overall protein production process.PdbxEntitySrcGenCloneRecombinationgetPdbxEntitySrcGenCloneRecombination()This category contains details for the recombination-based cloning steps used in the overall protein production process.PdbxEntitySrcGenDepositorInfogetPdbxEntitySrcGenDepositorInfo()Data items in the PDBX_ENTITY_SRC_GEN_DEPOSITOR_INFO category record details of the source from which the entity was obtained in cases where the source was genetically manipulated.PdbxEntitySrcGenExpressgetPdbxEntitySrcGenExpress()This category contains details for the EXPRESSION steps used in the overall protein production process.PdbxEntitySrcGenExpressTimepointgetPdbxEntitySrcGenExpressTimepoint()This category contains details for OD time series used to monitor a given EXPRESSION step used in the overall protein production process.PdbxEntitySrcGenFractgetPdbxEntitySrcGenFract()This category contains details for the fraction steps used in the overall protein production process.PdbxEntitySrcGenLysisgetPdbxEntitySrcGenLysis()This category contains details for the cell lysis steps used in the overall protein production process.PdbxEntitySrcGenProdDigestgetPdbxEntitySrcGenProdDigest()This category contains details for the DIGEST steps used in the overall protein production process.PdbxEntitySrcGenProdOthergetPdbxEntitySrcGenProdOther()This category contains details for process steps that are not explicitly catered for elsewhere.PdbxEntitySrcGenProdOtherParametergetPdbxEntitySrcGenProdOtherParameter()This category contains parameters and values required to capture information about a particular process stepPdbxEntitySrcGenProdPcrgetPdbxEntitySrcGenProdPcr()This category contains details for the PCR steps used in the overall protein production process.PdbxEntitySrcGenProteolysisgetPdbxEntitySrcGenProteolysis()This category contains details for the protein purification tag removal steps used in the overall protein production processPdbxEntitySrcGenPuregetPdbxEntitySrcGenPure()This category contains details for the final purified protein product.PdbxEntitySrcGenRefoldgetPdbxEntitySrcGenRefold()This category contains details for the refolding steps used in the overall protein production process.PdbxEntitySrcSyngetPdbxEntitySrcSyn()The data items in category PDBX_ENTITY_SRC_SYN record the source details about chemically synthesized molecules.PdbxEntryDetailsgetPdbxEntryDetails()Data items in the PDBX_ENTRY_DETAILS category provide additional details about this entry.PdbxExptlCrystalCryoTreatmentgetPdbxExptlCrystalCryoTreatment()Data items in the PDBX_EXPTL_CRYSTAL_CRYO_TREATMENT category record details cryogenic treatments applied to this crystal.PdbxExptlCrystalGrowCompgetPdbxExptlCrystalGrowComp()Data items in the PDBX_EXPTL_CRYSTAL_GROW_COMP category record details about the components of the solutions that were 'mixed' to produce the crystal.PdbxExptlCrystalGrowSolgetPdbxExptlCrystalGrowSol()Data items in the PDBX_EXPTL_CRYSTAL_GROW_SOL category record details about the solutions that were 'mixed' to produce the crystal.PdbxExptlPdgetPdbxExptlPd()Data items in the pdbx_exptl_pd record information about powder sample preparations.PdbxFamilyGroupIndexgetPdbxFamilyGroupIndex()Data items in the PDBX_FAMILY_GROUP_INDEX category record the family membership in family groups.PdbxFamilyPrdAuditgetPdbxFamilyPrdAudit()Data items in the PDBX_FAMILY_PRD_AUDIT category records the status and tracking information for this family.PdbxFeatureAssemblygetPdbxFeatureAssembly()Data items in the PDBX_FEATURE_ASSEMBLY category records information about properties pertaining to this structural assembly.PdbxFeatureDomaingetPdbxFeatureDomain()Data items in the PDBX_FEATURE_DOMAIN category records information about properties pertaining to this structure domain.PdbxFeatureEntrygetPdbxFeatureEntry()Data items in the PDBX_FEATURE_ENTRY category records information about properties pertaining to this structure entry.PdbxFeatureMonomergetPdbxFeatureMonomer()Data items in the PDBX_FEATURE_MONOMER category records information about properties pertaining to particular monomers in this structure.PdbxFeatureSequenceRangegetPdbxFeatureSequenceRange()Data items in the PDBX_FEATURE_SEQUENCE_RANGE category records information about properties pertaining to this structure sequence_range.PdbxHelicalSymmetrygetPdbxHelicalSymmetry()Data items in the PDBX_HELICAL_SYMMETRY category record details about the helical symmetry group associated with this entry.PdbxHelicalSymmetryDepositorInfogetPdbxHelicalSymmetryDepositorInfo()Data items in the PDBX_HELICAL_SYMMETRY_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_HELICAL_SYMMETRY.PdbxHybridgetPdbxHybrid()Data items in the PDBX_HYBRID category are used to describe the chimeric characteristics of a DNA/RNA structure.PdbxInhibitorInfogetPdbxInhibitorInfo()Data items in the PDBX_INHIBITOR_INFO category are still used until the 'entity' categories are entered into the database, even though the inhibitor is repeated.PdbxIonInfogetPdbxIonInfo()Data items in the PDBX_ION_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated.PdbxLinkedEntitygetPdbxLinkedEntity()Data items in the PDBX_LINKED_ENTITY category record information about molecules composed of linked entities.PdbxLinkedEntityInstanceListgetPdbxLinkedEntityInstanceList()Data items in the PDBX_LINKED_ENTITY_INSTANCE_LIST category identify instance molecules represented as linked entities within an entry.PdbxLinkedEntityLinkListgetPdbxLinkedEntityLinkList()Data items in the PDBX_LINKED_ENTITY_LINK_LIST category give details about the linkages with molecules represented as linked entities.PdbxLinkedEntityListgetPdbxLinkedEntityList()Data items in the PDBX_LINKED_ENTITY_LIST category record the list of entity constituents for this molecule.PdbxMissingAtomNonpolygetPdbxMissingAtomNonpoly()Data items in the PDBX_MISSING_ATOM_NONPOLY category list the atoms missing in nonpolymer residues.PdbxMissingAtomPolygetPdbxMissingAtomPoly()Data items in the PDBX_MISSING_ATOM_POLY category lists atoms missing in polymer residues.PdbxMissingResidueListgetPdbxMissingResidueList()Provides a place-holder for PDB REMARK 465 data.PdbxMoleculegetPdbxMolecule()Data items in the PDBX_MOLECULE category identify reference molecules within a PDB entry.PdbxMoleculeFeaturesgetPdbxMoleculeFeatures()Data items in the PDBX_MOLECULE_FEATURES category record features of molecules within a PDB entry.PdbxMoleculeFeaturesDepositorInfogetPdbxMoleculeFeaturesDepositorInfo()Data items in the PDBX_MOLECULE_FEATURES_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_MOLECULE_FEATURES.PdbxNaStrandInfogetPdbxNaStrandInfo()Data items in the PDBX_NA_STRAND_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated.PdbxNaStructKeywdsgetPdbxNaStructKeywds()Data items in the PDBX_NA_STRUCT_KEYWDS category record give details about structural features of the NA.PdbxNmrAssignedChemShiftListgetPdbxNmrAssignedChemShiftList()Items in the assigned_chem_shift_list category provide information about a list of reported assigned chemical shift values.PdbxNmrChemShiftExperimentgetPdbxNmrChemShiftExperiment()Items in the chem_shift_experiment category provide pointers to the NMR experiments and samples used to collect the data for a set of reported assigned chemical shifts.PdbxNmrChemShiftRefgetPdbxNmrChemShiftRef()Items in the pdbx_nmr_chem_shift_ref category provide the chemical shift referencing values used in assigning the chemical shift positions for peaks in spectral peak lists and assigned atom chemical shifts.PdbxNmrChemShiftReferencegetPdbxNmrChemShiftReference()Items in the chem_shift_reference category define a set of chemical shift referencing parameters.PdbxNmrChemShiftSoftwaregetPdbxNmrChemShiftSoftware()Items in the chem_shift_software category provide pointers to the software category and methods category.PdbxNmrComputinggetPdbxNmrComputing()The table in this section is used to describe the software that was used for data collection, data processing, data analysis, structure calculations and refinement.PdbxNmrConstraintFilegetPdbxNmrConstraintFile()Items in the pdbx_nmr_constraint_file category record the name of the constraint file, the software used to calculate conformers with the constraint file, and the characteristics of the constraints in the constraint file.PdbxNmrConstraintsgetPdbxNmrConstraints()This section provides a tabulation of constraint data.PdbxNmrDetailsgetPdbxNmrDetails()Experimental details of the NMR study that have not been described elsewhere in this deposition.PdbxNmrEnsemblegetPdbxNmrEnsemble()This category contains the information that describes the ensemble of deposited structures.PdbxNmrEnsembleRmsgetPdbxNmrEnsembleRms()Structural statistics are derived from molecular dynamics and simulated annealing programs.PdbxNmrExptlgetPdbxNmrExptl()In this section, enter information on those experiments that were used to generate constraint data.PdbxNmrExptlSamplegetPdbxNmrExptlSample()The chemical constituents of each NMR sample.PdbxNmrExptlSampleConditionsgetPdbxNmrExptlSampleConditions()The experimental conditions used to for each sample.PdbxNmrForceConstantsgetPdbxNmrForceConstants()The final force constants, including units, employed for the various experimental constraints, covalent geometry constraints, and the non-bonded interaction terms in the target function used for simulated annealing.PdbxNmrRefinegetPdbxNmrRefine()Describe the method and details of the refinement of the deposited structure.PdbxNmrRepresentativegetPdbxNmrRepresentative()An average structure is often calculated in addition to the ensemble, or one of the ensemble is selected as a representative structure.PdbxNmrSampleDetailsgetPdbxNmrSampleDetails()Complete description of each NMR sample, including the solvent system used.PdbxNmrSoftwaregetPdbxNmrSoftware()Description of the software that was used for data collection, data processing, data analysis, structure calculations and refinement.PdbxNmrSoftwareTaskgetPdbxNmrSoftwareTask()Items in the pdbx_nmr_software_task category provide information about software workflow in the NMR experiment.PdbxNmrSpectralDimgetPdbxNmrSpectralDim()Items in the spectral_dim category describe the parameters of each dimension in the NMR experiment used to generate the spectral peak list.PdbxNmrSpectralPeakListgetPdbxNmrSpectralPeakList()Items in the pdbx_nmr_spectral_peak_list category provide information about a list of reported spectral peak characteristic values.PdbxNmrSpectralPeakSoftwaregetPdbxNmrSpectralPeakSoftware()Items in the pdbx_nmr_spectral_peak_software category provide pointers to the software category and methods category where descriptions of software applications and methods can be found.PdbxNmrSpectrometergetPdbxNmrSpectrometer()The details about each spectrometer used to collect data for this deposition.PdbxNmrSystematicChemShiftOffsetgetPdbxNmrSystematicChemShiftOffset()Items in the pdbx_nmr_systematic_chem_shift_offset category define chemical shift offsets that systematically affect all chemical shifts in a set of assigned chemical shifts for a specific nuclei.PdbxNmrUploadgetPdbxNmrUpload()Items in the pdbx_nmr_upload category provide information about the data files uploaded by a depositor using the deposition system.PdbxNonpolySchemegetPdbxNonpolyScheme()The PDBX_NONPOLY_SCHEME category provides residue level nomenclature mapping for non-polymer entities.PdbxNonstandardListgetPdbxNonstandardList()The information in this category is exclusively used to store the HET records of a PDB file.PdbxPdbCompndgetPdbxPdbCompnd()This is a place holder for the PDB COMPND.PdbxPdbSourcegetPdbxPdbSource()This is a place holder for the PDB SOURCE.PdbxPhasingDmgetPdbxPhasingDm()Data items in the PDBX_PHASING_DM category record details about density modificationPdbxPhasingDmShellgetPdbxPhasingDmShell()Data items in the PDBX_PHASING_DM_SHELL category record details about density modification in resolution shell.PdbxPhasingMADSetgetPdbxPhasingMADSet()Record details about each phasing set: (Note: the phasing set is different from data set.PdbxPhasingMADSetShellgetPdbxPhasingMADSetShell()The same as category pdbx_phasing_MAD_set, but broken into shells.PdbxPhasingMADSetSitegetPdbxPhasingMADSetSite()record the details (coordinates etc.) of anomalous scatters.PdbxPhasingMADShellgetPdbxPhasingMADShell()Data items in the PDBX_PHASING_MAD_SHELL category record details about the phasing of the structure, when methods involving multiple anomalous dispersion techniques are involved (note: the values are overall, but broken down into shells of resolution)PdbxPhasingMRgetPdbxPhasingMR()Data items in the PDBX_PHASING_MR category record details about molecular replacement.PdbxPointSymmetrygetPdbxPointSymmetry()Data items in the PDBX_POINT_SYMMETRY category record details about the point symmetry group associated with this entry.PdbxPointSymmetryDepositorInfogetPdbxPointSymmetryDepositorInfo()Data items in the PDBX_POINT_SYMMETRY_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_POINT_SYMMETRY.PdbxPolySeqSchemegetPdbxPolySeqScheme()The PDBX_POLY_SEQ_SCHEME category provides residue level nomenclature mapping for polymer entities.PdbxPostProcessDetailsgetPdbxPostProcessDetails()Data items in the PDBX_POST_PROCESS_DETAILS identify problems or errors encountered in the post-processing of this entry.PdbxPostProcessStatusgetPdbxPostProcessStatus()Data items in the PDBX_POST_PROCESS_DETAILS record the status of post-processed entries.PdbxPrdAuditgetPdbxPrdAudit()Data items in the PDBX_PRD_AUDIT category records the status and tracking information for this molecule.PdbxPrereleaseSeqgetPdbxPrereleaseSeq()This category provides a placeholder for pre-release sequence information.PdbxProteinInfogetPdbxProteinInfo()Data items in the PDBX_PROTEIN_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated.PdbxReferenceEntityLinkgetPdbxReferenceEntityLink()Data items in the PDBX_REFERENCE_ENTITY_LINK category give details about the linkages between entities within reference molecules.PdbxReferenceEntityListgetPdbxReferenceEntityList()Data items in the PDBX_REFERENCE_ENTITY_LIST category record the list of entities within each reference molecule.PdbxReferenceEntityNonpolygetPdbxReferenceEntityNonpoly()Data items in the PDBX_REFERENCE_ENTITY_NONPOLY category record the list of entities within each reference molecule.PdbxReferenceEntityPolygetPdbxReferenceEntityPoly()Data items in the PDBX_REFERENCE_ENTITY_POLY category record details about the polymer, such as the type of the polymer, the number of monomers and whether it has nonstandard features.PdbxReferenceEntityPolyLinkgetPdbxReferenceEntityPolyLink()Data items in the PDBX_REFERENCE_ENTITY_POLY_LINK category give details about polymer linkages including both standard and non-standard linkages between polymer componnents.PdbxReferenceEntityPolySeqgetPdbxReferenceEntityPolySeq()Data items in the PDBX_REFERENCE_ENTITY_POLY_SEQ category specify the sequence of monomers in a polymer.PdbxReferenceEntitySequencegetPdbxReferenceEntitySequence()Additional features associated with the reference entity.PdbxReferenceEntitySrcNatgetPdbxReferenceEntitySrcNat()Data items in the PDBX_REFERENCE_ENTITY_SRC_NAT category record details of the source from which the entity was obtained.PdbxReferenceEntitySubcomponentsgetPdbxReferenceEntitySubcomponents()Data items in the PDBX_REFERENCE_ENTITY_SUBCOMPONENTS category records subcomponent sequence from which this entity could be built.PdbxReferenceLinkedEntitygetPdbxReferenceLinkedEntity()Data items in the pdbx_reference_linked_entity category describe common observed interaction patterns within linked entities.PdbxReferenceLinkedEntityCompLinkgetPdbxReferenceLinkedEntityCompLink()Data items in the pdbx_reference_linked_entity_comp_link category enumerate inter-entity linkages between the components of common observed interaction patterns described in the pdbx_reference_linked_entity category.PdbxReferenceLinkedEntityCompListgetPdbxReferenceLinkedEntityCompList()Data items in the pdbx_reference_linked_entity_comp_list category lists the constituents of common observed interaction patterns described in the pdbx_reference_linked_entity category.PdbxReferenceLinkedEntityLinkgetPdbxReferenceLinkedEntityLink()Data items in the pdbx_reference_linked_entity_link category enumerate linkages between the entities in common observed interaction patterns described in the pdbx_reference_linked_entity category.PdbxReferenceMoleculegetPdbxReferenceMolecule()Data items in the PDBX_REFERENCE_MOLECULE category record reference information about small polymer molecules.PdbxReferenceMoleculeAnnotationgetPdbxReferenceMoleculeAnnotation()Data items in the PDBX_REFERENCE_MOLECULE_ANNOTATION category specify additional annotation relevant to the molecular entities.PdbxReferenceMoleculeDetailsgetPdbxReferenceMoleculeDetails()Data items in the PDBX_REFERENCE_MOLECULE_DETAILS category records textual details about small polymer molecules.PdbxReferenceMoleculeFamilygetPdbxReferenceMoleculeFamily()Data items in the PDBX_REFERENCE_MOLECULE_FAMILY category identify entity families.PdbxReferenceMoleculeFeaturesgetPdbxReferenceMoleculeFeatures()Additional features associated with the reference entity.PdbxReferenceMoleculeListgetPdbxReferenceMoleculeList()Data items in the PDBX_REFERENCE_MOLECULE_LIST category record reference information about small polymer molecules.PdbxReferenceMoleculeRelatedStructuresgetPdbxReferenceMoleculeRelatedStructures()Data items in the PDBX_REFERENCE_MOLECULE_RELATED_STRUCTURES category record details of the structural examples in related databases for this entity.PdbxReferenceMoleculeSynonymsgetPdbxReferenceMoleculeSynonyms()Data items in the PDBX_REFERENCE_MOLECULE_SYNONYMS category records synonym names for reference entities.PdbxReferencePublicationListgetPdbxReferencePublicationList()Data items in the PDBX_REFERENCE_PUBLICATION_LIST hold reference information related to PDB citation data.PdbxRefinegetPdbxRefine()Data items in the PDBX_REFINE category record details about additional structure refinement parameters which are needed to complete legacy REMARK 3 refinement templates in PDB format files.PdbxRefineAuxFilegetPdbxRefineAuxFile()Auxilary parameter and topology files used in refinement.PdbxRefineComponentgetPdbxRefineComponent()Data items in the PDBX_REFINE_COMPONENT category record statistics of the final model relative to the density map.PdbxRefineLsRestrNcsgetPdbxRefineLsRestrNcs()Holds details of NCS restraints in cases where multiple conditions are provided for each domain.PdbxRefineTlsgetPdbxRefineTls()Data items in the REFINE_TLS category record details about TLS parameters used in structure refinement.PdbxRefineTlsGroupgetPdbxRefineTlsGroup()Data items in the PDBX_REFINE_TLS_GROUP category record details about a fragment of a TLS group.PdbxReflnsTwingetPdbxReflnsTwin()Details decribing crystallographic twinning.PdbxRelatedExpDataSetgetPdbxRelatedExpDataSet()Data items in the PDBX_RELATED_DATA_SET category record references to experimental data sets related to the entry.PdbxRemediationAtomSiteMappinggetPdbxRemediationAtomSiteMapping()Data items in the PDBX_REMEDIATION_ATOM_SITE_MAPPING category records mapping information between selected molecular entities that have been chemically redefined.PdbxReRefinementgetPdbxReRefinement()Describes the origin of the experimental data used in this entry.PdbxRmchOutliergetPdbxRmchOutlier()Data items in the PDBX_RMCH_OUTLIER category list the residues with torsion angles outside the expected Ramachandran regions.PdbxRmsDevsCovalentgetPdbxRmsDevsCovalent()Data items in the PDBX_RMS_DEVS_COVALENT record the summary RMS deviations for nucleic acid covalent geometry relative to small molecule crystal standards.PdbxRmsDevsCovByMonomergetPdbxRmsDevsCovByMonomer()Data items in the PDBX_RMS_DEVS_COV_BY_MONOMER record the RMS deviations covalent geometry for each momoner relative to small molecule crystal standards.PdbxRobotSystemgetPdbxRobotSystem()The details about each robotic system used to collect data for this project.PdbxSeqMapDepositorInfogetPdbxSeqMapDepositorInfo()Data items in the PDBX_SEQ_MAP_DEPOSITOR_INFO record the details about the mapping sample and coordinate sequences.PdbxSequenceAnnotationgetPdbxSequenceAnnotation()PDBX_SEQUENCE_ANNOTATION holds internal details about molecular sequences described in the context of PDB chains.PdbxSequencePatterngetPdbxSequencePattern()Data items in the PDBX_SEQUENCE_PATTERN category record the number of occurences of common step sequence patterns (e.g.PdbxSequenceRangegetPdbxSequenceRange()Data items in the PDBX_SEQUENCE_RANGE category identify the beginning and ending points of polypeptide sequence segments.PdbxSerialCrystallographyDataReductiongetPdbxSerialCrystallographyDataReduction()Data items in the PDBX_SERIAL_CRYSTALLOGRAPHY_DATA_REDUCTION category record details about data processing that are unique to XFEL experiments.PdbxSerialCrystallographyMeasurementgetPdbxSerialCrystallographyMeasurement()Data items in the PDBX_SERIAL_CRYSTALLOGRAPHY_MEASUREMENT category record details the beam that is impinging on the samplePdbxSerialCrystallographySampleDeliverygetPdbxSerialCrystallographySampleDelivery()Data items in the PDBX_SERIAL_CRYSTALLOGRAPHY_SAMPLE_DELIVERY category record general details about the sample deliveryPdbxSerialCrystallographySampleDeliveryFixedTargetgetPdbxSerialCrystallographySampleDeliveryFixedTarget()Data items in the PDBX_SERIAL_CRYSTALLOGRAPHY_SAMPLE_DELIVERY_FIXED_TARGET category record details about sample delivery using a fixed taget.PdbxSerialCrystallographySampleDeliveryInjectiongetPdbxSerialCrystallographySampleDeliveryInjection()Data items in the PDBX_SERIAL_CRYSTALLOGRAPHY_SAMPLE_DELIVERY_INJECTION category record details about sample delivery by injectionPdbxSGProjectgetPdbxSGProject()Data items in the PDBX_CONTACT_AUTHOR category record details about the Structural Genomics Project and name and initials for each Center.PdbxSolnScattergetPdbxSolnScatter()Data items in the PDBX_SOLN_SCATTER category record details about a solution scattering experimentPdbxSolnScatterModelgetPdbxSolnScatterModel()Data items in the PDBX_SOLN_SCATTER_MODEL category record details about the homology model fitting to the solution scatter data.PdbxSolventAtomSiteMappinggetPdbxSolventAtomSiteMapping()Data items in the PDBX_SOLVENT_ATOM_SITE_MAPPING category records mapping information between solvent atoms before and after symmetry repositioning.PdbxSolventInfogetPdbxSolventInfo()Data items in the PDBX_SOLVENT_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated.PdbxSourcegetPdbxSource()Data item will still be used until the ENTITY category is fully adopted by NDBQuery.PdbxStereochemistrygetPdbxStereochemistry()Data items in the PDBX_STEREOCHEMISTRY identify chiral centers and associated chiral volumes.PdbxStructAssemblygetPdbxStructAssembly()Data items in the PDBX_STRUCT_ASSEMBLY category record details about the structural elements that form macromolecular assemblies.PdbxStructAssemblyAuthClassificationgetPdbxStructAssemblyAuthClassification()Provides reason a particular assembly in pdbx_struct_assembly is of interest.PdbxStructAssemblyAuthEvidencegetPdbxStructAssemblyAuthEvidence()Provides author supplied evidentiary support for assemblies in pdbx_struct_assembly.PdbxStructAssemblyAuthEvidenceDepositorInfogetPdbxStructAssemblyAuthEvidenceDepositorInfo()Provides author supplied evidentiary support for assemblies in pdbx_struct_assembly.PdbxStructAssemblyDepositorInfogetPdbxStructAssemblyDepositorInfo()Data items in the PDBX_STRUCT_ASSEMBLY_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_ASSEMBLY.PdbxStructAssemblyGengetPdbxStructAssemblyGen()Data items in the PDBX_STRUCT_ASSEMBLY_GEN category record details about the generation of each macromolecular assemblies.PdbxStructAssemblyGenDepositorInfogetPdbxStructAssemblyGenDepositorInfo()Data items in the PDBX_STRUCT_ASSEMBLY_GEN_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_ASSEMBLY_GEN.PdbxStructAssemblyPropgetPdbxStructAssemblyProp()Properties and features of structural assemblies.PdbxStructAssemblyPropDepositorInfogetPdbxStructAssemblyPropDepositorInfo()Data items in the PDBX_STRUCT_ASSEMBLY_PROP_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_ASSEMBLY_PROP.PdbxStructAsymGengetPdbxStructAsymGen()Data items in the PDBX_STRUCT_ASYM_GEN category record details about the generation of the crystallographic asymmetric unit.PdbxStructBiolFuncgetPdbxStructBiolFunc()Data items in the PDBX_STRUCT_BIOL_FUNC category record details about the function of a particular biological assembly.PdbxStructChemCompDiagnosticsgetPdbxStructChemCompDiagnostics()Data items in the PDBX_STRUCT_CHEM_COMP_DIAGNOSTICS category provides structural diagnostics in chemical components instances.PdbxStructChemCompFeaturegetPdbxStructChemCompFeature()Data items in the PDBX_STRUCT_CHEM_COMP_FEATURE category provides structural annotations in chemical components instances.PdbxStructConnAnglegetPdbxStructConnAngle()Data items in the PDBX_STRUCT_CONN_ANGLE category record the angles in connections between portions of the structure.PdbxStructEntityInstgetPdbxStructEntityInst()Data items in the PDBX_STRUCT_ENTITY_INST category record details about the structural elements in the deposited entry.PdbxStructGroupComponentRangegetPdbxStructGroupComponentRange()Data items in the PDBX_STRUCT_GROUP_COMPONENT_RANGE category define a structural group as a continuous span chemical components.PdbxStructGroupComponentsgetPdbxStructGroupComponents()Data items in the PDBX_STRUCT_GROUP_COMPONENTS category list component-level group assignments within the entry.PdbxStructGroupListgetPdbxStructGroupList()Data items in the PDBX_STRUCT_GROUP_LIST define groups of related components or atoms.PdbxStructInfogetPdbxStructInfo()Special features of this structural entry.PdbxStructLegacyOperListgetPdbxStructLegacyOperList()Data items in the PDBX_STRUCT_LEGACY_OPER_LIST category describe Cartesian rotation and translation operations required to generate or transform the coordinates deposited with this entry.PdbxStructLinkgetPdbxStructLink()Data items in the PDBX_STRUCT_LINK category record details about covalent linkages in the structure.PdbxStructModResiduegetPdbxStructModResidue()Data items in the PDBX_STRUCT_MOD_RESIDUE category list the modified polymer components in the entry and provide some details describing the nature of the modification.PdbxStructMsymGengetPdbxStructMsymGen()Data items in the PDBX_STRUCT_MSYM_GEN category record details about the generation of the minimal asymmetric unit.PdbxStructNcsVirusGengetPdbxStructNcsVirusGen()Data items in the PDBX_STRUCT_NCS_VIRUS_GEN category record details about the generation of virus structures from NCS matrix operators.PdbxStructOperListgetPdbxStructOperList()Data items in the PDBX_STRUCT_OPER_LIST category describe Cartesian rotation and translation operations required to generate or transform the coordinates deposited with this entry.PdbxStructOperListDepositorInfogetPdbxStructOperListDepositorInfo()Data items in the PDBX_STRUCT_OPER_LIST_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_OPER_LIST.PdbxStructPackGengetPdbxStructPackGen()Data items in the PDBX_STRUCT_PACK_GEN category record details about the generation of the packing picture(s).PdbxStructRefSeqDeletiongetPdbxStructRefSeqDeletion()Data items in the PDBX_STRUCT_REF_SEQ_INSERTION category annotate deletions in the sequence of the entity described in the referenced database entry.PdbxStructRefSeqDepositorInfogetPdbxStructRefSeqDepositorInfo()Data items in the PDBX_STRUCT_REF_SEQ_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory STRUCT_REF_SEQ.PdbxStructRefSeqDifDepositorInfogetPdbxStructRefSeqDifDepositorInfo()Data items in the PDBX_STRUCT_REF_SEQ_DIF_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory STRUCT_REF_SEQ_DIF.PdbxStructRefSeqFeaturegetPdbxStructRefSeqFeature()Data items in the PDBX_STRUCT_REF_SEQ_FEATURE category provide a mechanism for identifying and annotating sequence features.PdbxStructRefSeqFeaturePropgetPdbxStructRefSeqFeatureProp()Data items in the PDBX_STRUCT_REF_SEQ_FEATURE_PROP category provide a mechanism for identifying and annotating properties of sequence features.PdbxStructRefSeqInsertiongetPdbxStructRefSeqInsertion()Data items in the PDBX_STRUCT_REF_SEQ_INSERTION category annotate insertions in the sequence of the entity described in the referenced database entry.PdbxStructSheetHbondgetPdbxStructSheetHbond()Data items in the PDBX_STRUCT_SHEET_HBOND category record details about the hydrogen bonding between residue ranges in a beta sheet.PdbxStructSpecialSymmetrygetPdbxStructSpecialSymmetry()Data items in the PDBX_STRUCT_SPECIAL_SYMMETRY category list the molecular components that lie on special symmetry positions.PdbxSugarPhosphateGeometrygetPdbxSugarPhosphateGeometry()Data items in the PDBX_SUGAR_PHOSPHATE_GEOMETRY record the RMS deviations covalent geometry for each momoner relative to small molecule crystal standards.PdbxSummaryFlagsgetPdbxSummaryFlags()Container category for a list of feature flags associated with each structure entry.PdbxSupportingExpDataSetgetPdbxSupportingExpDataSet()Data items in the PDBX_SUPPORTING_EXP_DATA_SET category record to experimental data set dependencies for this entry.PdbxTableinfogetPdbxTableinfo()PdbxTrnaInfogetPdbxTrnaInfo()Data items in the PDBX_TRNA_INFO category are still used until the 'entity' categories are entered into the database, even though the T-RNA is repeated.PdbxUnobsOrZeroOccAtomsgetPdbxUnobsOrZeroOccAtoms()Data items in the PDBX_UNOBS_OR_ZERO_OCC_ATOMS category list the atoms within the entry that are either unobserved or have zero occupancy/PdbxUnobsOrZeroOccResiduesgetPdbxUnobsOrZeroOccResidues()Data items in the PDBX_UNOBS_OR_ZERO_OCC_RESIDUES category list the residues within the entry that are not observed or have zero occupancy.PdbxUnpairgetPdbxUnpair()These records give information about residues which do not pair (h-bond) in the asymmetric unit.PdbxValAnglegetPdbxValAngle()The PDBX_VAL_ANGLE category lists the covalent bond angles in this entry deviating by greater than 6*sigma from standard values.PdbxValBondgetPdbxValBond()The PDBX_VAL_BOND category lists the covalent bond angles in this entry deviating by greater than 6*sigma from standard values.PdbxValChiralgetPdbxValChiral()Data items in the PDBX_VAL_CHIRAL category list the atoms with nonstandard chiralities.PdbxValContactgetPdbxValContact()The PDBX_VAL_CONTACT category lists non-bonded atoms within the assymetric unit of the entry that are in close contact.PdbxValidateChiralgetPdbxValidateChiral()Data items in the PDBX_VALIDATE_CHIRAL category list the residues that contain unexpected configuration of chiral centers.PdbxValidateCloseContactgetPdbxValidateCloseContact()Data items in the PDBX_VALIDATE_CLOSE_CONTACT category list the atoms within the entry that are in close contact with regard the distances expected from either covalent bonding or closest approach by van der Waals contacts.PdbxValidateMainChainPlanegetPdbxValidateMainChainPlane()Data items in the PDBX_VALIDATE_MAIN_CHAIN_PLANE category list the residues that contain unexpected deviations from planes for main chain atoms as defined by the improper torsion angle describing planarity: PLANARITY = C(i-1) - CA(i-1) - N(i) - O(i-1) ==> planar < 5 as a pseudo torsionPdbxValidatePeptideOmegagetPdbxValidatePeptideOmega()Data items in the PDBX_VALIDATE_PEPTIDE_OMEGA category list the residues that contain peptide bonds deviate significantly from both cis and trans conformation.PdbxValidatePlanesgetPdbxValidatePlanes()Data items in the PDBX_VALIDATE_PLANES category list the residues that contain unexpected deviations from planes centers.PdbxValidatePlanesAtomgetPdbxValidatePlanesAtom()Data items in the PDBX_VALIDATE_PLANES_ATOM category list the residues that contain unexpected deviations from planes centers.PdbxValidatePolymerLinkagegetPdbxValidatePolymerLinkage()Data items in the PDBX_VALIDATE_POLYMER_LINKAGE category list the polymer linkages within the entry that are outside of typlical covalent distances.PdbxValidateRmsdAnglegetPdbxValidateRmsdAngle()Data items in the PDBX_VALIDATE_RMSD_ANGLE category list the the covalent bond angles found in an entry that have values which deviate from expected values by more than 6*rmsd for the particular entry from the expected standard valuePdbxValidateRmsdBondgetPdbxValidateRmsdBond()Data items in the PDBX_VALIDATE_RMSD_BOND category list the covalent bonds that have values which deviate from expected values by more than 6*rmsd.PdbxValidateSymmContactgetPdbxValidateSymmContact()Data items in the PDBX_VALIDATE_SYMM_CONTACT category list the atoms within the entry that are in close contact with regard the distances expected from either covalent bonding or closest approach by van der Waals contacts.PdbxValidateTorsiongetPdbxValidateTorsion()Data items in the PDBX_VALIDATE_TORSION category list the residues with torsion angles outside the expected ramachandran regionsPdbxValSymContactgetPdbxValSymContact()The PDBX_VAL_SYM_CONTACT category lists symmetry related contacts amoung non-bonded atoms.PdbxVersiongetPdbxVersion()Data items in the PDBX_VERSION category record details about the version of this entry.PdbxViewCategorygetPdbxViewCategory()Data items in the PDBX_VIEW_CATEGORY specify the categories belonging to a category view group.PdbxViewCategoryGroupgetPdbxViewCategoryGroup()Data items in the PDBX_VIEW_CATEGORY_GROUP identify collections of related mmCIF categories.PdbxViewItemgetPdbxViewItem()Data items in the PDBX_VIEW_ITEM specify the mmCIF data items belonging to a view category.PdbxVirtualAnglegetPdbxVirtualAngle()Data items in the PDBX_VIRTUAL_ANGLE category record details about the molecular virtual angles, as calculated from the contents of the ATOM, CELL, and SYMMETRY data.PdbxVirtualBondgetPdbxVirtualBond()Data items in the PDBX_VIRTUAL_BOND category record details about virtual bonds, as calculated from the contents of the ATOM, CELL, and SYMMETRY data.PdbxVirtualTorsiongetPdbxVirtualTorsion()Data items in the PDBX_VIRTUAL_TORSION category record details about virtual torsion angles, as calculated from the contents of the ATOM, CELL, and SYMMETRY data.PdbxXplorFilegetPdbxXplorFile()Parameter and topology files used in X-PLOR/CNS refinement.PhasinggetPhasing()Data items in the PHASING category record details about the phasing of the structure, listing the various methods used in the phasing process.PhasingAveraginggetPhasingAveraging()Data items in the PHASING_AVERAGING category record details about the phasing of the structure where methods involving averaging of multiple observations of the molecule in the asymmetric unit are involved.PhasingIsomorphousgetPhasingIsomorphous()Data items in the PHASING_ISOMORPHOUS category record details about the phasing of the structure where a model isomorphous to the structure being phased was used to generate the initial phases.PhasingMADgetPhasingMAD()Data items in the PHASING_MAD category record details about the phasing of the structure where methods involving multiple-wavelength anomalous-dispersion techniques are involved.PhasingMADClustgetPhasingMADClust()Data items in the PHASING_MAD_CLUST category record details about a cluster of experiments that contributed to the generation of a set of phases.PhasingMADExptgetPhasingMADExpt()Data items in the PHASING_MAD_EXPT category record details about a MAD phasing experiment, such as the number of experiments that were clustered together to produce a set of phases or the statistics for those phases.PhasingMADRatiogetPhasingMADRatio()Data items in the PHASING_MAD_RATIO category record the ratios of phasing statistics between pairs of data sets in a MAD phasing experiment, in given shells of resolution.PhasingMADSetgetPhasingMADSet()Data items in the PHASING_MAD_SET category record details about the individual data sets used in a MAD phasing experiment.PhasingMIRgetPhasingMIR()Data items in the PHASING_MIR category record details about the phasing of the structure where methods involving isomorphous replacement are involved.PhasingMIRDergetPhasingMIRDer()Data items in the PHASING_MIR_DER category record details about individual derivatives used in the phasing of the structure when methods involving isomorphous replacement are involved.PhasingMIRDerReflngetPhasingMIRDerRefln()Data items in the PHASING_MIR_DER_REFLN category record details about the calculated structure factors obtained in an MIR phasing experiment.PhasingMIRDerShellgetPhasingMIRDerShell()Data items in the PHASING_MIR_DER_SHELL category record statistics, broken down into shells of resolution, for an MIR phasing experiment.PhasingMIRDerSitegetPhasingMIRDerSite()Data items in the PHASING_MIR_DER_SITE category record details about the heavy-atom sites in an MIR phasing experiment.PhasingMIRShellgetPhasingMIRShell()Data items in the PHASING_MIR_SHELL category record statistics for an isomorphous replacement phasing experiment.broken down into shells of resolution.PhasingSetgetPhasingSet()Data items in the PHASING_SET category record details about the data sets used in a phasing experiment.PhasingSetReflngetPhasingSetRefln()Data items in the PHASING_SET_REFLN category record the values of the measured structure factors used in a phasing experiment.PublgetPubl()Data items in the PUBL category are used when submitting a manuscript for publication.PublAuthorgetPublAuthor()Data items in the PUBL_AUTHOR category record details of the authors of a manuscript submitted for publication.PublBodygetPublBody()Data items in the PUBL_BODY category permit the labelling of different text sections within the body of a paper.PublManuscriptInclgetPublManuscriptIncl()Data items in the PUBL_MANUSCRIPT_INCL category allow the authors of a manuscript submitted for publication to list data names that should be added to the standard request list used by the journal printing software.RefinegetRefine()Data items in the REFINE category record details about the structure-refinement parameters.RefineAnalyzegetRefineAnalyze()Data items in the REFINE_ANALYZE category record details about the refined structure that are often used to analyze the refinement and assess its quality.RefineBIsogetRefineBIso()Data items in the REFINE_B_ISO category record details about the treatment of isotropic B factors (displacement parameters) during refinement.RefineFunctMinimizedgetRefineFunctMinimized()Data items in the REFINE_FUNCT_MINIMIZED category record details about the individual terms of the function minimized during refinement.RefineHistgetRefineHist()Data items in the REFINE_HIST category record details about the steps during the refinement of the structure.RefineLsClassgetRefineLsClass()Data items in the REFINE_LS_CLASS category record details about the reflections used for the structure refinement for each reflection class separately.RefineLsRestrgetRefineLsRestr()Data items in the REFINE_LS_RESTR category record details about the restraints applied to various classes of parameters during the least-squares refinement.RefineLsRestrNcsgetRefineLsRestrNcs()Data items in the REFINE_LS_RESTR_NCS category record details about the restraints applied to atom positions in domains related by noncrystallographic symmetry during least-squares refinement, and also about the deviation of the restrained atomic parameters at the end of the refinement.RefineLsRestrTypegetRefineLsRestrType()Data items in the REFINE_LS_RESTR_TYPE category record details about the restraint types used in the least-squares refinement.RefineLsShellgetRefineLsShell()Data items in the REFINE_LS_SHELL category record details about the results of the least-squares refinement broken down into shells of resolution.RefineOccupancygetRefineOccupancy()Data items in the REFINE_OCCUPANCY category record details about the treatment of atom occupancies during refinement.ReflngetRefln()Data items in the REFLN category record details about the reflection data used to determine the ATOM_SITE data items.ReflnsgetReflns()Data items in the REFLNS category record details about the reflection data used to determine the ATOM_SITE data items.ReflnsClassgetReflnsClass()Data items in the REFLNS_CLASS category record details of the reflections used to determine the structural parameters for each reflection class.ReflnsScalegetReflnsScale()Data items in the REFLNS_SCALE category record details about the structure-factor scales.ReflnsShellgetReflnsShell()Data items in the REFLNS_SHELL category record details about the reflection data used to determine the ATOM_SITE data items broken down into shells of resolution.ReflnSysAbsgetReflnSysAbs()Data items in the REFLN_SYS_ABS category record details about the reflection data that should be systematically absent, given the designated space group.List<Block>getSaveFrames()All save frames associated to thisBlock.SoftwaregetSoftware()Data items in the SOFTWARE category record details about the software used in the structure analysis, which implies any software used in the generation of any data items associated with the structure determination and structure representation.SpaceGroupgetSpaceGroup()Contains all the data items that refer to the space group as a whole, such as its name or crystal system.SpaceGroupSymopgetSpaceGroupSymop()Contains information about the symmetry operations of the space group.StructgetStruct()Data items in the STRUCT category record details about the description of the crystallographic structure.StructAsymgetStructAsym()Data items in the STRUCT_ASYM category record details about the structural elements in the asymmetric unit.StructBiolgetStructBiol()Data items in the STRUCT_BIOL category record details about the structural elements that form each structure of biological significance.StructBiolGengetStructBiolGen()Data items in the STRUCT_BIOL_GEN category record details about the generation of each biological unit.StructBiolKeywordsgetStructBiolKeywords()Data items in the STRUCT_BIOL_KEYWORDS category record keywords that describe each biological unit.StructBiolViewgetStructBiolView()Data items in the STRUCT_BIOL_VIEW category record details about how to draw and annotate an informative view of the biological structure.StructConfgetStructConf()Data items in the STRUCT_CONF category record details about the backbone conformation of a segment of polymer.StructConfTypegetStructConfType()Data items in the STRUCT_CONF_TYPE category record details about the criteria used to identify backbone conformations of a segment of polymer.StructConngetStructConn()Data items in the STRUCT_CONN category record details about the connections between portions of the structure.StructConnTypegetStructConnType()Data items in the STRUCT_CONN_TYPE category record details about the criteria used to identify interactions between portions of the structure.StructKeywordsgetStructKeywords()Data items in the STRUCT_KEYWORDS category specify keywords that describe the chemical structure in this entry.StructMonDetailsgetStructMonDetails()Data items in the STRUCT_MON_DETAILS category record details about specifics of calculations summarized in data items in the STRUCT_MON_PROT and STRUCT_MON_NUCL categories.StructMonNuclgetStructMonNucl()Data items in the STRUCT_MON_NUCL category record details about structural properties of a nucleic acid when analyzed at the monomer level.StructMonProtgetStructMonProt()Data items in the STRUCT_MON_PROT category record details about structural properties of a protein when analyzed at the monomer level.StructMonProtCisgetStructMonProtCis()Data items in the STRUCT_MON_PROT_CIS category identify monomers that have been found to have the peptide bond in the cis conformation.StructNcsDomgetStructNcsDom()Data items in the STRUCT_NCS_DOM category record information about the domains in an ensemble of domains related by one or more noncrystallographic symmetry operators.StructNcsDomLimgetStructNcsDomLim()Data items in the STRUCT_NCS_DOM_LIM category identify the start and end points of polypeptide chain segments that form all or part of a domain in an ensemble of domains related by noncrystallographic symmetry.StructNcsEnsgetStructNcsEns()Data items in the STRUCT_NCS_ENS category record information about ensembles of domains related by noncrystallographic symmetry.StructNcsEnsGengetStructNcsEnsGen()Data items in the STRUCT_NCS_ENS_GEN category list domains related by a noncrystallographic symmetry operation and identify the operator.StructNcsOpergetStructNcsOper()Data items in the STRUCT_NCS_OPER category describe the noncrystallographic symmetry operations.StructRefgetStructRef()Data items in the STRUCT_REF category allow the author of a data block to relate the entities or biological units described in the data block to information archived in external databases.StructRefSeqgetStructRefSeq()Data items in the STRUCT_REF_SEQ category provide a mechanism for indicating and annotating a region (or regions) of alignment between the sequence of an entity or biological unit described in the data block and the sequence in the referenced database entry.StructRefSeqDifgetStructRefSeqDif()Data items in the STRUCT_REF_SEQ_DIF category provide a mechanism for indicating and annotating point differences between the sequence of the entity or biological unit described in the data block and the sequence of the referenced database entry.StructSheetgetStructSheet()Data items in the STRUCT_SHEET category record details about the beta-sheets.StructSheetHbondgetStructSheetHbond()Data items in the STRUCT_SHEET_HBOND category record details about the hydrogen bonding between residue ranges in a beta- sheet.StructSheetOrdergetStructSheetOrder()Data items in the STRUCT_SHEET_ORDER category record details about the order of the residue ranges that form a beta-sheet.StructSheetRangegetStructSheetRange()Data items in the STRUCT_SHEET_RANGE category record details about the residue ranges that form a beta-sheet.StructSheetTopologygetStructSheetTopology()Data items in the STRUCT_SHEET_TOPOLOGY category record details about the topology of the residue ranges that form a beta-sheet.StructSitegetStructSite()Data items in the STRUCT_SITE category record details about portions of the structure that contribute to structurally relevant sites (e.g.StructSiteGengetStructSiteGen()Data items in the STRUCT_SITE_GEN category record details about the generation of portions of the structure that contribute to structurally relevant sites.StructSiteKeywordsgetStructSiteKeywords()Data items in the STRUCT_SITE_KEYWORDS category record keywords describing the site.StructSiteViewgetStructSiteView()Data items in the STRUCT_SITE_VIEW category record details about how to draw and annotate an informative view of the site.SymmetrygetSymmetry()Data items in the SYMMETRY category record details about the space-group symmetry.SymmetryEquivgetSymmetryEquiv()Data items in the SYMMETRY_EQUIV category list the symmetry-equivalent positions for the space group.ValenceParamgetValenceParam()Data items in the VALENCE_PARAM category define the parameters used for calculating bond valences from bond lengths.ValenceRefgetValenceRef()Data items in the VALENCE_REF category list the references from which the bond-valence parameters have been taken.-
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.rcsb.cif.model.Block
categories, categoryNames, saveFrames
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Method Detail
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getBlockHeader
public String getBlockHeader()
Description copied from interface:BlockThe header of thisBlock.- Specified by:
getBlockHeaderin interfaceBlock- Returns:
Stringof the header
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getCategory
public Category getCategory(String name)
Description copied from interface:BlockRetrieve a particularCategoryby name.- Specified by:
getCategoryin interfaceBlock- Parameters:
name- the category name- Returns:
- the corresponding
Category, if none exists a instance ofBaseCategoryis returned as proxy
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getColumn
public Column getColumn(String name)
Description copied from interface:BlockRetrieve aColumnby name. This is relevant for CCDC files that identify columns by 'flat' names such as "cell_length_a"- Specified by:
getColumnin interfaceBlock- Parameters:
name- the category name and column name, joined by an underscore- Returns:
- the corresponding
Column, if none exists a instance ofBaseColumnis returned as proxy
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getCategoryNames
public List<String> getCategoryNames()
Description copied from interface:Block- Specified by:
getCategoryNamesin interfaceBlock- Returns:
- collection of all
Categorynames
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getSaveFrames
public List<Block> getSaveFrames()
Description copied from interface:BlockAll save frames associated to thisBlock.- Specified by:
getSaveFramesin interfaceBlock- Returns:
- collection of save frames
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getAtomSite
public AtomSite getAtomSite()
Description copied from interface:BlockData items in the ATOM_SITE category record details about the atom sites in a macromolecular crystal structure, such as the positional coordinates, atomic displacement parameters, magnetic moments and directions. The data items for describing anisotropic atomic displacement factors are only used if the corresponding items are not given in the ATOM_SITE_ANISOTROP category.- Specified by:
getAtomSitein interfaceBlock- Returns:
- AtomSite
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getAtomSiteAnisotrop
public AtomSiteAnisotrop getAtomSiteAnisotrop()
Description copied from interface:BlockData items in the ATOM_SITE_ANISOTROP category record details about anisotropic displacement parameters. If the ATOM_SITE_ANISOTROP category is used for storing these data, the corresponding ATOM_SITE data items are not used.- Specified by:
getAtomSiteAnisotropin interfaceBlock- Returns:
- AtomSiteAnisotrop
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getAtomSites
public AtomSites getAtomSites()
Description copied from interface:BlockData items in the ATOM_SITES category record details about the crystallographic cell and cell transformations, which are common to all atom sites.- Specified by:
getAtomSitesin interfaceBlock- Returns:
- AtomSites
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getAtomSitesAlt
public AtomSitesAlt getAtomSitesAlt()
Description copied from interface:BlockData items in the ATOM_SITES_ALT category record details about the structural ensembles that should be generated from atom sites or groups of atom sites that are modelled in alternative conformations in this data block.- Specified by:
getAtomSitesAltin interfaceBlock- Returns:
- AtomSitesAlt
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getAtomSitesAltEns
public AtomSitesAltEns getAtomSitesAltEns()
Description copied from interface:BlockData items in the ATOM_SITES_ALT_ENS category record details about the ensemble structure generated from atoms with various alternative conformation IDs.- Specified by:
getAtomSitesAltEnsin interfaceBlock- Returns:
- AtomSitesAltEns
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getAtomSitesAltGen
public AtomSitesAltGen getAtomSitesAltGen()
Description copied from interface:BlockData items in the ATOM_SITES_ALT_GEN category record details about the interpretation of multiple conformations in the structure.- Specified by:
getAtomSitesAltGenin interfaceBlock- Returns:
- AtomSitesAltGen
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getAtomSitesFootnote
public AtomSitesFootnote getAtomSitesFootnote()
Description copied from interface:BlockData items in the ATOM_SITES_FOOTNOTE category record detailed comments about an atom site or a group of atom sites.- Specified by:
getAtomSitesFootnotein interfaceBlock- Returns:
- AtomSitesFootnote
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getAtomType
public AtomType getAtomType()
Description copied from interface:BlockData items in the ATOM_TYPE category record details about the properties of the atoms that occupy the atom sites, such as the atomic scattering factors.- Specified by:
getAtomTypein interfaceBlock- Returns:
- AtomType
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getAudit
public Audit getAudit()
Description copied from interface:BlockData items in the AUDIT category record details about the creation and subsequent updating of the data block. Note that these items apply only to the creation and updating of the data block, and should not be confused with the data items in the JOURNAL category that record different stages in the publication of the material in the data block.
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getAuditAuthor
public AuditAuthor getAuditAuthor()
Description copied from interface:BlockData items in the AUDIT_AUTHOR category record details about the author(s) of the data block.- Specified by:
getAuditAuthorin interfaceBlock- Returns:
- AuditAuthor
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getAuditConform
public AuditConform getAuditConform()
Description copied from interface:BlockData items in the AUDIT_CONFORM category describe the dictionary versions against which the data names appearing in the current data block are conformant.- Specified by:
getAuditConformin interfaceBlock- Returns:
- AuditConform
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getAuditContactAuthor
public AuditContactAuthor getAuditContactAuthor()
Description copied from interface:BlockData items in the AUDIT_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the content of this data block.- Specified by:
getAuditContactAuthorin interfaceBlock- Returns:
- AuditContactAuthor
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getCell
public Cell getCell()
Description copied from interface:BlockData items in the CELL category record details about the crystallographic cell parameters.
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getCellMeasurement
public CellMeasurement getCellMeasurement()
Description copied from interface:BlockData items in the CELL_MEASUREMENT category record details about the measurement of the crystallographic cell parameters.- Specified by:
getCellMeasurementin interfaceBlock- Returns:
- CellMeasurement
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getCellMeasurementRefln
public CellMeasurementRefln getCellMeasurementRefln()
Description copied from interface:BlockData items in the CELL_MEASUREMENT_REFLN category record details about the reflections used to determine the crystallographic cell parameters. The CELL_MEASUREMENT_REFLN data items would in general be used only for diffractometer data.- Specified by:
getCellMeasurementReflnin interfaceBlock- Returns:
- CellMeasurementRefln
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getChemComp
public ChemComp getChemComp()
Description copied from interface:BlockData items in the CHEM_COMP category give details about each of the chemical components from which the relevant chemical structures can be constructed, such as name, mass or charge. The related categories CHEM_COMP_ATOM, CHEM_COMP_BOND, CHEM_COMP_ANGLE etc. describe the detailed geometry of these chemical components.- Specified by:
getChemCompin interfaceBlock- Returns:
- ChemComp
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getChemCompAngle
public ChemCompAngle getChemCompAngle()
Description copied from interface:BlockData items in the CHEM_COMP_ANGLE category record details about angles in a chemical component. Angles are designated by three atoms, with the second atom forming the vertex of the angle. Target values may be specified as angles in degrees, as a distance between the first and third atoms, or both.- Specified by:
getChemCompAnglein interfaceBlock- Returns:
- ChemCompAngle
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getChemCompAtom
public ChemCompAtom getChemCompAtom()
Description copied from interface:BlockData items in the CHEM_COMP_ATOM category record details about the atoms in a chemical component. Specifying the atomic coordinates for the components in this category is an alternative to specifying the structure of the component via bonds, angles, planes etc. in the appropriate CHEM_COMP subcategories.- Specified by:
getChemCompAtomin interfaceBlock- Returns:
- ChemCompAtom
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getChemCompBond
public ChemCompBond getChemCompBond()
Description copied from interface:BlockData items in the CHEM_COMP_BOND category record details about the bonds between atoms in a chemical component. Target values may be specified as bond orders, as a distance between the two atoms, or both.- Specified by:
getChemCompBondin interfaceBlock- Returns:
- ChemCompBond
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getChemCompChir
public ChemCompChir getChemCompChir()
Description copied from interface:BlockData items in the CHEM_COMP_CHIR category provide details about the chiral centres in a chemical component. The atoms bonded to the chiral atom are specified in the CHEM_COMP_CHIR_ATOM category.- Specified by:
getChemCompChirin interfaceBlock- Returns:
- ChemCompChir
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getChemCompChirAtom
public ChemCompChirAtom getChemCompChirAtom()
Description copied from interface:BlockData items in the CHEM_COMP_CHIR_ATOM category enumerate the atoms bonded to a chiral atom within a chemical component.- Specified by:
getChemCompChirAtomin interfaceBlock- Returns:
- ChemCompChirAtom
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getChemCompLink
public ChemCompLink getChemCompLink()
Description copied from interface:BlockData items in the CHEM_COMP_LINK category give details about the links between chemical components.- Specified by:
getChemCompLinkin interfaceBlock- Returns:
- ChemCompLink
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getChemCompPlane
public ChemCompPlane getChemCompPlane()
Description copied from interface:BlockData items in the CHEM_COMP_PLANE category provide identifiers for the planes in a chemical component. The atoms in the plane are specified in the CHEM_COMP_PLANE_ATOM category.- Specified by:
getChemCompPlanein interfaceBlock- Returns:
- ChemCompPlane
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getChemCompPlaneAtom
public ChemCompPlaneAtom getChemCompPlaneAtom()
Description copied from interface:BlockData items in the CHEM_COMP_PLANE_ATOM category enumerate the atoms in a plane within a chemical component.- Specified by:
getChemCompPlaneAtomin interfaceBlock- Returns:
- ChemCompPlaneAtom
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getChemCompTor
public ChemCompTor getChemCompTor()
Description copied from interface:BlockData items in the CHEM_COMP_TOR category record details about the torsion angles in a chemical component. As torsion angles can have more than one target value, the target values are specified in the CHEM_COMP_TOR_VALUE category.- Specified by:
getChemCompTorin interfaceBlock- Returns:
- ChemCompTor
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getChemCompTorValue
public ChemCompTorValue getChemCompTorValue()
Description copied from interface:BlockData items in the CHEM_COMP_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_COMP_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both.- Specified by:
getChemCompTorValuein interfaceBlock- Returns:
- ChemCompTorValue
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getChemLink
public ChemLink getChemLink()
Description copied from interface:BlockData items in the CHEM_LINK category give details about the links between chemical components.- Specified by:
getChemLinkin interfaceBlock- Returns:
- ChemLink
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getChemLinkAngle
public ChemLinkAngle getChemLinkAngle()
Description copied from interface:BlockData items in the CHEM_LINK_ANGLE category record details about angles in a link between chemical components.- Specified by:
getChemLinkAnglein interfaceBlock- Returns:
- ChemLinkAngle
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getChemLinkBond
public ChemLinkBond getChemLinkBond()
Description copied from interface:BlockData items in the CHEM_LINK_BOND category record details about bonds in a link between components in the chemical structure.- Specified by:
getChemLinkBondin interfaceBlock- Returns:
- ChemLinkBond
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getChemLinkChir
public ChemLinkChir getChemLinkChir()
Description copied from interface:BlockData items in the CHEM_LINK_CHIR category provide details about the chiral centres in a link between two chemical components. The atoms bonded to the chiral atom are specified in the CHEM_LINK_CHIR_ATOM category.- Specified by:
getChemLinkChirin interfaceBlock- Returns:
- ChemLinkChir
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getChemLinkChirAtom
public ChemLinkChirAtom getChemLinkChirAtom()
Description copied from interface:BlockData items in the CHEM_LINK_CHIR_ATOM category enumerate the atoms bonded to a chiral atom in a link between two chemical components.- Specified by:
getChemLinkChirAtomin interfaceBlock- Returns:
- ChemLinkChirAtom
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getChemLinkPlane
public ChemLinkPlane getChemLinkPlane()
Description copied from interface:BlockData items in the CHEM_LINK_PLANE category provide identifiers for the planes in a link between two chemical components. The atoms in the plane are specified in the CHEM_LINK_PLANE_ATOM category.- Specified by:
getChemLinkPlanein interfaceBlock- Returns:
- ChemLinkPlane
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getChemLinkPlaneAtom
public ChemLinkPlaneAtom getChemLinkPlaneAtom()
Description copied from interface:BlockData items in the CHEM_LINK_PLANE_ATOM category enumerate the atoms in a plane in a link between two chemical components.- Specified by:
getChemLinkPlaneAtomin interfaceBlock- Returns:
- ChemLinkPlaneAtom
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getChemLinkTor
public ChemLinkTor getChemLinkTor()
Description copied from interface:BlockData items in the CHEM_LINK_TOR category record details about the torsion angles in a link between two chemical components. As torsion angles can have more than one target value, the target values are specified in the CHEM_LINK_TOR_VALUE category.- Specified by:
getChemLinkTorin interfaceBlock- Returns:
- ChemLinkTor
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getChemLinkTorValue
public ChemLinkTorValue getChemLinkTorValue()
Description copied from interface:BlockData items in the CHEM_LINK_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_LINK_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both.- Specified by:
getChemLinkTorValuein interfaceBlock- Returns:
- ChemLinkTorValue
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getChemical
public Chemical getChemical()
Description copied from interface:BlockData items in the CHEMICAL category would not in general be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL category record details about the composition and chemical properties of the compounds. The formula data items must agree with those that specify the density, unit-cell and Z values.- Specified by:
getChemicalin interfaceBlock- Returns:
- Chemical
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getChemicalConnAtom
public ChemicalConnAtom getChemicalConnAtom()
Description copied from interface:BlockData items in the CHEMICAL_CONN_ATOM category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the two-dimensional (2D) chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_ATOM data items provide information about the chemical properties of the atoms in the structure. In cases where crystallographic and molecular symmetry elements coincide, they must also contain symmetry-generated atoms, so that the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND data items will always describe a complete chemical entity.- Specified by:
getChemicalConnAtomin interfaceBlock- Returns:
- ChemicalConnAtom
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getChemicalConnBond
public ChemicalConnBond getChemicalConnBond()
Description copied from interface:BlockData items in the CHEMICAL_CONN_BOND category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the two-dimensional (2D) chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_BOND data items specify the connections between the atoms in the CHEMICAL_CONN_ATOM list and the nature of the chemical bond between these atoms.- Specified by:
getChemicalConnBondin interfaceBlock- Returns:
- ChemicalConnBond
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getChemicalFormula
public ChemicalFormula getChemicalFormula()
Description copied from interface:BlockData items in the CHEMICAL_FORMULA category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_FORMULA category specify the composition and chemical properties of the compound. The formula data items must agree with those that specify the density, unit-cell and Z values. The following rules apply to the construction of the data items _chemical_formula.analytical, _chemical_formula.structural and _chemical_formula.sum. For the data item _chemical_formula.moiety, the formula construction is broken up into residues or moieties, i.e. groups of atoms that form a molecular unit or molecular ion. The rules given below apply within each moiety but different requirements apply to the way that moieties are connected (see _chemical_formula.moiety). (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count). (4) Where a group of elements is enclosed in parentheses, the multiplier for the group must follow the closing parenthesis. That is, all element and group multipliers are assumed to be printed as subscripted numbers. (An exception to this rule exists for _chemical_formula.moiety formulae where pre- and post-multipliers are permitted for molecular units.) (5) Unless the elements are ordered in a manner that corresponds to their chemical structure, as in _chemical_formula.structural, the order of the elements within any group or moiety should be: C, then H, then the other elements in alphabetical order of their symbol. This is the 'Hill' system used by Chemical Abstracts. This ordering is used in _chemical_formula.moiety and _chemical_formula.sum.- Specified by:
getChemicalFormulain interfaceBlock- Returns:
- ChemicalFormula
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getCitation
public Citation getCitation()
Description copied from interface:BlockData items in the CITATION category record details about the literature cited as being relevant to the contents of the data block.- Specified by:
getCitationin interfaceBlock- Returns:
- Citation
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getCitationAuthor
public CitationAuthor getCitationAuthor()
Description copied from interface:BlockData items in the CITATION_AUTHOR category record details about the authors associated with the citations in the CITATION list.- Specified by:
getCitationAuthorin interfaceBlock- Returns:
- CitationAuthor
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getCitationEditor
public CitationEditor getCitationEditor()
Description copied from interface:BlockData items in the CITATION_EDITOR category record details about the editors associated with the books or book chapters cited in the CITATION list.- Specified by:
getCitationEditorin interfaceBlock- Returns:
- CitationEditor
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getComputing
public Computing getComputing()
Description copied from interface:BlockData items in the COMPUTING category record details about the computer programs used in the crystal structure analysis. Data items in this category would not, in general, be used in a macromolecular CIF. The category SOFTWARE, which allows a more detailed description of computer programs and their attributes to be given, would be used instead.- Specified by:
getComputingin interfaceBlock- Returns:
- Computing
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getDatabase
public Database getDatabase()
Description copied from interface:BlockData items in the DATABASE category have been superseded by data items in the DATABASE_2 category. They are included here only for compliance with older CIFs.- Specified by:
getDatabasein interfaceBlock- Returns:
- Database
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getDatabase2
public Database2 getDatabase2()
Description copied from interface:BlockData items in the DATABASE_2 category record details about the database identifiers of the data block. These data items are assigned by database managers and should only appear in a data block if they originate from that source. The name of this category, DATABASE_2, arose because the category name DATABASE was already in use in the core CIF dictionary, but was used differently from the way it needed to be used in the mmCIF dictionary. Since CIF data names cannot be changed once they have been adopted, a new category had to be created.- Specified by:
getDatabase2in interfaceBlock- Returns:
- Database2
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getDatabasePDBCaveat
public DatabasePDBCaveat getDatabasePDBCaveat()
Description copied from interface:BlockData items in the DATABASE_PDB_CAVEAT category record details about features of the data block flagged as 'caveats' by the Protein Data Bank (PDB). These data items are included only for consistency with PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file.- Specified by:
getDatabasePDBCaveatin interfaceBlock- Returns:
- DatabasePDBCaveat
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getDatabasePDBMatrix
public DatabasePDBMatrix getDatabasePDBMatrix()
Description copied from interface:BlockThe DATABASE_PDB_MATRIX category provides placeholders for transformation matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file.- Specified by:
getDatabasePDBMatrixin interfaceBlock- Returns:
- DatabasePDBMatrix
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getDatabasePDBRemark
public DatabasePDBRemark getDatabasePDBRemark()
Description copied from interface:BlockData items in the DATABASE_PDB_REMARK category record details about the data block as archived by the Protein Data Bank (PDB). Some data appearing in PDB REMARK records can be algorithmically extracted into the appropriate data items in the data block. These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. NOTE: These remark records in this category are not uniformly annotated by the PDB and may not be consistent with nomenclature or labeling used in the entry.- Specified by:
getDatabasePDBRemarkin interfaceBlock- Returns:
- DatabasePDBRemark
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getDatabasePDBRev
public DatabasePDBRev getDatabasePDBRev()
Description copied from interface:BlockData items in the DATABASE_PDB_REV category record details about the history of the data block as archived by the Protein Data Bank (PDB). These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source.- Specified by:
getDatabasePDBRevin interfaceBlock- Returns:
- DatabasePDBRev
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getDatabasePDBRevRecord
public DatabasePDBRevRecord getDatabasePDBRevRecord()
Description copied from interface:BlockData items in the DATABASE_PDB_REV_RECORD category record details about specific record types that were changed in a given revision of a PDB entry. These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source.- Specified by:
getDatabasePDBRevRecordin interfaceBlock- Returns:
- DatabasePDBRevRecord
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getDatabasePDBTvect
public DatabasePDBTvect getDatabasePDBTvect()
Description copied from interface:BlockThe DATABASE_PDB_TVECT category provides placeholders for the TVECT matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if the data block was created by reformatting a PDB format file.- Specified by:
getDatabasePDBTvectin interfaceBlock- Returns:
- DatabasePDBTvect
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getDiffrn
public Diffrn getDiffrn()
Description copied from interface:BlockData items in the DIFFRN category record details about the diffraction data and their measurement.
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getDiffrnAttenuator
public DiffrnAttenuator getDiffrnAttenuator()
Description copied from interface:BlockData items in the DIFFRN_ATTENUATOR category record details about the diffraction attenuator scales employed.- Specified by:
getDiffrnAttenuatorin interfaceBlock- Returns:
- DiffrnAttenuator
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getDiffrnDetector
public DiffrnDetector getDiffrnDetector()
Description copied from interface:BlockData items in the DIFFRN_DETECTOR category describe the detector used to measure the scattered radiation, including any analyser and post-sample collimation.- Specified by:
getDiffrnDetectorin interfaceBlock- Returns:
- DiffrnDetector
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getDiffrnMeasurement
public DiffrnMeasurement getDiffrnMeasurement()
Description copied from interface:BlockData items in the DIFFRN_MEASUREMENT category record details about the device used to orient and/or position the crystal during data measurement and the manner in which the diffraction data were measured.- Specified by:
getDiffrnMeasurementin interfaceBlock- Returns:
- DiffrnMeasurement
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getDiffrnOrientMatrix
public DiffrnOrientMatrix getDiffrnOrientMatrix()
Description copied from interface:BlockData items in the DIFFRN_ORIENT_MATRIX category record details about the orientation matrix used in the measurement of the diffraction data.- Specified by:
getDiffrnOrientMatrixin interfaceBlock- Returns:
- DiffrnOrientMatrix
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getDiffrnOrientRefln
public DiffrnOrientRefln getDiffrnOrientRefln()
Description copied from interface:BlockData items in the DIFFRN_ORIENT_REFLN category record details about the reflections that define the orientation matrix used in the measurement of the diffraction intensities.- Specified by:
getDiffrnOrientReflnin interfaceBlock- Returns:
- DiffrnOrientRefln
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getDiffrnRadiation
public DiffrnRadiation getDiffrnRadiation()
Description copied from interface:BlockData items in the DIFFRN_RADIATION category describe the radiation used in measuring the diffraction intensities, its collimation and monochromatization before the sample. Post-sample treatment of the beam is described by data items in the DIFFRN_DETECTOR category.- Specified by:
getDiffrnRadiationin interfaceBlock- Returns:
- DiffrnRadiation
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getDiffrnRadiationWavelength
public DiffrnRadiationWavelength getDiffrnRadiationWavelength()
Description copied from interface:BlockData items in the DIFFRN_RADIATION_WAVELENGTH category describe the wavelength of the radiation used to measure the diffraction intensities. Items may be looped to identify and assign weights to distinct components of a polychromatic beam.- Specified by:
getDiffrnRadiationWavelengthin interfaceBlock- Returns:
- DiffrnRadiationWavelength
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getDiffrnRefln
public DiffrnRefln getDiffrnRefln()
Description copied from interface:BlockData items in the DIFFRN_REFLN category record details about the intensities in the diffraction data set identified by _diffrn_refln.diffrn_id. The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements in the particular diffraction data set identified by _diffrn_reflns.diffrn_id.- Specified by:
getDiffrnReflnin interfaceBlock- Returns:
- DiffrnRefln
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getDiffrnReflns
public DiffrnReflns getDiffrnReflns()
Description copied from interface:BlockData items in the DIFFRN_REFLNS category record details about the set of intensities measured in the diffraction experiment. The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements in a diffraction data set.- Specified by:
getDiffrnReflnsin interfaceBlock- Returns:
- DiffrnReflns
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getDiffrnScaleGroup
public DiffrnScaleGroup getDiffrnScaleGroup()
Description copied from interface:BlockData items in the DIFFRN_SCALE_GROUP category record details of the scaling factors applied to place all intensities in the reflection lists on a common scale. Scaling groups might, for example, correspond to each film in a multi-film data set or each crystal in a multi-crystal data set.- Specified by:
getDiffrnScaleGroupin interfaceBlock- Returns:
- DiffrnScaleGroup
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getDiffrnSource
public DiffrnSource getDiffrnSource()
Description copied from interface:BlockData items in the DIFFRN_SOURCE category record details of the source of radiation used in the diffraction experiment.- Specified by:
getDiffrnSourcein interfaceBlock- Returns:
- DiffrnSource
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getDiffrnStandardRefln
public DiffrnStandardRefln getDiffrnStandardRefln()
Description copied from interface:BlockData items in the DIFFRN_STANDARD_REFLN category record details about the reflections treated as standards during the measurement of a set of diffraction intensities. Note that these are the individual standard reflections, not the results of the analysis of the standard reflections.- Specified by:
getDiffrnStandardReflnin interfaceBlock- Returns:
- DiffrnStandardRefln
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getDiffrnStandards
public DiffrnStandards getDiffrnStandards()
Description copied from interface:BlockData items in the DIFFRN_STANDARDS category record details about the set of standard reflections used to monitor intensity stability during the measurement of diffraction intensities. Note that these records describe properties common to the set of standard reflections, not the standard reflections themselves.- Specified by:
getDiffrnStandardsin interfaceBlock- Returns:
- DiffrnStandards
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getEntity
public Entity getEntity()
Description copied from interface:BlockData items in the ENTITY category record details (such as chemical composition, name and source) about the molecular entities that are present in the crystallographic structure. Items in the various ENTITY subcategories provide a full chemical description of these molecular entities. Entities are of three types: polymer, non-polymer and water. Note that the water category includes only water; ordered solvent such as sulfate ion or acetone would be described as individual non-polymer entities. The ENTITY category is specific to macromolecular CIF applications and replaces the function of the CHEMICAL category in the CIF core. It is important to remember that the ENTITY data are not the result of the crystallographic experiment; those results are represented by the ATOM_SITE data items. ENTITY data items describe the chemistry of the molecules under investigation and can most usefully be thought of as the ideal groups to which the structure is restrained or constrained during refinement. It is also important to remember that entities do not correspond directly to the enumeration of the contents of the asymmetric unit. Entities are described only once, even in those structures that contain multiple observations of an entity. The STRUCT_ASYM data items, which reference the entity list, describe and label the contents of the asymmetric unit.
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getEntityKeywords
public EntityKeywords getEntityKeywords()
Description copied from interface:BlockData items in the ENTITY_KEYWORDS category specify keywords relevant to the molecular entities. Note that this list of keywords is separate from the list that is used for the STRUCT_BIOL data items and is intended to provide only the information that one would know about the molecular entity *if one did not know its structure*. Hence polypeptides are simply polypeptides, not cytokines or beta-alpha-barrels, and polyribonucleic acids are simply poly-RNA, not transfer- RNA.- Specified by:
getEntityKeywordsin interfaceBlock- Returns:
- EntityKeywords
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getEntityLink
public EntityLink getEntityLink()
Description copied from interface:BlockData items in the ENTITY_LINK category give details about the links between entities.- Specified by:
getEntityLinkin interfaceBlock- Returns:
- EntityLink
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getEntityNameCom
public EntityNameCom getEntityNameCom()
Description copied from interface:BlockData items in the ENTITY_NAME_COM category record the common name or names associated with the entity. In some cases, the entity name may not be the same as the name of the biological structure. For example, haemoglobin alpha chain would be the entity common name, not haemoglobin.- Specified by:
getEntityNameComin interfaceBlock- Returns:
- EntityNameCom
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getEntityNameSys
public EntityNameSys getEntityNameSys()
Description copied from interface:BlockData items in the ENTITY_NAME_SYS category record the systematic name or names associated with the entity and the system that was used to construct the systematic name. In some cases, the entity name may not be the same as the name of the biological structure.- Specified by:
getEntityNameSysin interfaceBlock- Returns:
- EntityNameSys
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getEntityPoly
public EntityPoly getEntityPoly()
Description copied from interface:BlockData items in the ENTITY_POLY category record details about the polymer, such as the type of the polymer, the number of monomers and whether it has nonstandard features.- Specified by:
getEntityPolyin interfaceBlock- Returns:
- EntityPoly
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getEntityPolySeq
public EntityPolySeq getEntityPolySeq()
Description copied from interface:BlockData items in the ENTITY_POLY_SEQ category specify the sequence of monomers in a polymer. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID. The corresponding ATOM_SITE entries should reflect this heterogeneity.- Specified by:
getEntityPolySeqin interfaceBlock- Returns:
- EntityPolySeq
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getEntry
public Entry getEntry()
Description copied from interface:BlockThere is only one item in the ENTRY category, _entry.id. This data item gives a name to this entry and is indirectly a key to the categories (such as CELL, GEOM, EXPTL) that describe information pertinent to the entire data block.
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getEntryLink
public EntryLink getEntryLink()
Description copied from interface:BlockData items in the ENTRY_LINK category record the relationships between the current data block identified by _entry.id and other data blocks within the current file which may be referenced in the current data block.- Specified by:
getEntryLinkin interfaceBlock- Returns:
- EntryLink
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getExptl
public Exptl getExptl()
Description copied from interface:BlockData items in the EXPTL category record details about the experimental work prior to the intensity measurements and details about the absorption-correction technique employed.
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getExptlCrystal
public ExptlCrystal getExptlCrystal()
Description copied from interface:BlockData items in the EXPTL_CRYSTAL category record the results of experimental measurements on the crystal or crystals used, such as shape, size or density.- Specified by:
getExptlCrystalin interfaceBlock- Returns:
- ExptlCrystal
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getExptlCrystalFace
public ExptlCrystalFace getExptlCrystalFace()
Description copied from interface:BlockData items in the EXPTL_CRYSTAL_FACE category record details of the crystal faces.- Specified by:
getExptlCrystalFacein interfaceBlock- Returns:
- ExptlCrystalFace
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getExptlCrystalGrow
public ExptlCrystalGrow getExptlCrystalGrow()
Description copied from interface:BlockData items in the EXPTL_CRYSTAL_GROW category record details about the conditions and methods used to grow the crystal.- Specified by:
getExptlCrystalGrowin interfaceBlock- Returns:
- ExptlCrystalGrow
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getExptlCrystalGrowComp
public ExptlCrystalGrowComp getExptlCrystalGrowComp()
Description copied from interface:BlockData items in the EXPTL_CRYSTAL_GROW_COMP category record details about the components of the solutions that were 'mixed' (by whatever means) to produce the crystal. In general, solution 1 is the solution that contains the molecule to be crystallized and solution 2 is the solution that contains the precipitant. However, the number of solutions required to describe the crystallization protocol is not limited to 2. Details of the crystallization protocol should be given in _exptl_crystal_grow_comp.details using the solutions described in EXPTL_CRYSTAL_GROW_COMP.- Specified by:
getExptlCrystalGrowCompin interfaceBlock- Returns:
- ExptlCrystalGrowComp
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getGeom
public Geom getGeom()
Description copied from interface:BlockData items in the GEOM and related (GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_HBOND and GEOM_TORSION) categories record details about the molecular geometry as calculated from the contents of the ATOM, CELL and SYMMETRY data. Geometry data are therefore redundant, in that they can be calculated from other more fundamental quantities in the data block. However, they provide a check on the correctness of both sets of data and enable the most important geometric data to be identified for publication by setting the appropriate publication flag.
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getGeomAngle
public GeomAngle getGeomAngle()
Description copied from interface:BlockData items in the GEOM_ANGLE category record details about the bond angles as calculated from the contents of the ATOM, CELL and SYMMETRY data.- Specified by:
getGeomAnglein interfaceBlock- Returns:
- GeomAngle
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getGeomBond
public GeomBond getGeomBond()
Description copied from interface:BlockData items in the GEOM_BOND category record details about the bond lengths as calculated from the contents of the ATOM, CELL and SYMMETRY data.- Specified by:
getGeomBondin interfaceBlock- Returns:
- GeomBond
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getGeomContact
public GeomContact getGeomContact()
Description copied from interface:BlockData items in the GEOM_CONTACT category record details about interatomic contacts as calculated from the contents of the ATOM, CELL and SYMMETRY data.- Specified by:
getGeomContactin interfaceBlock- Returns:
- GeomContact
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getGeomHbond
public GeomHbond getGeomHbond()
Description copied from interface:BlockData items in the GEOM_HBOND category record details about hydrogen bonds as calculated from the contents of the ATOM, CELL and SYMMETRY data.- Specified by:
getGeomHbondin interfaceBlock- Returns:
- GeomHbond
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getGeomTorsion
public GeomTorsion getGeomTorsion()
Description copied from interface:BlockData items in the GEOM_TORSION category record details about torsion angles as calculated from the contents of the ATOM, CELL and SYMMETRY data. The vector direction _geom_torsion.atom_site_id_2 to _geom_torsion.atom_site_id_3 is the viewing direction, and the torsion angle is the angle of twist required to superimpose the projection of the vector between site 2 and site 1 onto the projection of the vector between site 3 and site 4. Clockwise torsions are positive, anticlockwise torsions are negative. Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523.- Specified by:
getGeomTorsionin interfaceBlock- Returns:
- GeomTorsion
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getJournal
public Journal getJournal()
Description copied from interface:BlockData items in the JOURNAL category record details about the book-keeping by the journal staff when processing a data block submitted for publication. The creator of a data block will not normally specify these data. The data names are not defined in the dictionary because they are for journal use only.- Specified by:
getJournalin interfaceBlock- Returns:
- Journal
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getJournalIndex
public JournalIndex getJournalIndex()
Description copied from interface:BlockData items in the JOURNAL_INDEX category are used to list terms used to generate the journal indexes. The creator of a data block will not normally specify these data items.- Specified by:
getJournalIndexin interfaceBlock- Returns:
- JournalIndex
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getPhasing
public Phasing getPhasing()
Description copied from interface:BlockData items in the PHASING category record details about the phasing of the structure, listing the various methods used in the phasing process. Details about the application of each method are listed in the appropriate subcategories.- Specified by:
getPhasingin interfaceBlock- Returns:
- Phasing
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getPhasingAveraging
public PhasingAveraging getPhasingAveraging()
Description copied from interface:BlockData items in the PHASING_AVERAGING category record details about the phasing of the structure where methods involving averaging of multiple observations of the molecule in the asymmetric unit are involved.- Specified by:
getPhasingAveragingin interfaceBlock- Returns:
- PhasingAveraging
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getPhasingIsomorphous
public PhasingIsomorphous getPhasingIsomorphous()
Description copied from interface:BlockData items in the PHASING_ISOMORPHOUS category record details about the phasing of the structure where a model isomorphous to the structure being phased was used to generate the initial phases.- Specified by:
getPhasingIsomorphousin interfaceBlock- Returns:
- PhasingIsomorphous
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getPhasingMAD
public PhasingMAD getPhasingMAD()
Description copied from interface:BlockData items in the PHASING_MAD category record details about the phasing of the structure where methods involving multiple-wavelength anomalous-dispersion techniques are involved.- Specified by:
getPhasingMADin interfaceBlock- Returns:
- PhasingMAD
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getPhasingMADClust
public PhasingMADClust getPhasingMADClust()
Description copied from interface:BlockData items in the PHASING_MAD_CLUST category record details about a cluster of experiments that contributed to the generation of a set of phases.- Specified by:
getPhasingMADClustin interfaceBlock- Returns:
- PhasingMADClust
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getPhasingMADExpt
public PhasingMADExpt getPhasingMADExpt()
Description copied from interface:BlockData items in the PHASING_MAD_EXPT category record details about a MAD phasing experiment, such as the number of experiments that were clustered together to produce a set of phases or the statistics for those phases.- Specified by:
getPhasingMADExptin interfaceBlock- Returns:
- PhasingMADExpt
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getPhasingMADRatio
public PhasingMADRatio getPhasingMADRatio()
Description copied from interface:BlockData items in the PHASING_MAD_RATIO category record the ratios of phasing statistics between pairs of data sets in a MAD phasing experiment, in given shells of resolution.- Specified by:
getPhasingMADRatioin interfaceBlock- Returns:
- PhasingMADRatio
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getPhasingMADSet
public PhasingMADSet getPhasingMADSet()
Description copied from interface:BlockData items in the PHASING_MAD_SET category record details about the individual data sets used in a MAD phasing experiment.- Specified by:
getPhasingMADSetin interfaceBlock- Returns:
- PhasingMADSet
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getPhasingMIR
public PhasingMIR getPhasingMIR()
Description copied from interface:BlockData items in the PHASING_MIR category record details about the phasing of the structure where methods involving isomorphous replacement are involved. All isomorphous-replacement-based techniques are covered by this category, including single isomorphous replacement (SIR), multiple isomorphous replacement (MIR) and single or multiple isomorphous replacement plus anomalous scattering (SIRAS, MIRAS).- Specified by:
getPhasingMIRin interfaceBlock- Returns:
- PhasingMIR
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getPhasingMIRDer
public PhasingMIRDer getPhasingMIRDer()
Description copied from interface:BlockData items in the PHASING_MIR_DER category record details about individual derivatives used in the phasing of the structure when methods involving isomorphous replacement are involved. A derivative in this context does not necessarily equate with a data set; for instance, the same data set could be used to one resolution limit as an isomorphous scatterer and to a different resolution (and with a different sigma cutoff) as an anomalous scatterer. These would be treated as two distinct derivatives, although both derivatives would point to the same data sets via _phasing_MIR_der.der_set_id and _phasing_MIR_der.native_set_id.- Specified by:
getPhasingMIRDerin interfaceBlock- Returns:
- PhasingMIRDer
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getPhasingMIRDerRefln
public PhasingMIRDerRefln getPhasingMIRDerRefln()
Description copied from interface:BlockData items in the PHASING_MIR_DER_REFLN category record details about the calculated structure factors obtained in an MIR phasing experiment. This list may contain information from a number of different derivatives; _phasing_MIR_der_refln.der_id indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.) It is not necessary for the data items describing the measured value of F to appear in this list, as they will be given in the PHASING_SET_REFLN category. However, these items can also be listed here for completeness.- Specified by:
getPhasingMIRDerReflnin interfaceBlock- Returns:
- PhasingMIRDerRefln
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getPhasingMIRDerShell
public PhasingMIRDerShell getPhasingMIRDerShell()
Description copied from interface:BlockData items in the PHASING_MIR_DER_SHELL category record statistics, broken down into shells of resolution, for an MIR phasing experiment. This list may contain information from a number of different derivatives; _phasing_MIR_der_shell.der_id indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.)- Specified by:
getPhasingMIRDerShellin interfaceBlock- Returns:
- PhasingMIRDerShell
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getPhasingMIRDerSite
public PhasingMIRDerSite getPhasingMIRDerSite()
Description copied from interface:BlockData items in the PHASING_MIR_DER_SITE category record details about the heavy-atom sites in an MIR phasing experiment. This list may contain information from a number of different derivatives; _phasing_MIR_der_site.der_id indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.)- Specified by:
getPhasingMIRDerSitein interfaceBlock- Returns:
- PhasingMIRDerSite
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getPhasingMIRShell
public PhasingMIRShell getPhasingMIRShell()
Description copied from interface:BlockData items in the PHASING_MIR_SHELL category record statistics for an isomorphous replacement phasing experiment.broken down into shells of resolution.- Specified by:
getPhasingMIRShellin interfaceBlock- Returns:
- PhasingMIRShell
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getPhasingSet
public PhasingSet getPhasingSet()
Description copied from interface:BlockData items in the PHASING_SET category record details about the data sets used in a phasing experiment. A given data set may be used in a number of different ways; for instance, a single data set could be used both as an isomorphous derivative and as a component of a multiple-wavelength calculation. This category establishes identifiers for each data set and permits the archiving of a subset of experimental information for each data set (cell constants, wavelength, temperature etc.). This and related categories of data items are provided so that derivative intensity and phase information can be stored in the same data block as the information for the refined structure. If all the possible experimental information for each data set (raw data sets, crystal growth conditions etc.) is to be archived, these data items should be recorded in a separate data block.- Specified by:
getPhasingSetin interfaceBlock- Returns:
- PhasingSet
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getPhasingSetRefln
public PhasingSetRefln getPhasingSetRefln()
Description copied from interface:BlockData items in the PHASING_SET_REFLN category record the values of the measured structure factors used in a phasing experiment. This list may contain information from a number of different data sets; _phasing_set_refln.set_id indicates the data set to which a given record corresponds.- Specified by:
getPhasingSetReflnin interfaceBlock- Returns:
- PhasingSetRefln
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getPubl
public Publ getPubl()
Description copied from interface:BlockData items in the PUBL category are used when submitting a manuscript for publication.
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getPublAuthor
public PublAuthor getPublAuthor()
Description copied from interface:BlockData items in the PUBL_AUTHOR category record details of the authors of a manuscript submitted for publication.- Specified by:
getPublAuthorin interfaceBlock- Returns:
- PublAuthor
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getPublBody
public PublBody getPublBody()
Description copied from interface:BlockData items in the PUBL_BODY category permit the labelling of different text sections within the body of a paper. Note that these should not be used in a paper which has a standard format with sections tagged by specific data names (such as in Acta Crystallographica Section C). Typically, each journal will supply a list of the specific items it requires in its Notes for Authors.- Specified by:
getPublBodyin interfaceBlock- Returns:
- PublBody
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getPublManuscriptIncl
public PublManuscriptIncl getPublManuscriptIncl()
Description copied from interface:BlockData items in the PUBL_MANUSCRIPT_INCL category allow the authors of a manuscript submitted for publication to list data names that should be added to the standard request list used by the journal printing software.- Specified by:
getPublManuscriptInclin interfaceBlock- Returns:
- PublManuscriptIncl
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getRefine
public Refine getRefine()
Description copied from interface:BlockData items in the REFINE category record details about the structure-refinement parameters.
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getRefineAnalyze
public RefineAnalyze getRefineAnalyze()
Description copied from interface:BlockData items in the REFINE_ANALYZE category record details about the refined structure that are often used to analyze the refinement and assess its quality. A given computer program may or may not produce values corresponding to these data names.- Specified by:
getRefineAnalyzein interfaceBlock- Returns:
- RefineAnalyze
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getRefineBIso
public RefineBIso getRefineBIso()
Description copied from interface:BlockData items in the REFINE_B_ISO category record details about the treatment of isotropic B factors (displacement parameters) during refinement.- Specified by:
getRefineBIsoin interfaceBlock- Returns:
- RefineBIso
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getRefineFunctMinimized
public RefineFunctMinimized getRefineFunctMinimized()
Description copied from interface:BlockData items in the REFINE_FUNCT_MINIMIZED category record details about the individual terms of the function minimized during refinement.- Specified by:
getRefineFunctMinimizedin interfaceBlock- Returns:
- RefineFunctMinimized
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getRefineHist
public RefineHist getRefineHist()
Description copied from interface:BlockData items in the REFINE_HIST category record details about the steps during the refinement of the structure. These data items are not meant to be as thorough a description of the refinement as is provided for the final model in other categories; rather, these data items provide a mechanism for sketching out the progress of the refinement, supported by a small set of representative statistics.- Specified by:
getRefineHistin interfaceBlock- Returns:
- RefineHist
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getRefineLsRestr
public RefineLsRestr getRefineLsRestr()
Description copied from interface:BlockData items in the REFINE_LS_RESTR category record details about the restraints applied to various classes of parameters during the least-squares refinement.- Specified by:
getRefineLsRestrin interfaceBlock- Returns:
- RefineLsRestr
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getRefineLsRestrNcs
public RefineLsRestrNcs getRefineLsRestrNcs()
Description copied from interface:BlockData items in the REFINE_LS_RESTR_NCS category record details about the restraints applied to atom positions in domains related by noncrystallographic symmetry during least-squares refinement, and also about the deviation of the restrained atomic parameters at the end of the refinement. It is expected that these values will only be reported once for each set of restrained domains.- Specified by:
getRefineLsRestrNcsin interfaceBlock- Returns:
- RefineLsRestrNcs
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getRefineLsRestrType
public RefineLsRestrType getRefineLsRestrType()
Description copied from interface:BlockData items in the REFINE_LS_RESTR_TYPE category record details about the restraint types used in the least-squares refinement.- Specified by:
getRefineLsRestrTypein interfaceBlock- Returns:
- RefineLsRestrType
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getRefineLsShell
public RefineLsShell getRefineLsShell()
Description copied from interface:BlockData items in the REFINE_LS_SHELL category record details about the results of the least-squares refinement broken down into shells of resolution.- Specified by:
getRefineLsShellin interfaceBlock- Returns:
- RefineLsShell
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getRefineOccupancy
public RefineOccupancy getRefineOccupancy()
Description copied from interface:BlockData items in the REFINE_OCCUPANCY category record details about the treatment of atom occupancies during refinement.- Specified by:
getRefineOccupancyin interfaceBlock- Returns:
- RefineOccupancy
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getRefln
public Refln getRefln()
Description copied from interface:BlockData items in the REFLN category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped.
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getReflnSysAbs
public ReflnSysAbs getReflnSysAbs()
Description copied from interface:BlockData items in the REFLN_SYS_ABS category record details about the reflection data that should be systematically absent, given the designated space group.- Specified by:
getReflnSysAbsin interfaceBlock- Returns:
- ReflnSysAbs
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getReflns
public Reflns getReflns()
Description copied from interface:BlockData items in the REFLNS category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped.
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getReflnsScale
public ReflnsScale getReflnsScale()
Description copied from interface:BlockData items in the REFLNS_SCALE category record details about the structure-factor scales. They are referenced from within the REFLN list through _refln.scale_group_code.- Specified by:
getReflnsScalein interfaceBlock- Returns:
- ReflnsScale
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getReflnsShell
public ReflnsShell getReflnsShell()
Description copied from interface:BlockData items in the REFLNS_SHELL category record details about the reflection data used to determine the ATOM_SITE data items broken down into shells of resolution.- Specified by:
getReflnsShellin interfaceBlock- Returns:
- ReflnsShell
-
getSoftware
public Software getSoftware()
Description copied from interface:BlockData items in the SOFTWARE category record details about the software used in the structure analysis, which implies any software used in the generation of any data items associated with the structure determination and structure representation. These data items allow computer programs to be referenced in more detail than data items in the COMPUTING category do.- Specified by:
getSoftwarein interfaceBlock- Returns:
- Software
-
getStruct
public Struct getStruct()
Description copied from interface:BlockData items in the STRUCT category record details about the description of the crystallographic structure.
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getStructAsym
public StructAsym getStructAsym()
Description copied from interface:BlockData items in the STRUCT_ASYM category record details about the structural elements in the asymmetric unit.- Specified by:
getStructAsymin interfaceBlock- Returns:
- StructAsym
-
getStructBiol
public StructBiol getStructBiol()
Description copied from interface:BlockData items in the STRUCT_BIOL category record details about the structural elements that form each structure of biological significance. A given crystal structure may contain many different biological structures. A given structural component in the asymmetric unit may be part of more than one biological unit. A given biological structure may involve crystallographic symmetry. For instance, in a structure of a lysozyme-FAB structure, the light- and heavy-chain components of the FAB could be one biological unit, while the two chains of the FAB and the lysozyme could constitute a second biological unit.- Specified by:
getStructBiolin interfaceBlock- Returns:
- StructBiol
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getStructBiolGen
public StructBiolGen getStructBiolGen()
Description copied from interface:BlockData items in the STRUCT_BIOL_GEN category record details about the generation of each biological unit. The STRUCT_BIOL_GEN data items provide the specifications of the components that constitute that biological unit, which may include symmetry elements.- Specified by:
getStructBiolGenin interfaceBlock- Returns:
- StructBiolGen
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getStructBiolKeywords
public StructBiolKeywords getStructBiolKeywords()
Description copied from interface:BlockData items in the STRUCT_BIOL_KEYWORDS category record keywords that describe each biological unit.- Specified by:
getStructBiolKeywordsin interfaceBlock- Returns:
- StructBiolKeywords
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getStructBiolView
public StructBiolView getStructBiolView()
Description copied from interface:BlockData items in the STRUCT_BIOL_VIEW category record details about how to draw and annotate an informative view of the biological structure.- Specified by:
getStructBiolViewin interfaceBlock- Returns:
- StructBiolView
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getStructConf
public StructConf getStructConf()
Description copied from interface:BlockData items in the STRUCT_CONF category record details about the backbone conformation of a segment of polymer. Data items in the STRUCT_CONF_TYPE category define the criteria used to identify the backbone conformations.- Specified by:
getStructConfin interfaceBlock- Returns:
- StructConf
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getStructConfType
public StructConfType getStructConfType()
Description copied from interface:BlockData items in the STRUCT_CONF_TYPE category record details about the criteria used to identify backbone conformations of a segment of polymer.- Specified by:
getStructConfTypein interfaceBlock- Returns:
- StructConfType
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getStructConn
public StructConn getStructConn()
Description copied from interface:BlockData items in the STRUCT_CONN category record details about the connections between portions of the structure. These can be hydrogen bonds, salt bridges, disulfide bridges and so on. The STRUCT_CONN_TYPE records define the criteria used to identify these connections.- Specified by:
getStructConnin interfaceBlock- Returns:
- StructConn
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getStructConnType
public StructConnType getStructConnType()
Description copied from interface:BlockData items in the STRUCT_CONN_TYPE category record details about the criteria used to identify interactions between portions of the structure.- Specified by:
getStructConnTypein interfaceBlock- Returns:
- StructConnType
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getStructKeywords
public StructKeywords getStructKeywords()
Description copied from interface:BlockData items in the STRUCT_KEYWORDS category specify keywords that describe the chemical structure in this entry.- Specified by:
getStructKeywordsin interfaceBlock- Returns:
- StructKeywords
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getStructMonDetails
public StructMonDetails getStructMonDetails()
Description copied from interface:BlockData items in the STRUCT_MON_DETAILS category record details about specifics of calculations summarized in data items in the STRUCT_MON_PROT and STRUCT_MON_NUCL categories. These can include the coefficients used in map calculations, the radii used for including points in a calculation and so on.- Specified by:
getStructMonDetailsin interfaceBlock- Returns:
- StructMonDetails
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getStructMonNucl
public StructMonNucl getStructMonNucl()
Description copied from interface:BlockData items in the STRUCT_MON_NUCL category record details about structural properties of a nucleic acid when analyzed at the monomer level. Analogous data items for proteins are given in the STRUCT_MON_PROT category. For items where the value of the property depends on the method employed to calculate it, details of the method of calculation are given using data items in the STRUCT_MON_DETAILS category.- Specified by:
getStructMonNuclin interfaceBlock- Returns:
- StructMonNucl
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getStructMonProt
public StructMonProt getStructMonProt()
Description copied from interface:BlockData items in the STRUCT_MON_PROT category record details about structural properties of a protein when analyzed at the monomer level. Analogous data items for nucleic acids are given in the STRUCT_MON_NUCL category. For items where the value of the property depends on the method employed to calculate it, details of the method of calculation are given using data items in the STRUCT_MON_DETAILS category.- Specified by:
getStructMonProtin interfaceBlock- Returns:
- StructMonProt
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getStructMonProtCis
public StructMonProtCis getStructMonProtCis()
Description copied from interface:BlockData items in the STRUCT_MON_PROT_CIS category identify monomers that have been found to have the peptide bond in the cis conformation. The criterion used to select residues to be designated as containing cis peptide bonds is given in _struct_mon_details.prot_cis.- Specified by:
getStructMonProtCisin interfaceBlock- Returns:
- StructMonProtCis
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getStructNcsDom
public StructNcsDom getStructNcsDom()
Description copied from interface:BlockData items in the STRUCT_NCS_DOM category record information about the domains in an ensemble of domains related by one or more noncrystallographic symmetry operators. A domain need not correspond to a complete polypeptide chain; it can be composed of one or more segments in a single chain, or by segments from more than one chain.- Specified by:
getStructNcsDomin interfaceBlock- Returns:
- StructNcsDom
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getStructNcsDomLim
public StructNcsDomLim getStructNcsDomLim()
Description copied from interface:BlockData items in the STRUCT_NCS_DOM_LIM category identify the start and end points of polypeptide chain segments that form all or part of a domain in an ensemble of domains related by noncrystallographic symmetry.- Specified by:
getStructNcsDomLimin interfaceBlock- Returns:
- StructNcsDomLim
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getStructNcsEns
public StructNcsEns getStructNcsEns()
Description copied from interface:BlockData items in the STRUCT_NCS_ENS category record information about ensembles of domains related by noncrystallographic symmetry. The point group of the ensemble when taken as a whole may be specified, as well as any special aspects of the ensemble that require description.- Specified by:
getStructNcsEnsin interfaceBlock- Returns:
- StructNcsEns
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getStructNcsEnsGen
public StructNcsEnsGen getStructNcsEnsGen()
Description copied from interface:BlockData items in the STRUCT_NCS_ENS_GEN category list domains related by a noncrystallographic symmetry operation and identify the operator.- Specified by:
getStructNcsEnsGenin interfaceBlock- Returns:
- StructNcsEnsGen
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getStructNcsOper
public StructNcsOper getStructNcsOper()
Description copied from interface:BlockData items in the STRUCT_NCS_OPER category describe the noncrystallographic symmetry operations. Each operator is specified as a matrix and a subsequent translation vector. Operators need not represent proper rotations.- Specified by:
getStructNcsOperin interfaceBlock- Returns:
- StructNcsOper
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getStructRef
public StructRef getStructRef()
Description copied from interface:BlockData items in the STRUCT_REF category allow the author of a data block to relate the entities or biological units described in the data block to information archived in external databases. For references to the sequence of a polymer, the value of the data item _struct_ref.seq_align is used to indicate whether the correspondence between the sequence of the entity or biological unit in the data block and the sequence in the referenced database entry is 'complete' or 'partial'. If this value is 'partial', the region (or regions) of the alignment may be delimited using data items in the STRUCT_REF_SEQ category. Similarly, the value of _struct_ref.seq_dif is used to indicate whether the two sequences contain point differences. If the value is 'yes', the differences may be identified and annotated using data items in the STRUCT_REF_SEQ_DIF category.- Specified by:
getStructRefin interfaceBlock- Returns:
- StructRef
-
getStructRefSeq
public StructRefSeq getStructRefSeq()
Description copied from interface:BlockData items in the STRUCT_REF_SEQ category provide a mechanism for indicating and annotating a region (or regions) of alignment between the sequence of an entity or biological unit described in the data block and the sequence in the referenced database entry.- Specified by:
getStructRefSeqin interfaceBlock- Returns:
- StructRefSeq
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getStructRefSeqDif
public StructRefSeqDif getStructRefSeqDif()
Description copied from interface:BlockData items in the STRUCT_REF_SEQ_DIF category provide a mechanism for indicating and annotating point differences between the sequence of the entity or biological unit described in the data block and the sequence of the referenced database entry.- Specified by:
getStructRefSeqDifin interfaceBlock- Returns:
- StructRefSeqDif
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getStructSheet
public StructSheet getStructSheet()
Description copied from interface:BlockData items in the STRUCT_SHEET category record details about the beta-sheets.- Specified by:
getStructSheetin interfaceBlock- Returns:
- StructSheet
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getStructSheetHbond
public StructSheetHbond getStructSheetHbond()
Description copied from interface:BlockData items in the STRUCT_SHEET_HBOND category record details about the hydrogen bonding between residue ranges in a beta- sheet. It is necessary to treat hydrogen bonding independently of the designation of ranges, because the hydrogen bonding may begin in different places for the interactions of a given strand with the one preceding it and the one following it in the sheet.- Specified by:
getStructSheetHbondin interfaceBlock- Returns:
- StructSheetHbond
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getStructSheetOrder
public StructSheetOrder getStructSheetOrder()
Description copied from interface:BlockData items in the STRUCT_SHEET_ORDER category record details about the order of the residue ranges that form a beta-sheet. All order links are pairwise and the specified pairs are assumed to be adjacent to one another in the sheet. These data items are an alternative to the STRUCT_SHEET_TOPOLOGY data items and they allow all manner of sheets to be described.- Specified by:
getStructSheetOrderin interfaceBlock- Returns:
- StructSheetOrder
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getStructSheetRange
public StructSheetRange getStructSheetRange()
Description copied from interface:BlockData items in the STRUCT_SHEET_RANGE category record details about the residue ranges that form a beta-sheet. Residues are included in a range if they made beta-sheet-type hydrogen-bonding interactions with at least one adjacent strand and if there are at least two residues in the range.- Specified by:
getStructSheetRangein interfaceBlock- Returns:
- StructSheetRange
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getStructSheetTopology
public StructSheetTopology getStructSheetTopology()
Description copied from interface:BlockData items in the STRUCT_SHEET_TOPOLOGY category record details about the topology of the residue ranges that form a beta-sheet. All topology links are pairwise and the specified pairs are assumed to be successive in the amino-acid sequence. These data items are useful in describing various simple and complex folds, but they become inadequate when the strands in the sheet come from more than one chain. The STRUCT_SHEET_ORDER data items can be used to describe single- and multiple-chain-containing sheets.- Specified by:
getStructSheetTopologyin interfaceBlock- Returns:
- StructSheetTopology
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getStructSite
public StructSite getStructSite()
Description copied from interface:BlockData items in the STRUCT_SITE category record details about portions of the structure that contribute to structurally relevant sites (e.g. active sites, substrate-binding subsites, metal-coordination sites).- Specified by:
getStructSitein interfaceBlock- Returns:
- StructSite
-
getStructSiteGen
public StructSiteGen getStructSiteGen()
Description copied from interface:BlockData items in the STRUCT_SITE_GEN category record details about the generation of portions of the structure that contribute to structurally relevant sites.- Specified by:
getStructSiteGenin interfaceBlock- Returns:
- StructSiteGen
-
getStructSiteKeywords
public StructSiteKeywords getStructSiteKeywords()
Description copied from interface:BlockData items in the STRUCT_SITE_KEYWORDS category record keywords describing the site.- Specified by:
getStructSiteKeywordsin interfaceBlock- Returns:
- StructSiteKeywords
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getStructSiteView
public StructSiteView getStructSiteView()
Description copied from interface:BlockData items in the STRUCT_SITE_VIEW category record details about how to draw and annotate an informative view of the site.- Specified by:
getStructSiteViewin interfaceBlock- Returns:
- StructSiteView
-
getSymmetry
public Symmetry getSymmetry()
Description copied from interface:BlockData items in the SYMMETRY category record details about the space-group symmetry.- Specified by:
getSymmetryin interfaceBlock- Returns:
- Symmetry
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getSymmetryEquiv
public SymmetryEquiv getSymmetryEquiv()
Description copied from interface:BlockData items in the SYMMETRY_EQUIV category list the symmetry-equivalent positions for the space group.- Specified by:
getSymmetryEquivin interfaceBlock- Returns:
- SymmetryEquiv
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getAuditLink
public AuditLink getAuditLink()
Description copied from interface:BlockData items in the AUDIT_LINK category record details about the relationships between data blocks in the current CIF.- Specified by:
getAuditLinkin interfaceBlock- Returns:
- AuditLink
-
getDiffrnReflnsClass
public DiffrnReflnsClass getDiffrnReflnsClass()
Description copied from interface:BlockData items in the DIFFRN_REFLNS_CLASS category record details about the classes of reflections measured in the diffraction experiment.- Specified by:
getDiffrnReflnsClassin interfaceBlock- Returns:
- DiffrnReflnsClass
-
getRefineLsClass
public RefineLsClass getRefineLsClass()
Description copied from interface:BlockData items in the REFINE_LS_CLASS category record details about the reflections used for the structure refinement for each reflection class separately.- Specified by:
getRefineLsClassin interfaceBlock- Returns:
- RefineLsClass
-
getReflnsClass
public ReflnsClass getReflnsClass()
Description copied from interface:BlockData items in the REFLNS_CLASS category record details of the reflections used to determine the structural parameters for each reflection class.- Specified by:
getReflnsClassin interfaceBlock- Returns:
- ReflnsClass
-
getSpaceGroup
public SpaceGroup getSpaceGroup()
Description copied from interface:BlockContains all the data items that refer to the space group as a whole, such as its name or crystal system. They may be looped, for example, in a list of space groups and their properties. Only a subset of the SPACE_GROUP category items appear in this dictionary. The remainder are found in the symmetry CIF dictionary. Space-group types are identified by their number as given in International Tables for Crystallography Vol. A. Specific settings of the space groups can be identified either by their Hall symbol or by specifying their symmetry operations. The commonly used Hermann-Mauguin symbol determines the space-group type uniquely but several different Hermann-Mauguin symbols may refer to the same space-group type. A Hermann-Mauguin symbol contains information on the choice of the basis, but not on the choice of origin. Different formats for the Hermann-Mauguin symbol are found in the symmetry CIF dictionary.- Specified by:
getSpaceGroupin interfaceBlock- Returns:
- SpaceGroup
-
getSpaceGroupSymop
public SpaceGroupSymop getSpaceGroupSymop()
Description copied from interface:BlockContains information about the symmetry operations of the space group.- Specified by:
getSpaceGroupSymopin interfaceBlock- Returns:
- SpaceGroupSymop
-
getValenceParam
public ValenceParam getValenceParam()
Description copied from interface:BlockData items in the VALENCE_PARAM category define the parameters used for calculating bond valences from bond lengths. In addition to the parameters, a pointer is given to the reference (in VALENCE_REF) from which the bond-valence parameters were taken.- Specified by:
getValenceParamin interfaceBlock- Returns:
- ValenceParam
-
getValenceRef
public ValenceRef getValenceRef()
Description copied from interface:BlockData items in the VALENCE_REF category list the references from which the bond-valence parameters have been taken.- Specified by:
getValenceRefin interfaceBlock- Returns:
- ValenceRef
-
getPdbxAudit
public PdbxAudit getPdbxAudit()
Description copied from interface:BlockThe PDBX_AUDIT holds current version information.- Specified by:
getPdbxAuditin interfaceBlock- Returns:
- PdbxAudit
-
getPdbxVersion
public PdbxVersion getPdbxVersion()
Description copied from interface:BlockData items in the PDBX_VERSION category record details about the version of this entry.- Specified by:
getPdbxVersionin interfaceBlock- Returns:
- PdbxVersion
-
getPdbxAuditAuthor
public PdbxAuditAuthor getPdbxAuditAuthor()
Description copied from interface:BlockData items in the PDBX_AUDIT_AUTHOR category record details about the author(s) of the data block.- Specified by:
getPdbxAuditAuthorin interfaceBlock- Returns:
- PdbxAuditAuthor
-
getPdbxDatabaseMessage
public PdbxDatabaseMessage getPdbxDatabaseMessage()
Description copied from interface:BlockThe PDBX_DATABASE_MESSAGE category provides information about correspondance related to a structure deposition.- Specified by:
getPdbxDatabaseMessagein interfaceBlock- Returns:
- PdbxDatabaseMessage
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getPdbxDatabasePDBObsSpr
public PdbxDatabasePDBObsSpr getPdbxDatabasePDBObsSpr()
Description copied from interface:BlockThe PDBX_DATABASE_PDB_OBS_SPR category provides placeholders for information on obsolete/superseded PDB entries- Specified by:
getPdbxDatabasePDBObsSprin interfaceBlock- Returns:
- PdbxDatabasePDBObsSpr
-
getPdbxDatabaseProc
public PdbxDatabaseProc getPdbxDatabaseProc()
Description copied from interface:BlockInternal records to track the data processing cycle.- Specified by:
getPdbxDatabaseProcin interfaceBlock- Returns:
- PdbxDatabaseProc
-
getPdbxDatabaseRemark
public PdbxDatabaseRemark getPdbxDatabaseRemark()
Description copied from interface:BlockData items in the PDBX_DATABASE_REMARK category record keep additional information about the entry. They are mostly used to create 'non-standard' PDB REMARK annotations (6-99).- Specified by:
getPdbxDatabaseRemarkin interfaceBlock- Returns:
- PdbxDatabaseRemark
-
getPdbxDatabaseStatus
public PdbxDatabaseStatus getPdbxDatabaseStatus()
Description copied from interface:BlockThese are internal RCSB records to keep track of data processing and status of the entry.- Specified by:
getPdbxDatabaseStatusin interfaceBlock- Returns:
- PdbxDatabaseStatus
-
getPdbxEntityName
public PdbxEntityName getPdbxEntityName()
Description copied from interface:BlockThe PDBX_ENTITY_NAME records additional name information for each entity.- Specified by:
getPdbxEntityNamein interfaceBlock- Returns:
- PdbxEntityName
-
getPdbxPrereleaseSeq
public PdbxPrereleaseSeq getPdbxPrereleaseSeq()
Description copied from interface:BlockThis category provides a placeholder for pre-release sequence information. After release this category should be discarded.- Specified by:
getPdbxPrereleaseSeqin interfaceBlock- Returns:
- PdbxPrereleaseSeq
-
getPdbxPolySeqScheme
public PdbxPolySeqScheme getPdbxPolySeqScheme()
Description copied from interface:BlockThe PDBX_POLY_SEQ_SCHEME category provides residue level nomenclature mapping for polymer entities.- Specified by:
getPdbxPolySeqSchemein interfaceBlock- Returns:
- PdbxPolySeqScheme
-
getPdbxNonpolyScheme
public PdbxNonpolyScheme getPdbxNonpolyScheme()
Description copied from interface:BlockThe PDBX_NONPOLY_SCHEME category provides residue level nomenclature mapping for non-polymer entities.- Specified by:
getPdbxNonpolySchemein interfaceBlock- Returns:
- PdbxNonpolyScheme
-
getPdbxRefine
public PdbxRefine getPdbxRefine()
Description copied from interface:BlockData items in the PDBX_REFINE category record details about additional structure refinement parameters which are needed to complete legacy REMARK 3 refinement templates in PDB format files.- Specified by:
getPdbxRefinein interfaceBlock- Returns:
- PdbxRefine
-
getPdbxStructSheetHbond
public PdbxStructSheetHbond getPdbxStructSheetHbond()
Description copied from interface:BlockData items in the PDBX_STRUCT_SHEET_HBOND category record details about the hydrogen bonding between residue ranges in a beta sheet. This category is provided for cases where only a single hydrogen bond is used to register the two residue ranges. Category STRUCT_SHEET_HBOND should be used when the initial and terminal hydrogen bonds for strand pair are known.- Specified by:
getPdbxStructSheetHbondin interfaceBlock- Returns:
- PdbxStructSheetHbond
-
getPdbxXplorFile
public PdbxXplorFile getPdbxXplorFile()
Description copied from interface:BlockParameter and topology files used in X-PLOR/CNS refinement.- Specified by:
getPdbxXplorFilein interfaceBlock- Returns:
- PdbxXplorFile
-
getPdbxRefineAuxFile
public PdbxRefineAuxFile getPdbxRefineAuxFile()
Description copied from interface:BlockAuxilary parameter and topology files used in refinement.- Specified by:
getPdbxRefineAuxFilein interfaceBlock- Returns:
- PdbxRefineAuxFile
-
getPdbxDatabaseRelated
public PdbxDatabaseRelated getPdbxDatabaseRelated()
Description copied from interface:BlockData items in PDBX_DATABASE_RELATED contain references to entries that are related to the this entry.- Specified by:
getPdbxDatabaseRelatedin interfaceBlock- Returns:
- PdbxDatabaseRelated
-
getPdbxEntityAssembly
public PdbxEntityAssembly getPdbxEntityAssembly()
Description copied from interface:BlockThe PDBX_ENTITY_ASSEMBLY category provides a chemical description of the biological assembly studied in terms of its constituent entities.- Specified by:
getPdbxEntityAssemblyin interfaceBlock- Returns:
- PdbxEntityAssembly
-
getPdbxExptlCrystalGrowComp
public PdbxExptlCrystalGrowComp getPdbxExptlCrystalGrowComp()
Description copied from interface:BlockData items in the PDBX_EXPTL_CRYSTAL_GROW_COMP category record details about the components of the solutions that were 'mixed' to produce the crystal.- Specified by:
getPdbxExptlCrystalGrowCompin interfaceBlock- Returns:
- PdbxExptlCrystalGrowComp
-
getPdbxExptlCrystalGrowSol
public PdbxExptlCrystalGrowSol getPdbxExptlCrystalGrowSol()
Description copied from interface:BlockData items in the PDBX_EXPTL_CRYSTAL_GROW_SOL category record details about the solutions that were 'mixed' to produce the crystal.- Specified by:
getPdbxExptlCrystalGrowSolin interfaceBlock- Returns:
- PdbxExptlCrystalGrowSol
-
getPdbxExptlCrystalCryoTreatment
public PdbxExptlCrystalCryoTreatment getPdbxExptlCrystalCryoTreatment()
Description copied from interface:BlockData items in the PDBX_EXPTL_CRYSTAL_CRYO_TREATMENT category record details cryogenic treatments applied to this crystal.- Specified by:
getPdbxExptlCrystalCryoTreatmentin interfaceBlock- Returns:
- PdbxExptlCrystalCryoTreatment
-
getPdbxRefineTls
public PdbxRefineTls getPdbxRefineTls()
Description copied from interface:BlockData items in the REFINE_TLS category record details about TLS parameters used in structure refinement. Note that the intention is primarily to describe directly refined TLS parameters, although other methods of obtaining TLS parameters may be covered, see item _pdbx_refine_tls.method- Specified by:
getPdbxRefineTlsin interfaceBlock- Returns:
- PdbxRefineTls
-
getPdbxRefineTlsGroup
public PdbxRefineTlsGroup getPdbxRefineTlsGroup()
Description copied from interface:BlockData items in the PDBX_REFINE_TLS_GROUP category record details about a fragment of a TLS group. Properties of the TLS group are recorded in PDBX_REFINE_TLS- Specified by:
getPdbxRefineTlsGroupin interfaceBlock- Returns:
- PdbxRefineTlsGroup
-
getPdbxContactAuthor
public PdbxContactAuthor getPdbxContactAuthor()
Description copied from interface:BlockData items in the PDBX_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the contents of this data block. This category atomizes information to a greater degree than the standard AUDIT_CONTACT_AUTHOR category.- Specified by:
getPdbxContactAuthorin interfaceBlock- Returns:
- PdbxContactAuthor
-
getPdbxSGProject
public PdbxSGProject getPdbxSGProject()
Description copied from interface:BlockData items in the PDBX_CONTACT_AUTHOR category record details about the Structural Genomics Project and name and initials for each Center.- Specified by:
getPdbxSGProjectin interfaceBlock- Returns:
- PdbxSGProject
-
getPdbxAtomSiteAnisoTls
public PdbxAtomSiteAnisoTls getPdbxAtomSiteAnisoTls()
Description copied from interface:BlockData items in the PDBX_ATOM_SITE_ANISO_TLS category record details about the TLS contribution to anisotropic displacement parameters.- Specified by:
getPdbxAtomSiteAnisoTlsin interfaceBlock- Returns:
- PdbxAtomSiteAnisoTls
-
getPdbxNmrDetails
public PdbxNmrDetails getPdbxNmrDetails()
Description copied from interface:BlockExperimental details of the NMR study that have not been described elsewhere in this deposition.- Specified by:
getPdbxNmrDetailsin interfaceBlock- Returns:
- PdbxNmrDetails
-
getPdbxNmrSampleDetails
public PdbxNmrSampleDetails getPdbxNmrSampleDetails()
Description copied from interface:BlockComplete description of each NMR sample, including the solvent system used.- Specified by:
getPdbxNmrSampleDetailsin interfaceBlock- Returns:
- PdbxNmrSampleDetails
-
getPdbxNmrExptlSample
public PdbxNmrExptlSample getPdbxNmrExptlSample()
Description copied from interface:BlockThe chemical constituents of each NMR sample. Each sample is identified by a number and each component in the sample is identified by name.- Specified by:
getPdbxNmrExptlSamplein interfaceBlock- Returns:
- PdbxNmrExptlSample
-
getPdbxNmrExptlSampleConditions
public PdbxNmrExptlSampleConditions getPdbxNmrExptlSampleConditions()
Description copied from interface:BlockThe experimental conditions used to for each sample. Each set of conditions is identified by a numerical code.- Specified by:
getPdbxNmrExptlSampleConditionsin interfaceBlock- Returns:
- PdbxNmrExptlSampleConditions
-
getPdbxNmrSpectrometer
public PdbxNmrSpectrometer getPdbxNmrSpectrometer()
Description copied from interface:BlockThe details about each spectrometer used to collect data for this deposition.- Specified by:
getPdbxNmrSpectrometerin interfaceBlock- Returns:
- PdbxNmrSpectrometer
-
getPdbxNmrExptl
public PdbxNmrExptl getPdbxNmrExptl()
Description copied from interface:BlockIn this section, enter information on those experiments that were used to generate constraint data. For each NMR experiment indicate which sample and which sample conditions were used for the experiment.- Specified by:
getPdbxNmrExptlin interfaceBlock- Returns:
- PdbxNmrExptl
-
getPdbxNmrSoftware
public PdbxNmrSoftware getPdbxNmrSoftware()
Description copied from interface:BlockDescription of the software that was used for data collection, data processing, data analysis, structure calculations and refinement. The description should include the name of the software, the author of the software and the version used.- Specified by:
getPdbxNmrSoftwarein interfaceBlock- Returns:
- PdbxNmrSoftware
-
getPdbxNmrConstraints
public PdbxNmrConstraints getPdbxNmrConstraints()
Description copied from interface:BlockThis section provides a tabulation of constraint data.- Specified by:
getPdbxNmrConstraintsin interfaceBlock- Returns:
- PdbxNmrConstraints
-
getPdbxNmrEnsemble
public PdbxNmrEnsemble getPdbxNmrEnsemble()
Description copied from interface:BlockThis category contains the information that describes the ensemble of deposited structures. If only an average structure has been deposited skip this section.- Specified by:
getPdbxNmrEnsemblein interfaceBlock- Returns:
- PdbxNmrEnsemble
-
getPdbxNmrEnsembleRms
public PdbxNmrEnsembleRms getPdbxNmrEnsembleRms()
Description copied from interface:BlockStructural statistics are derived from molecular dynamics and simulated annealing programs.- Specified by:
getPdbxNmrEnsembleRmsin interfaceBlock- Returns:
- PdbxNmrEnsembleRms
-
getPdbxNmrRepresentative
public PdbxNmrRepresentative getPdbxNmrRepresentative()
Description copied from interface:BlockAn average structure is often calculated in addition to the ensemble, or one of the ensemble is selected as a representative structure. This section describes selection of the representative structure.- Specified by:
getPdbxNmrRepresentativein interfaceBlock- Returns:
- PdbxNmrRepresentative
-
getPdbxNmrRefine
public PdbxNmrRefine getPdbxNmrRefine()
Description copied from interface:BlockDescribe the method and details of the refinement of the deposited structure.- Specified by:
getPdbxNmrRefinein interfaceBlock- Returns:
- PdbxNmrRefine
-
getPdbxNmrForceConstants
public PdbxNmrForceConstants getPdbxNmrForceConstants()
Description copied from interface:BlockThe final force constants, including units, employed for the various experimental constraints, covalent geometry constraints, and the non-bonded interaction terms in the target function used for simulated annealing.- Specified by:
getPdbxNmrForceConstantsin interfaceBlock- Returns:
- PdbxNmrForceConstants
-
getNdbStructConfNa
public NdbStructConfNa getNdbStructConfNa()
Description copied from interface:BlockData items in the NDB_STRUCT_CONF_NA category describes secondary structure features in this entry.- Specified by:
getNdbStructConfNain interfaceBlock- Returns:
- NdbStructConfNa
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getNdbStructFeatureNa
public NdbStructFeatureNa getNdbStructFeatureNa()
Description copied from interface:BlockData items in the NDB_STRUCT_FEATURE_NA category describes tertiary and other special structural features in this entry.- Specified by:
getNdbStructFeatureNain interfaceBlock- Returns:
- NdbStructFeatureNa
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getNdbStructNaBasePair
public NdbStructNaBasePair getNdbStructNaBasePair()
Description copied from interface:BlockData items in the NDB_STRUCT_NA_BASE_PAIR category record details of base pairing interactions.- Specified by:
getNdbStructNaBasePairin interfaceBlock- Returns:
- NdbStructNaBasePair
-
getNdbStructNaBasePairStep
public NdbStructNaBasePairStep getNdbStructNaBasePairStep()
Description copied from interface:BlockData items in the NDB_STRUCT_NA_BASE_PAIR_STEP category record details of base pair step interactions.- Specified by:
getNdbStructNaBasePairStepin interfaceBlock- Returns:
- NdbStructNaBasePairStep
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getNdbOriginalNdbCoordinates
public NdbOriginalNdbCoordinates getNdbOriginalNdbCoordinates()
Description copied from interface:BlockPlaceholder category for PDB coordinate data.- Specified by:
getNdbOriginalNdbCoordinatesin interfaceBlock- Returns:
- NdbOriginalNdbCoordinates
-
getPdbxEntityNonpoly
public PdbxEntityNonpoly getPdbxEntityNonpoly()
- Specified by:
getPdbxEntityNonpolyin interfaceBlock- Returns:
- PdbxEntityNonpoly
-
getPdbxPhasingDm
public PdbxPhasingDm getPdbxPhasingDm()
Description copied from interface:BlockData items in the PDBX_PHASING_DM category record details about density modification- Specified by:
getPdbxPhasingDmin interfaceBlock- Returns:
- PdbxPhasingDm
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getPdbxPhasingDmShell
public PdbxPhasingDmShell getPdbxPhasingDmShell()
Description copied from interface:BlockData items in the PDBX_PHASING_DM_SHELL category record details about density modification in resolution shell.- Specified by:
getPdbxPhasingDmShellin interfaceBlock- Returns:
- PdbxPhasingDmShell
-
getPdbxPhasingMADShell
public PdbxPhasingMADShell getPdbxPhasingMADShell()
Description copied from interface:BlockData items in the PDBX_PHASING_MAD_SHELL category record details about the phasing of the structure, when methods involving multiple anomalous dispersion techniques are involved (note: the values are overall, but broken down into shells of resolution)- Specified by:
getPdbxPhasingMADShellin interfaceBlock- Returns:
- PdbxPhasingMADShell
-
getPdbxPhasingMADSet
public PdbxPhasingMADSet getPdbxPhasingMADSet()
Description copied from interface:BlockRecord details about each phasing set: (Note: the phasing set is different from data set. for example: if there are three data sets, the inflection point (IP), the peak (PK) and the high remote (HR), the combination of the phasing set will be IP_iso, PK_iso (the isomorphous repleacement with HR as 'native'), IP_ano, PK_ano and HR_ano (the anomalous difference with itself). Therefore, there are five set used for phasing.- Specified by:
getPdbxPhasingMADSetin interfaceBlock- Returns:
- PdbxPhasingMADSet
-
getPdbxPhasingMADSetShell
public PdbxPhasingMADSetShell getPdbxPhasingMADSetShell()
Description copied from interface:BlockThe same as category pdbx_phasing_MAD_set, but broken into shells.- Specified by:
getPdbxPhasingMADSetShellin interfaceBlock- Returns:
- PdbxPhasingMADSetShell
-
getPdbxPhasingMADSetSite
public PdbxPhasingMADSetSite getPdbxPhasingMADSetSite()
Description copied from interface:Blockrecord the details (coordinates etc.) of anomalous scatters.- Specified by:
getPdbxPhasingMADSetSitein interfaceBlock- Returns:
- PdbxPhasingMADSetSite
-
getPdbxPhasingMR
public PdbxPhasingMR getPdbxPhasingMR()
Description copied from interface:BlockData items in the PDBX_PHASING_MR category record details about molecular replacement.- Specified by:
getPdbxPhasingMRin interfaceBlock- Returns:
- PdbxPhasingMR
-
getPdbxRefineComponent
public PdbxRefineComponent getPdbxRefineComponent()
Description copied from interface:BlockData items in the PDBX_REFINE_COMPONENT category record statistics of the final model relative to the density map.- Specified by:
getPdbxRefineComponentin interfaceBlock- Returns:
- PdbxRefineComponent
-
getPdbxEntityProdProtocol
public PdbxEntityProdProtocol getPdbxEntityProdProtocol()
Description copied from interface:BlockThis category contains descriptive protocols for the production of this entity.- Specified by:
getPdbxEntityProdProtocolin interfaceBlock- Returns:
- PdbxEntityProdProtocol
-
getPdbxEntitySrcGenProdOther
public PdbxEntitySrcGenProdOther getPdbxEntitySrcGenProdOther()
Description copied from interface:BlockThis category contains details for process steps that are not explicitly catered for elsewhere. It provides some basic details as well as placeholders for a list of parameters and values (the category PDBX_ENTITY_SRC_GEN_PROD_OTHER_PARAMETER). Note that processes that have been modelled explicitly should not be represented using this category.- Specified by:
getPdbxEntitySrcGenProdOtherin interfaceBlock- Returns:
- PdbxEntitySrcGenProdOther
-
getPdbxEntitySrcGenProdOtherParameter
public PdbxEntitySrcGenProdOtherParameter getPdbxEntitySrcGenProdOtherParameter()
Description copied from interface:BlockThis category contains parameters and values required to capture information about a particular process step- Specified by:
getPdbxEntitySrcGenProdOtherParameterin interfaceBlock- Returns:
- PdbxEntitySrcGenProdOtherParameter
-
getPdbxEntitySrcGenProdPcr
public PdbxEntitySrcGenProdPcr getPdbxEntitySrcGenProdPcr()
Description copied from interface:BlockThis category contains details for the PCR steps used in the overall protein production process. The PCR is assumed to be applied to the result of the previous production step, or the gene source if this is the first production step.- Specified by:
getPdbxEntitySrcGenProdPcrin interfaceBlock- Returns:
- PdbxEntitySrcGenProdPcr
-
getPdbxEntitySrcGenProdDigest
public PdbxEntitySrcGenProdDigest getPdbxEntitySrcGenProdDigest()
Description copied from interface:BlockThis category contains details for the DIGEST steps used in the overall protein production process. The digestion is assumed to be applied to the result of the previous production step, or the gene source if this is the first production step.- Specified by:
getPdbxEntitySrcGenProdDigestin interfaceBlock- Returns:
- PdbxEntitySrcGenProdDigest
-
getPdbxEntitySrcGenClone
public PdbxEntitySrcGenClone getPdbxEntitySrcGenClone()
Description copied from interface:BlockThis category contains details for the cloning steps used in the overall protein production process. Each row in PDBX_ENTITY_SRC_GEN_CLONE should have an equivalent row in either PDBX_ENTITY_SRC_GEN_CLONE_LIGATION or PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION. If only summary information is provided data in the later two categories may be omitted.- Specified by:
getPdbxEntitySrcGenClonein interfaceBlock- Returns:
- PdbxEntitySrcGenClone
-
getPdbxEntitySrcGenCloneLigation
public PdbxEntitySrcGenCloneLigation getPdbxEntitySrcGenCloneLigation()
Description copied from interface:BlockThis category contains details for the ligation-based cloning steps used in the overall protein production process. _pdbx_entity_src_gen_clone_ligation.clone_step_id in this category must point at a defined _pdbx_entity_src_gen_clone.step_id. The details in PDBX_ENTITY_SRC_GEN_CLONE_LIGATION extend the details in PDBX_ENTITY_SRC_GEN_CLONE to cover ligation dependent cloning steps.- Specified by:
getPdbxEntitySrcGenCloneLigationin interfaceBlock- Returns:
- PdbxEntitySrcGenCloneLigation
-
getPdbxEntitySrcGenCloneRecombination
public PdbxEntitySrcGenCloneRecombination getPdbxEntitySrcGenCloneRecombination()
Description copied from interface:BlockThis category contains details for the recombination-based cloning steps used in the overall protein production process. It is assumed that these reactions will use commercially available kits. _pdbx_entity_src_gen_clone_recombination.clone_step_id in this category must point at a defined _pdbx_entity_src_gen_clone.step_id. The details in PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION extend the details in PDBX_ENTITY_SRC_GEN_CLONE to cover recombination dependent cloning steps.- Specified by:
getPdbxEntitySrcGenCloneRecombinationin interfaceBlock- Returns:
- PdbxEntitySrcGenCloneRecombination
-
getPdbxEntitySrcGenExpress
public PdbxEntitySrcGenExpress getPdbxEntitySrcGenExpress()
Description copied from interface:BlockThis category contains details for the EXPRESSION steps used in the overall protein production process. It is hoped that this category will cover all forms of cell-based expression by reading induction as induction/transformation/transfection.- Specified by:
getPdbxEntitySrcGenExpressin interfaceBlock- Returns:
- PdbxEntitySrcGenExpress
-
getPdbxEntitySrcGenExpressTimepoint
public PdbxEntitySrcGenExpressTimepoint getPdbxEntitySrcGenExpressTimepoint()
Description copied from interface:BlockThis category contains details for OD time series used to monitor a given EXPRESSION step used in the overall protein production process.- Specified by:
getPdbxEntitySrcGenExpressTimepointin interfaceBlock- Returns:
- PdbxEntitySrcGenExpressTimepoint
-
getPdbxEntitySrcGenLysis
public PdbxEntitySrcGenLysis getPdbxEntitySrcGenLysis()
Description copied from interface:BlockThis category contains details for the cell lysis steps used in the overall protein production process.- Specified by:
getPdbxEntitySrcGenLysisin interfaceBlock- Returns:
- PdbxEntitySrcGenLysis
-
getPdbxEntitySrcGenRefold
public PdbxEntitySrcGenRefold getPdbxEntitySrcGenRefold()
Description copied from interface:BlockThis category contains details for the refolding steps used in the overall protein production process.- Specified by:
getPdbxEntitySrcGenRefoldin interfaceBlock- Returns:
- PdbxEntitySrcGenRefold
-
getPdbxEntitySrcGenProteolysis
public PdbxEntitySrcGenProteolysis getPdbxEntitySrcGenProteolysis()
Description copied from interface:BlockThis category contains details for the protein purification tag removal steps used in the overall protein production process- Specified by:
getPdbxEntitySrcGenProteolysisin interfaceBlock- Returns:
- PdbxEntitySrcGenProteolysis
-
getPdbxEntitySrcGenChrom
public PdbxEntitySrcGenChrom getPdbxEntitySrcGenChrom()
Description copied from interface:BlockThis category contains details for the chromatographic steps used in the purification of the protein.- Specified by:
getPdbxEntitySrcGenChromin interfaceBlock- Returns:
- PdbxEntitySrcGenChrom
-
getPdbxEntitySrcGenFract
public PdbxEntitySrcGenFract getPdbxEntitySrcGenFract()
Description copied from interface:BlockThis category contains details for the fraction steps used in the overall protein production process. Examples of fractionation steps are centrifugation and magnetic bead pull-down purification.- Specified by:
getPdbxEntitySrcGenFractin interfaceBlock- Returns:
- PdbxEntitySrcGenFract
-
getPdbxEntitySrcGenPure
public PdbxEntitySrcGenPure getPdbxEntitySrcGenPure()
Description copied from interface:BlockThis category contains details for the final purified protein product. Note that this category does not contain the amino acid sequence of the protein. The sequence will be found in the ENTITY_POLY_SEQ entry with matching entity_id. Only one PDBX_ENTITY_SRC_GEN_PURE category is allowed per entity, hence there is no step_id for this category.- Specified by:
getPdbxEntitySrcGenPurein interfaceBlock- Returns:
- PdbxEntitySrcGenPure
-
getPdbxEntitySrcGenCharacter
public PdbxEntitySrcGenCharacter getPdbxEntitySrcGenCharacter()
Description copied from interface:BlockThis category contains details of protein characterisation. It refers to the characteristion of the product of a specific step.- Specified by:
getPdbxEntitySrcGenCharacterin interfaceBlock- Returns:
- PdbxEntitySrcGenCharacter
-
getPdbxConstruct
public PdbxConstruct getPdbxConstruct()
Description copied from interface:BlockData items in the PDBX_CONSTRUCT category specify a sequence of nucleic acids or amino acids. It is a catch-all that may be used to provide details of sequences known to be relevant to the project as well as primers, plasmids, proteins and such like that are either used or produced during the protein production process. Molecules described here are not necessarily complete, so for instance it would be possible to include either a complete plasmid or just its insert. This category may be considered as an abbreviated form of _entity where the molecules described are not required to appear in the final co-ordinates. Note that the details provided here all pertain to a single entry as defined at deposition. It is anticipated that _pdbx_construct.id would also be composed of a sequence that is unique within a given site prefixed by a code that identifies that site and would, therefore, be GLOBALLY unique. Thus this category could also be used locally to store details about the different constructs used during protein production without reference to the entry_id (which only becomes a meaningful concept during deposition).- Specified by:
getPdbxConstructin interfaceBlock- Returns:
- PdbxConstruct
-
getPdbxConstructFeature
public PdbxConstructFeature getPdbxConstructFeature()
Description copied from interface:BlockData items in the PDBX_CONSTRUCT_FEATURE category may be used to specify various properties of a nucleic acid sequence used during protein production.- Specified by:
getPdbxConstructFeaturein interfaceBlock- Returns:
- PdbxConstructFeature
-
getPdbxRobotSystem
public PdbxRobotSystem getPdbxRobotSystem()
Description copied from interface:BlockThe details about each robotic system used to collect data for this project.- Specified by:
getPdbxRobotSystemin interfaceBlock- Returns:
- PdbxRobotSystem
-
getPdbxBuffer
public PdbxBuffer getPdbxBuffer()
Description copied from interface:BlockData items in the PDBX_BUFFER category record details of the sample buffer.- Specified by:
getPdbxBufferin interfaceBlock- Returns:
- PdbxBuffer
-
getPdbxBufferComponents
public PdbxBufferComponents getPdbxBufferComponents()
Description copied from interface:BlockConstituents of buffer in sample- Specified by:
getPdbxBufferComponentsin interfaceBlock- Returns:
- PdbxBufferComponents
-
getPdbxDomain
public PdbxDomain getPdbxDomain()
Description copied from interface:BlockData items in the PDBX_DOMAIN category record information about domain definitions. A domain need not correspond to a completely polypeptide chain; it can be composed of one or more segments in a single chain, or by segments from more than one chain.- Specified by:
getPdbxDomainin interfaceBlock- Returns:
- PdbxDomain
-
getPdbxDomainRange
public PdbxDomainRange getPdbxDomainRange()
Description copied from interface:BlockData items in the PDBX_DOMAIN_RANGE category identify the beginning and ending points of polypeptide chain segments that form all or part of a domain.- Specified by:
getPdbxDomainRangein interfaceBlock- Returns:
- PdbxDomainRange
-
getPdbxSequenceRange
public PdbxSequenceRange getPdbxSequenceRange()
Description copied from interface:BlockData items in the PDBX_SEQUENCE_RANGE category identify the beginning and ending points of polypeptide sequence segments.- Specified by:
getPdbxSequenceRangein interfaceBlock- Returns:
- PdbxSequenceRange
-
getPdbxFeatureEntry
public PdbxFeatureEntry getPdbxFeatureEntry()
Description copied from interface:BlockData items in the PDBX_FEATURE_ENTRY category records information about properties pertaining to this structure entry.- Specified by:
getPdbxFeatureEntryin interfaceBlock- Returns:
- PdbxFeatureEntry
-
getPdbxFeatureDomain
public PdbxFeatureDomain getPdbxFeatureDomain()
Description copied from interface:BlockData items in the PDBX_FEATURE_DOMAIN category records information about properties pertaining to this structure domain.- Specified by:
getPdbxFeatureDomainin interfaceBlock- Returns:
- PdbxFeatureDomain
-
getPdbxFeatureSequenceRange
public PdbxFeatureSequenceRange getPdbxFeatureSequenceRange()
Description copied from interface:BlockData items in the PDBX_FEATURE_SEQUENCE_RANGE category records information about properties pertaining to this structure sequence_range.- Specified by:
getPdbxFeatureSequenceRangein interfaceBlock- Returns:
- PdbxFeatureSequenceRange
-
getPdbxFeatureAssembly
public PdbxFeatureAssembly getPdbxFeatureAssembly()
Description copied from interface:BlockData items in the PDBX_FEATURE_ASSEMBLY category records information about properties pertaining to this structural assembly.- Specified by:
getPdbxFeatureAssemblyin interfaceBlock- Returns:
- PdbxFeatureAssembly
-
getPdbxFeatureMonomer
public PdbxFeatureMonomer getPdbxFeatureMonomer()
Description copied from interface:BlockData items in the PDBX_FEATURE_MONOMER category records information about properties pertaining to particular monomers in this structure.- Specified by:
getPdbxFeatureMonomerin interfaceBlock- Returns:
- PdbxFeatureMonomer
-
getPdbxExptlPd
public PdbxExptlPd getPdbxExptlPd()
Description copied from interface:BlockData items in the pdbx_exptl_pd record information about powder sample preparations.- Specified by:
getPdbxExptlPdin interfaceBlock- Returns:
- PdbxExptlPd
-
getPdbxReflnsTwin
public PdbxReflnsTwin getPdbxReflnsTwin()
Description copied from interface:BlockDetails decribing crystallographic twinning.- Specified by:
getPdbxReflnsTwinin interfaceBlock- Returns:
- PdbxReflnsTwin
-
getPdbxStructInfo
public PdbxStructInfo getPdbxStructInfo()
Description copied from interface:BlockSpecial features of this structural entry.- Specified by:
getPdbxStructInfoin interfaceBlock- Returns:
- PdbxStructInfo
-
getPdbxReRefinement
public PdbxReRefinement getPdbxReRefinement()
Description copied from interface:BlockDescribes the origin of the experimental data used in this entry.- Specified by:
getPdbxReRefinementin interfaceBlock- Returns:
- PdbxReRefinement
-
getPdbxStructAssemblyProp
public PdbxStructAssemblyProp getPdbxStructAssemblyProp()
Description copied from interface:BlockProperties and features of structural assemblies.- Specified by:
getPdbxStructAssemblyPropin interfaceBlock- Returns:
- PdbxStructAssemblyProp
-
getPdbxStructRefSeqFeature
public PdbxStructRefSeqFeature getPdbxStructRefSeqFeature()
Description copied from interface:BlockData items in the PDBX_STRUCT_REF_SEQ_FEATURE category provide a mechanism for identifying and annotating sequence features.- Specified by:
getPdbxStructRefSeqFeaturein interfaceBlock- Returns:
- PdbxStructRefSeqFeature
-
getPdbxStructRefSeqFeatureProp
public PdbxStructRefSeqFeatureProp getPdbxStructRefSeqFeatureProp()
Description copied from interface:BlockData items in the PDBX_STRUCT_REF_SEQ_FEATURE_PROP category provide a mechanism for identifying and annotating properties of sequence features.- Specified by:
getPdbxStructRefSeqFeaturePropin interfaceBlock- Returns:
- PdbxStructRefSeqFeatureProp
-
getPdbxStructChemCompDiagnostics
public PdbxStructChemCompDiagnostics getPdbxStructChemCompDiagnostics()
Description copied from interface:BlockData items in the PDBX_STRUCT_CHEM_COMP_DIAGNOSTICS category provides structural diagnostics in chemical components instances.- Specified by:
getPdbxStructChemCompDiagnosticsin interfaceBlock- Returns:
- PdbxStructChemCompDiagnostics
-
getPdbxChemCompFeature
public PdbxChemCompFeature getPdbxChemCompFeature()
Description copied from interface:BlockAdditional features associated with the chemical component.- Specified by:
getPdbxChemCompFeaturein interfaceBlock- Returns:
- PdbxChemCompFeature
-
getPdbxCoordinateModel
public PdbxCoordinateModel getPdbxCoordinateModel()
Description copied from interface:BlockThe details of the composition of the coordinate model.- Specified by:
getPdbxCoordinateModelin interfaceBlock- Returns:
- PdbxCoordinateModel
-
getPdbxStructChemCompFeature
public PdbxStructChemCompFeature getPdbxStructChemCompFeature()
Description copied from interface:BlockData items in the PDBX_STRUCT_CHEM_COMP_FEATURE category provides structural annotations in chemical components instances.- Specified by:
getPdbxStructChemCompFeaturein interfaceBlock- Returns:
- PdbxStructChemCompFeature
-
getPdbxDiffrnReflnsShell
public PdbxDiffrnReflnsShell getPdbxDiffrnReflnsShell()
Description copied from interface:BlockData items in the DIFFRN_REFLNS_SHELL category record details about the reflection data set within shells of resolution.- Specified by:
getPdbxDiffrnReflnsShellin interfaceBlock- Returns:
- PdbxDiffrnReflnsShell
-
getPdbxBondDistanceLimits
public PdbxBondDistanceLimits getPdbxBondDistanceLimits()
Description copied from interface:BlockThis category provides a table of upper and lower distance limits used as criteria in determining covalent bonds. The table is organized by atom type pairs.- Specified by:
getPdbxBondDistanceLimitsin interfaceBlock- Returns:
- PdbxBondDistanceLimits
-
getPdbxSolnScatter
public PdbxSolnScatter getPdbxSolnScatter()
Description copied from interface:BlockData items in the PDBX_SOLN_SCATTER category record details about a solution scattering experiment- Specified by:
getPdbxSolnScatterin interfaceBlock- Returns:
- PdbxSolnScatter
-
getPdbxSolnScatterModel
public PdbxSolnScatterModel getPdbxSolnScatterModel()
Description copied from interface:BlockData items in the PDBX_SOLN_SCATTER_MODEL category record details about the homology model fitting to the solution scatter data.- Specified by:
getPdbxSolnScatterModelin interfaceBlock- Returns:
- PdbxSolnScatterModel
-
getPdbxChemCompDescriptor
public PdbxChemCompDescriptor getPdbxChemCompDescriptor()
Description copied from interface:BlockData items in the CHEM_COMP_DESCRIPTOR category provide string descriptors of component chemical structure.- Specified by:
getPdbxChemCompDescriptorin interfaceBlock- Returns:
- PdbxChemCompDescriptor
-
getPdbxChemCompIdentifier
public PdbxChemCompIdentifier getPdbxChemCompIdentifier()
Description copied from interface:BlockData items in the CHEM_COMP_IDENTIFIER category provide identifiers for chemical components.- Specified by:
getPdbxChemCompIdentifierin interfaceBlock- Returns:
- PdbxChemCompIdentifier
-
getPdbxChemCompImport
public PdbxChemCompImport getPdbxChemCompImport()
Description copied from interface:BlockData items in the PDBX_CHEM_COMP_IMPORT category identify existing chemical components to be imported into the current component definition. Components in this list can be edited by instructions in categories pdbx_chem_comp_atom_edit and pdbx_chem_comp_bond_edit.- Specified by:
getPdbxChemCompImportin interfaceBlock- Returns:
- PdbxChemCompImport
-
getPdbxChemCompAtomEdit
public PdbxChemCompAtomEdit getPdbxChemCompAtomEdit()
Description copied from interface:BlockData items in the PDBX_CHEM_COMP_ATOM_EDIT category provide atom level editing instructions to be applied to imported chemical components.- Specified by:
getPdbxChemCompAtomEditin interfaceBlock- Returns:
- PdbxChemCompAtomEdit
-
getPdbxChemCompBondEdit
public PdbxChemCompBondEdit getPdbxChemCompBondEdit()
Description copied from interface:BlockData items in the PDBX_CHEM_COMP_BOND_EDIT category provide bond level editing instructions to be applied to imported chemical components.- Specified by:
getPdbxChemCompBondEditin interfaceBlock- Returns:
- PdbxChemCompBondEdit
-
getPdbxChemCompAudit
public PdbxChemCompAudit getPdbxChemCompAudit()
Description copied from interface:BlockData items in the PDBX_CHEM_COMP_AUDIT category records the status and tracking information for this component.- Specified by:
getPdbxChemCompAuditin interfaceBlock- Returns:
- PdbxChemCompAudit
-
getPdbxValidateCloseContact
public PdbxValidateCloseContact getPdbxValidateCloseContact()
Description copied from interface:BlockData items in the PDBX_VALIDATE_CLOSE_CONTACT category list the atoms within the entry that are in close contact with regard the distances expected from either covalent bonding or closest approach by van der Waals contacts. Contacts within the asymmetric unit are considered. For those contacts not involving hydrogen a limit of 2.2 Angstroms is used. For contacts involving a hydrogen atom a cutoff of 1.6 Angstroms is used.- Specified by:
getPdbxValidateCloseContactin interfaceBlock- Returns:
- PdbxValidateCloseContact
-
getPdbxValidateSymmContact
public PdbxValidateSymmContact getPdbxValidateSymmContact()
Description copied from interface:BlockData items in the PDBX_VALIDATE_SYMM_CONTACT category list the atoms within the entry that are in close contact with regard the distances expected from either covalent bonding or closest approach by van der Waals contacts. Contacts with for symmetry related contacts are considered. For those contacts not involving hydrogen a limit of 2.2 Angstroms is used. For contacts involving a hydrogen atom a cutoff of 1.6Angstrom is used.- Specified by:
getPdbxValidateSymmContactin interfaceBlock- Returns:
- PdbxValidateSymmContact
-
getPdbxValidateRmsdBond
public PdbxValidateRmsdBond getPdbxValidateRmsdBond()
Description copied from interface:BlockData items in the PDBX_VALIDATE_RMSD_BOND category list the covalent bonds that have values which deviate from expected values by more than 6*rmsd.- Specified by:
getPdbxValidateRmsdBondin interfaceBlock- Returns:
- PdbxValidateRmsdBond
-
getPdbxValidateRmsdAngle
public PdbxValidateRmsdAngle getPdbxValidateRmsdAngle()
Description copied from interface:BlockData items in the PDBX_VALIDATE_RMSD_ANGLE category list the the covalent bond angles found in an entry that have values which deviate from expected values by more than 6*rmsd for the particular entry from the expected standard value- Specified by:
getPdbxValidateRmsdAnglein interfaceBlock- Returns:
- PdbxValidateRmsdAngle
-
getPdbxValidateTorsion
public PdbxValidateTorsion getPdbxValidateTorsion()
Description copied from interface:BlockData items in the PDBX_VALIDATE_TORSION category list the residues with torsion angles outside the expected ramachandran regions- Specified by:
getPdbxValidateTorsionin interfaceBlock- Returns:
- PdbxValidateTorsion
-
getPdbxValidatePeptideOmega
public PdbxValidatePeptideOmega getPdbxValidatePeptideOmega()
Description copied from interface:BlockData items in the PDBX_VALIDATE_PEPTIDE_OMEGA category list the residues that contain peptide bonds deviate significantly from both cis and trans conformation. cis bonds, if any, are listed on cispep records. trans is defined as 180 +/- 30 and cis is defined as 0 +/- 30 degrees.- Specified by:
getPdbxValidatePeptideOmegain interfaceBlock- Returns:
- PdbxValidatePeptideOmega
-
getPdbxValidateChiral
public PdbxValidateChiral getPdbxValidateChiral()
Description copied from interface:BlockData items in the PDBX_VALIDATE_CHIRAL category list the residues that contain unexpected configuration of chiral centers. IMPROPER HA N C CB chirality CA IMPROPER HB1 HB2 CA CG stereo CB as this number approaches (+) or (-) 180.0, then the error in predicting the true chirality of the center increases. Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. HERE improper C---N----CA---CB done expected answer is around -120 mean -122.52 D-amino acid is +120.0- Specified by:
getPdbxValidateChiralin interfaceBlock- Returns:
- PdbxValidateChiral
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getPdbxValidatePlanes
public PdbxValidatePlanes getPdbxValidatePlanes()
Description copied from interface:BlockData items in the PDBX_VALIDATE_PLANES category list the residues that contain unexpected deviations from planes centers.- Specified by:
getPdbxValidatePlanesin interfaceBlock- Returns:
- PdbxValidatePlanes
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getPdbxValidatePlanesAtom
public PdbxValidatePlanesAtom getPdbxValidatePlanesAtom()
Description copied from interface:BlockData items in the PDBX_VALIDATE_PLANES_ATOM category list the residues that contain unexpected deviations from planes centers.- Specified by:
getPdbxValidatePlanesAtomin interfaceBlock- Returns:
- PdbxValidatePlanesAtom
-
getPdbxValidateMainChainPlane
public PdbxValidateMainChainPlane getPdbxValidateMainChainPlane()
Description copied from interface:BlockData items in the PDBX_VALIDATE_MAIN_CHAIN_PLANE category list the residues that contain unexpected deviations from planes for main chain atoms as defined by the improper torsion angle describing planarity: PLANARITY = C(i-1) - CA(i-1) - N(i) - O(i-1) ==> planar < 5 as a pseudo torsion- Specified by:
getPdbxValidateMainChainPlanein interfaceBlock- Returns:
- PdbxValidateMainChainPlane
-
getPdbxStructConnAngle
public PdbxStructConnAngle getPdbxStructConnAngle()
Description copied from interface:BlockData items in the PDBX_STRUCT_CONN_ANGLE category record the angles in connections between portions of the structure.- Specified by:
getPdbxStructConnAnglein interfaceBlock- Returns:
- PdbxStructConnAngle
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getPdbxUnobsOrZeroOccResidues
public PdbxUnobsOrZeroOccResidues getPdbxUnobsOrZeroOccResidues()
Description copied from interface:BlockData items in the PDBX_UNOBS_OR_ZERO_OCC_RESIDUES category list the residues within the entry that are not observed or have zero occupancy.- Specified by:
getPdbxUnobsOrZeroOccResiduesin interfaceBlock- Returns:
- PdbxUnobsOrZeroOccResidues
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getPdbxUnobsOrZeroOccAtoms
public PdbxUnobsOrZeroOccAtoms getPdbxUnobsOrZeroOccAtoms()
Description copied from interface:BlockData items in the PDBX_UNOBS_OR_ZERO_OCC_ATOMS category list the atoms within the entry that are either unobserved or have zero occupancy/- Specified by:
getPdbxUnobsOrZeroOccAtomsin interfaceBlock- Returns:
- PdbxUnobsOrZeroOccAtoms
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getPdbxEntryDetails
public PdbxEntryDetails getPdbxEntryDetails()
Description copied from interface:BlockData items in the PDBX_ENTRY_DETAILS category provide additional details about this entry.- Specified by:
getPdbxEntryDetailsin interfaceBlock- Returns:
- PdbxEntryDetails
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getPdbxStructModResidue
public PdbxStructModResidue getPdbxStructModResidue()
Description copied from interface:BlockData items in the PDBX_STRUCT_MOD_RESIDUE category list the modified polymer components in the entry and provide some details describing the nature of the modification.- Specified by:
getPdbxStructModResiduein interfaceBlock- Returns:
- PdbxStructModResidue
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getPdbxStructRefSeqInsertion
public PdbxStructRefSeqInsertion getPdbxStructRefSeqInsertion()
Description copied from interface:BlockData items in the PDBX_STRUCT_REF_SEQ_INSERTION category annotate insertions in the sequence of the entity described in the referenced database entry.- Specified by:
getPdbxStructRefSeqInsertionin interfaceBlock- Returns:
- PdbxStructRefSeqInsertion
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getPdbxStructRefSeqDeletion
public PdbxStructRefSeqDeletion getPdbxStructRefSeqDeletion()
Description copied from interface:BlockData items in the PDBX_STRUCT_REF_SEQ_INSERTION category annotate deletions in the sequence of the entity described in the referenced database entry.- Specified by:
getPdbxStructRefSeqDeletionin interfaceBlock- Returns:
- PdbxStructRefSeqDeletion
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getPdbxRemediationAtomSiteMapping
public PdbxRemediationAtomSiteMapping getPdbxRemediationAtomSiteMapping()
Description copied from interface:BlockData items in the PDBX_REMEDIATION_ATOM_SITE_MAPPING category records mapping information between selected molecular entities that have been chemically redefined. The prior and current atom nomenclature is tabulated in this category.- Specified by:
getPdbxRemediationAtomSiteMappingin interfaceBlock- Returns:
- PdbxRemediationAtomSiteMapping
-
getPdbxValidatePolymerLinkage
public PdbxValidatePolymerLinkage getPdbxValidatePolymerLinkage()
Description copied from interface:BlockData items in the PDBX_VALIDATE_POLYMER_LINKAGE category list the polymer linkages within the entry that are outside of typlical covalent distances.- Specified by:
getPdbxValidatePolymerLinkagein interfaceBlock- Returns:
- PdbxValidatePolymerLinkage
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getPdbxHelicalSymmetry
public PdbxHelicalSymmetry getPdbxHelicalSymmetry()
Description copied from interface:BlockData items in the PDBX_HELICAL_SYMMETRY category record details about the helical symmetry group associated with this entry.- Specified by:
getPdbxHelicalSymmetryin interfaceBlock- Returns:
- PdbxHelicalSymmetry
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getPdbxPointSymmetry
public PdbxPointSymmetry getPdbxPointSymmetry()
Description copied from interface:BlockData items in the PDBX_POINT_SYMMETRY category record details about the point symmetry group associated with this entry.- Specified by:
getPdbxPointSymmetryin interfaceBlock- Returns:
- PdbxPointSymmetry
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getPdbxStructEntityInst
public PdbxStructEntityInst getPdbxStructEntityInst()
Description copied from interface:BlockData items in the PDBX_STRUCT_ENTITY_INST category record details about the structural elements in the deposited entry. The entity instance is a method neutral identifier for the observed molecular entities in the deposited coordinate set.- Specified by:
getPdbxStructEntityInstin interfaceBlock- Returns:
- PdbxStructEntityInst
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getPdbxStructOperList
public PdbxStructOperList getPdbxStructOperList()
Description copied from interface:BlockData items in the PDBX_STRUCT_OPER_LIST category describe Cartesian rotation and translation operations required to generate or transform the coordinates deposited with this entry.- Specified by:
getPdbxStructOperListin interfaceBlock- Returns:
- PdbxStructOperList
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getPdbxStructAssembly
public PdbxStructAssembly getPdbxStructAssembly()
Description copied from interface:BlockData items in the PDBX_STRUCT_ASSEMBLY category record details about the structural elements that form macromolecular assemblies.- Specified by:
getPdbxStructAssemblyin interfaceBlock- Returns:
- PdbxStructAssembly
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getPdbxStructAssemblyGen
public PdbxStructAssemblyGen getPdbxStructAssemblyGen()
Description copied from interface:BlockData items in the PDBX_STRUCT_ASSEMBLY_GEN category record details about the generation of each macromolecular assemblies. The PDBX_STRUCT_ASSEMBLY_GEN data items provide the specifications of the components that constitute that assembly in terms of cartesian transformations.- Specified by:
getPdbxStructAssemblyGenin interfaceBlock- Returns:
- PdbxStructAssemblyGen
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getPdbxStructAsymGen
public PdbxStructAsymGen getPdbxStructAsymGen()
Description copied from interface:BlockData items in the PDBX_STRUCT_ASYM_GEN category record details about the generation of the crystallographic asymmetric unit. The PDBX_STRUCT_ASYM_GEN data items provide the specifications of the components that constitute the asymmetric unit in terms of cartesian transformations of deposited coordinates.- Specified by:
getPdbxStructAsymGenin interfaceBlock- Returns:
- PdbxStructAsymGen
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getPdbxStructMsymGen
public PdbxStructMsymGen getPdbxStructMsymGen()
Description copied from interface:BlockData items in the PDBX_STRUCT_MSYM_GEN category record details about the generation of the minimal asymmetric unit. For instance, this category can be used to provide this information for helical and point symmetry systems. The PDBX_STRUCT_MSYM_GEN data items provide the specifications of the components that constitute the asymmetric unit in terms of cartesian transformations of deposited coordinates.- Specified by:
getPdbxStructMsymGenin interfaceBlock- Returns:
- PdbxStructMsymGen
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getPdbxStructLegacyOperList
public PdbxStructLegacyOperList getPdbxStructLegacyOperList()
Description copied from interface:BlockData items in the PDBX_STRUCT_LEGACY_OPER_LIST category describe Cartesian rotation and translation operations required to generate or transform the coordinates deposited with this entry. This category provides a container for matrices used to construct icosahedral assemblies in legacy entries.- Specified by:
getPdbxStructLegacyOperListin interfaceBlock- Returns:
- PdbxStructLegacyOperList
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getPdbxChemCompAtomFeature
public PdbxChemCompAtomFeature getPdbxChemCompAtomFeature()
Description copied from interface:BlockData items in the PDBX_CHEM_COMP_ATOM_FEATURE category provide a selected list of atom level features for the chemical component.- Specified by:
getPdbxChemCompAtomFeaturein interfaceBlock- Returns:
- PdbxChemCompAtomFeature
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getPdbxReferenceMoleculeFamily
public PdbxReferenceMoleculeFamily getPdbxReferenceMoleculeFamily()
Description copied from interface:BlockData items in the PDBX_REFERENCE_MOLECULE_FAMILY category identify entity families.- Specified by:
getPdbxReferenceMoleculeFamilyin interfaceBlock- Returns:
- PdbxReferenceMoleculeFamily
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getPdbxReferenceMoleculeList
public PdbxReferenceMoleculeList getPdbxReferenceMoleculeList()
Description copied from interface:BlockData items in the PDBX_REFERENCE_MOLECULE_LIST category record reference information about small polymer molecules.- Specified by:
getPdbxReferenceMoleculeListin interfaceBlock- Returns:
- PdbxReferenceMoleculeList
-
getPdbxReferenceMolecule
public PdbxReferenceMolecule getPdbxReferenceMolecule()
Description copied from interface:BlockData items in the PDBX_REFERENCE_MOLECULE category record reference information about small polymer molecules.- Specified by:
getPdbxReferenceMoleculein interfaceBlock- Returns:
- PdbxReferenceMolecule
-
getPdbxReferenceEntityList
public PdbxReferenceEntityList getPdbxReferenceEntityList()
Description copied from interface:BlockData items in the PDBX_REFERENCE_ENTITY_LIST category record the list of entities within each reference molecule.- Specified by:
getPdbxReferenceEntityListin interfaceBlock- Returns:
- PdbxReferenceEntityList
-
getPdbxReferenceEntityNonpoly
public PdbxReferenceEntityNonpoly getPdbxReferenceEntityNonpoly()
Description copied from interface:BlockData items in the PDBX_REFERENCE_ENTITY_NONPOLY category record the list of entities within each reference molecule.- Specified by:
getPdbxReferenceEntityNonpolyin interfaceBlock- Returns:
- PdbxReferenceEntityNonpoly
-
getPdbxReferenceEntityLink
public PdbxReferenceEntityLink getPdbxReferenceEntityLink()
Description copied from interface:BlockData items in the PDBX_REFERENCE_ENTITY_LINK category give details about the linkages between entities within reference molecules.- Specified by:
getPdbxReferenceEntityLinkin interfaceBlock- Returns:
- PdbxReferenceEntityLink
-
getPdbxReferenceEntityPolyLink
public PdbxReferenceEntityPolyLink getPdbxReferenceEntityPolyLink()
Description copied from interface:BlockData items in the PDBX_REFERENCE_ENTITY_POLY_LINK category give details about polymer linkages including both standard and non-standard linkages between polymer componnents.- Specified by:
getPdbxReferenceEntityPolyLinkin interfaceBlock- Returns:
- PdbxReferenceEntityPolyLink
-
getPdbxReferenceEntityPoly
public PdbxReferenceEntityPoly getPdbxReferenceEntityPoly()
Description copied from interface:BlockData items in the PDBX_REFERENCE_ENTITY_POLY category record details about the polymer, such as the type of the polymer, the number of monomers and whether it has nonstandard features.- Specified by:
getPdbxReferenceEntityPolyin interfaceBlock- Returns:
- PdbxReferenceEntityPoly
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getPdbxReferenceEntityPolySeq
public PdbxReferenceEntityPolySeq getPdbxReferenceEntityPolySeq()
Description copied from interface:BlockData items in the PDBX_REFERENCE_ENTITY_POLY_SEQ category specify the sequence of monomers in a polymer.- Specified by:
getPdbxReferenceEntityPolySeqin interfaceBlock- Returns:
- PdbxReferenceEntityPolySeq
-
getPdbxReferenceEntitySequence
public PdbxReferenceEntitySequence getPdbxReferenceEntitySequence()
Description copied from interface:BlockAdditional features associated with the reference entity.- Specified by:
getPdbxReferenceEntitySequencein interfaceBlock- Returns:
- PdbxReferenceEntitySequence
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getPdbxReferenceEntitySrcNat
public PdbxReferenceEntitySrcNat getPdbxReferenceEntitySrcNat()
Description copied from interface:BlockData items in the PDBX_REFERENCE_ENTITY_SRC_NAT category record details of the source from which the entity was obtained.- Specified by:
getPdbxReferenceEntitySrcNatin interfaceBlock- Returns:
- PdbxReferenceEntitySrcNat
-
getPdbxReferenceMoleculeDetails
public PdbxReferenceMoleculeDetails getPdbxReferenceMoleculeDetails()
Description copied from interface:BlockData items in the PDBX_REFERENCE_MOLECULE_DETAILS category records textual details about small polymer molecules.- Specified by:
getPdbxReferenceMoleculeDetailsin interfaceBlock- Returns:
- PdbxReferenceMoleculeDetails
-
getPdbxReferenceMoleculeSynonyms
public PdbxReferenceMoleculeSynonyms getPdbxReferenceMoleculeSynonyms()
Description copied from interface:BlockData items in the PDBX_REFERENCE_MOLECULE_SYNONYMS category records synonym names for reference entities.- Specified by:
getPdbxReferenceMoleculeSynonymsin interfaceBlock- Returns:
- PdbxReferenceMoleculeSynonyms
-
getPdbxReferenceEntitySubcomponents
public PdbxReferenceEntitySubcomponents getPdbxReferenceEntitySubcomponents()
Description copied from interface:BlockData items in the PDBX_REFERENCE_ENTITY_SUBCOMPONENTS category records subcomponent sequence from which this entity could be built.- Specified by:
getPdbxReferenceEntitySubcomponentsin interfaceBlock- Returns:
- PdbxReferenceEntitySubcomponents
-
getPdbxReferenceMoleculeAnnotation
public PdbxReferenceMoleculeAnnotation getPdbxReferenceMoleculeAnnotation()
Description copied from interface:BlockData items in the PDBX_REFERENCE_MOLECULE_ANNOTATION category specify additional annotation relevant to the molecular entities.- Specified by:
getPdbxReferenceMoleculeAnnotationin interfaceBlock- Returns:
- PdbxReferenceMoleculeAnnotation
-
getPdbxReferenceMoleculeFeatures
public PdbxReferenceMoleculeFeatures getPdbxReferenceMoleculeFeatures()
Description copied from interface:BlockAdditional features associated with the reference entity.- Specified by:
getPdbxReferenceMoleculeFeaturesin interfaceBlock- Returns:
- PdbxReferenceMoleculeFeatures
-
getPdbxReferenceMoleculeRelatedStructures
public PdbxReferenceMoleculeRelatedStructures getPdbxReferenceMoleculeRelatedStructures()
Description copied from interface:BlockData items in the PDBX_REFERENCE_MOLECULE_RELATED_STRUCTURES category record details of the structural examples in related databases for this entity.- Specified by:
getPdbxReferenceMoleculeRelatedStructuresin interfaceBlock- Returns:
- PdbxReferenceMoleculeRelatedStructures
-
getPdbxStructGroupList
public PdbxStructGroupList getPdbxStructGroupList()
Description copied from interface:BlockData items in the PDBX_STRUCT_GROUP_LIST define groups of related components or atoms.- Specified by:
getPdbxStructGroupListin interfaceBlock- Returns:
- PdbxStructGroupList
-
getPdbxStructGroupComponents
public PdbxStructGroupComponents getPdbxStructGroupComponents()
Description copied from interface:BlockData items in the PDBX_STRUCT_GROUP_COMPONENTS category list component-level group assignments within the entry. Groups are defined and described in category PDBX_STRUCT_GROUP_LIST.- Specified by:
getPdbxStructGroupComponentsin interfaceBlock- Returns:
- PdbxStructGroupComponents
-
getPdbxStructGroupComponentRange
public PdbxStructGroupComponentRange getPdbxStructGroupComponentRange()
Description copied from interface:BlockData items in the PDBX_STRUCT_GROUP_COMPONENT_RANGE category define a structural group as a continuous span chemical components.- Specified by:
getPdbxStructGroupComponentRangein interfaceBlock- Returns:
- PdbxStructGroupComponentRange
-
getPdbxPrdAudit
public PdbxPrdAudit getPdbxPrdAudit()
Description copied from interface:BlockData items in the PDBX_PRD_AUDIT category records the status and tracking information for this molecule.- Specified by:
getPdbxPrdAuditin interfaceBlock- Returns:
- PdbxPrdAudit
-
getPdbxFamilyPrdAudit
public PdbxFamilyPrdAudit getPdbxFamilyPrdAudit()
Description copied from interface:BlockData items in the PDBX_FAMILY_PRD_AUDIT category records the status and tracking information for this family.- Specified by:
getPdbxFamilyPrdAuditin interfaceBlock- Returns:
- PdbxFamilyPrdAudit
-
getPdbxMolecule
public PdbxMolecule getPdbxMolecule()
Description copied from interface:BlockData items in the PDBX_MOLECULE category identify reference molecules within a PDB entry.- Specified by:
getPdbxMoleculein interfaceBlock- Returns:
- PdbxMolecule
-
getPdbxMoleculeFeatures
public PdbxMoleculeFeatures getPdbxMoleculeFeatures()
Description copied from interface:BlockData items in the PDBX_MOLECULE_FEATURES category record features of molecules within a PDB entry.- Specified by:
getPdbxMoleculeFeaturesin interfaceBlock- Returns:
- PdbxMoleculeFeatures
-
getPdbxFamilyGroupIndex
public PdbxFamilyGroupIndex getPdbxFamilyGroupIndex()
Description copied from interface:BlockData items in the PDBX_FAMILY_GROUP_INDEX category record the family membership in family groups.- Specified by:
getPdbxFamilyGroupIndexin interfaceBlock- Returns:
- PdbxFamilyGroupIndex
-
getPdbxDistantSolventAtoms
public PdbxDistantSolventAtoms getPdbxDistantSolventAtoms()
Description copied from interface:BlockData items in the PDBX_DISTANT_SOLVENT_ATOMS category list the solvent atoms remote from any macromolecule.- Specified by:
getPdbxDistantSolventAtomsin interfaceBlock- Returns:
- PdbxDistantSolventAtoms
-
getPdbxStructSpecialSymmetry
public PdbxStructSpecialSymmetry getPdbxStructSpecialSymmetry()
Description copied from interface:BlockData items in the PDBX_STRUCT_SPECIAL_SYMMETRY category list the molecular components that lie on special symmetry positions.- Specified by:
getPdbxStructSpecialSymmetryin interfaceBlock- Returns:
- PdbxStructSpecialSymmetry
-
getPdbxReferencePublicationList
public PdbxReferencePublicationList getPdbxReferencePublicationList()
Description copied from interface:BlockData items in the PDBX_REFERENCE_PUBLICATION_LIST hold reference information related to PDB citation data.- Specified by:
getPdbxReferencePublicationListin interfaceBlock- Returns:
- PdbxReferencePublicationList
-
getPdbxNmrAssignedChemShiftList
public PdbxNmrAssignedChemShiftList getPdbxNmrAssignedChemShiftList()
Description copied from interface:BlockItems in the assigned_chem_shift_list category provide information about a list of reported assigned chemical shift values.- Specified by:
getPdbxNmrAssignedChemShiftListin interfaceBlock- Returns:
- PdbxNmrAssignedChemShiftList
-
getPdbxNmrChemShiftExperiment
public PdbxNmrChemShiftExperiment getPdbxNmrChemShiftExperiment()
Description copied from interface:BlockItems in the chem_shift_experiment category provide pointers to the NMR experiments and samples used to collect the data for a set of reported assigned chemical shifts.- Specified by:
getPdbxNmrChemShiftExperimentin interfaceBlock- Returns:
- PdbxNmrChemShiftExperiment
-
getPdbxNmrChemShiftRef
public PdbxNmrChemShiftRef getPdbxNmrChemShiftRef()
Description copied from interface:BlockItems in the pdbx_nmr_chem_shift_ref category provide the chemical shift referencing values used in assigning the chemical shift positions for peaks in spectral peak lists and assigned atom chemical shifts.- Specified by:
getPdbxNmrChemShiftRefin interfaceBlock- Returns:
- PdbxNmrChemShiftRef
-
getPdbxNmrChemShiftReference
public PdbxNmrChemShiftReference getPdbxNmrChemShiftReference()
Description copied from interface:BlockItems in the chem_shift_reference category define a set of chemical shift referencing parameters.- Specified by:
getPdbxNmrChemShiftReferencein interfaceBlock- Returns:
- PdbxNmrChemShiftReference
-
getPdbxNmrChemShiftSoftware
public PdbxNmrChemShiftSoftware getPdbxNmrChemShiftSoftware()
Description copied from interface:BlockItems in the chem_shift_software category provide pointers to the software category and methods category.- Specified by:
getPdbxNmrChemShiftSoftwarein interfaceBlock- Returns:
- PdbxNmrChemShiftSoftware
-
getPdbxNmrConstraintFile
public PdbxNmrConstraintFile getPdbxNmrConstraintFile()
Description copied from interface:BlockItems in the pdbx_nmr_constraint_file category record the name of the constraint file, the software used to calculate conformers with the constraint file, and the characteristics of the constraints in the constraint file.- Specified by:
getPdbxNmrConstraintFilein interfaceBlock- Returns:
- PdbxNmrConstraintFile
-
getPdbxNmrSoftwareTask
public PdbxNmrSoftwareTask getPdbxNmrSoftwareTask()
Description copied from interface:BlockItems in the pdbx_nmr_software_task category provide information about software workflow in the NMR experiment.- Specified by:
getPdbxNmrSoftwareTaskin interfaceBlock- Returns:
- PdbxNmrSoftwareTask
-
getPdbxNmrSpectralDim
public PdbxNmrSpectralDim getPdbxNmrSpectralDim()
Description copied from interface:BlockItems in the spectral_dim category describe the parameters of each dimension in the NMR experiment used to generate the spectral peak list.- Specified by:
getPdbxNmrSpectralDimin interfaceBlock- Returns:
- PdbxNmrSpectralDim
-
getPdbxNmrSpectralPeakList
public PdbxNmrSpectralPeakList getPdbxNmrSpectralPeakList()
Description copied from interface:BlockItems in the pdbx_nmr_spectral_peak_list category provide information about a list of reported spectral peak characteristic values.- Specified by:
getPdbxNmrSpectralPeakListin interfaceBlock- Returns:
- PdbxNmrSpectralPeakList
-
getPdbxNmrSpectralPeakSoftware
public PdbxNmrSpectralPeakSoftware getPdbxNmrSpectralPeakSoftware()
Description copied from interface:BlockItems in the pdbx_nmr_spectral_peak_software category provide pointers to the software category and methods category where descriptions of software applications and methods can be found.- Specified by:
getPdbxNmrSpectralPeakSoftwarein interfaceBlock- Returns:
- PdbxNmrSpectralPeakSoftware
-
getPdbxNmrSystematicChemShiftOffset
public PdbxNmrSystematicChemShiftOffset getPdbxNmrSystematicChemShiftOffset()
Description copied from interface:BlockItems in the pdbx_nmr_systematic_chem_shift_offset category define chemical shift offsets that systematically affect all chemical shifts in a set of assigned chemical shifts for a specific nuclei.- Specified by:
getPdbxNmrSystematicChemShiftOffsetin interfaceBlock- Returns:
- PdbxNmrSystematicChemShiftOffset
-
getPdbxNmrUpload
public PdbxNmrUpload getPdbxNmrUpload()
Description copied from interface:BlockItems in the pdbx_nmr_upload category provide information about the data files uploaded by a depositor using the deposition system.- Specified by:
getPdbxNmrUploadin interfaceBlock- Returns:
- PdbxNmrUpload
-
getPdbxAuditSupport
public PdbxAuditSupport getPdbxAuditSupport()
Description copied from interface:BlockData items in the PDBX_AUDIT_SUPPORT category record details about funding support for the entry.- Specified by:
getPdbxAuditSupportin interfaceBlock- Returns:
- PdbxAuditSupport
-
getPdbxChemCompSubcomponentStructConn
public PdbxChemCompSubcomponentStructConn getPdbxChemCompSubcomponentStructConn()
Description copied from interface:BlockData items in the pdbx_chem_comp_subcomponent_struct_conn list the chemical interactions among the subcomponents in the chemical component.- Specified by:
getPdbxChemCompSubcomponentStructConnin interfaceBlock- Returns:
- PdbxChemCompSubcomponentStructConn
-
getPdbxChemCompSubcomponentEntityList
public PdbxChemCompSubcomponentEntityList getPdbxChemCompSubcomponentEntityList()
Description copied from interface:BlockData items in the pdbx_chem_comp_subcomponent_entity_list category list the constituent chemical entities and entity features in this chemical component.- Specified by:
getPdbxChemCompSubcomponentEntityListin interfaceBlock- Returns:
- PdbxChemCompSubcomponentEntityList
-
getEntitySrcNat
public EntitySrcNat getEntitySrcNat()
Description copied from interface:BlockData items in the ENTITY_SRC_NAT category record details of the source from which the entity was obtained in cases where the entity was isolated directly from a natural tissue.- Specified by:
getEntitySrcNatin interfaceBlock- Returns:
- EntitySrcNat
-
getEntitySrcGen
public EntitySrcGen getEntitySrcGen()
Description copied from interface:BlockData items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated. The following are treated separately: items pertaining to the tissue from which the gene was obtained, items pertaining to the host organism for gene expression and items pertaining to the actual producing organism (plasmid).- Specified by:
getEntitySrcGenin interfaceBlock- Returns:
- EntitySrcGen
-
getPdbxEntitySrcSyn
public PdbxEntitySrcSyn getPdbxEntitySrcSyn()
Description copied from interface:BlockThe data items in category PDBX_ENTITY_SRC_SYN record the source details about chemically synthesized molecules.- Specified by:
getPdbxEntitySrcSynin interfaceBlock- Returns:
- PdbxEntitySrcSyn
-
getPdbxEntityPolyCompLinkList
public PdbxEntityPolyCompLinkList getPdbxEntityPolyCompLinkList()
Description copied from interface:BlockData items in the PDBX_ENTITY_POLY_COMP_LINK_LIST category enumerate the the linkages between components within the polymer entity.- Specified by:
getPdbxEntityPolyCompLinkListin interfaceBlock- Returns:
- PdbxEntityPolyCompLinkList
-
getPdbxLinkedEntity
public PdbxLinkedEntity getPdbxLinkedEntity()
Description copied from interface:BlockData items in the PDBX_LINKED_ENTITY category record information about molecules composed of linked entities.- Specified by:
getPdbxLinkedEntityin interfaceBlock- Returns:
- PdbxLinkedEntity
-
getPdbxLinkedEntityInstanceList
public PdbxLinkedEntityInstanceList getPdbxLinkedEntityInstanceList()
Description copied from interface:BlockData items in the PDBX_LINKED_ENTITY_INSTANCE_LIST category identify instance molecules represented as linked entities within an entry.- Specified by:
getPdbxLinkedEntityInstanceListin interfaceBlock- Returns:
- PdbxLinkedEntityInstanceList
-
getPdbxLinkedEntityList
public PdbxLinkedEntityList getPdbxLinkedEntityList()
Description copied from interface:BlockData items in the PDBX_LINKED_ENTITY_LIST category record the list of entity constituents for this molecule.- Specified by:
getPdbxLinkedEntityListin interfaceBlock- Returns:
- PdbxLinkedEntityList
-
getPdbxLinkedEntityLinkList
public PdbxLinkedEntityLinkList getPdbxLinkedEntityLinkList()
Description copied from interface:BlockData items in the PDBX_LINKED_ENTITY_LINK_LIST category give details about the linkages with molecules represented as linked entities.- Specified by:
getPdbxLinkedEntityLinkListin interfaceBlock- Returns:
- PdbxLinkedEntityLinkList
-
getPdbxEntityDescriptor
public PdbxEntityDescriptor getPdbxEntityDescriptor()
Description copied from interface:BlockData items in the PDBX_ENTITY_DESCRIPTOR category provide string descriptors of entity chemical structure.- Specified by:
getPdbxEntityDescriptorin interfaceBlock- Returns:
- PdbxEntityDescriptor
-
getPdbxReferenceLinkedEntity
public PdbxReferenceLinkedEntity getPdbxReferenceLinkedEntity()
Description copied from interface:BlockData items in the pdbx_reference_linked_entity category describe common observed interaction patterns within linked entities.- Specified by:
getPdbxReferenceLinkedEntityin interfaceBlock- Returns:
- PdbxReferenceLinkedEntity
-
getPdbxReferenceLinkedEntityCompList
public PdbxReferenceLinkedEntityCompList getPdbxReferenceLinkedEntityCompList()
Description copied from interface:BlockData items in the pdbx_reference_linked_entity_comp_list category lists the constituents of common observed interaction patterns described in the pdbx_reference_linked_entity category.- Specified by:
getPdbxReferenceLinkedEntityCompListin interfaceBlock- Returns:
- PdbxReferenceLinkedEntityCompList
-
getPdbxReferenceLinkedEntityCompLink
public PdbxReferenceLinkedEntityCompLink getPdbxReferenceLinkedEntityCompLink()
Description copied from interface:BlockData items in the pdbx_reference_linked_entity_comp_link category enumerate inter-entity linkages between the components of common observed interaction patterns described in the pdbx_reference_linked_entity category.- Specified by:
getPdbxReferenceLinkedEntityCompLinkin interfaceBlock- Returns:
- PdbxReferenceLinkedEntityCompLink
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getPdbxReferenceLinkedEntityLink
public PdbxReferenceLinkedEntityLink getPdbxReferenceLinkedEntityLink()
Description copied from interface:BlockData items in the pdbx_reference_linked_entity_link category enumerate linkages between the entities in common observed interaction patterns described in the pdbx_reference_linked_entity category.- Specified by:
getPdbxReferenceLinkedEntityLinkin interfaceBlock- Returns:
- PdbxReferenceLinkedEntityLink
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getPdbxRelatedExpDataSet
public PdbxRelatedExpDataSet getPdbxRelatedExpDataSet()
Description copied from interface:BlockData items in the PDBX_RELATED_DATA_SET category record references to experimental data sets related to the entry.- Specified by:
getPdbxRelatedExpDataSetin interfaceBlock- Returns:
- PdbxRelatedExpDataSet
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getPdbxDatabaseStatusHistory
public PdbxDatabaseStatusHistory getPdbxDatabaseStatusHistory()
Description copied from interface:BlockThe pdbx_database_status_history category records the time evolution of entry processing status.- Specified by:
getPdbxDatabaseStatusHistoryin interfaceBlock- Returns:
- PdbxDatabaseStatusHistory
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getEmAssembly
public EmAssembly getEmAssembly()
Description copied from interface:BlockData items in the EM_ASSEMBLY category record details about the imaged EM sample.- Specified by:
getEmAssemblyin interfaceBlock- Returns:
- EmAssembly
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getEmEntityAssembly
public EmEntityAssembly getEmEntityAssembly()
Description copied from interface:BlockData items in the EM_ENTITY_ASSEMBLY category record details about each component of the complex.- Specified by:
getEmEntityAssemblyin interfaceBlock- Returns:
- EmEntityAssembly
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getEmVirusEntity
public EmVirusEntity getEmVirusEntity()
Description copied from interface:BlockData items in the EM_VIRUS_ENTITY category record details of the icosahedral virus.- Specified by:
getEmVirusEntityin interfaceBlock- Returns:
- EmVirusEntity
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getEmSamplePreparation
public EmSamplePreparation getEmSamplePreparation()
Description copied from interface:BlockData items in the EM_SAMPLE_PREPARATION category record details of sample conditions prior to and upon loading onto grid support.- Specified by:
getEmSamplePreparationin interfaceBlock- Returns:
- EmSamplePreparation
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getEmSampleSupport
public EmSampleSupport getEmSampleSupport()
Description copied from interface:BlockData items in the EM_SAMPLE_SUPPORT category record details of the electron microscope grid type, grid support film and pretreatment of whole before sample is applied- Specified by:
getEmSampleSupportin interfaceBlock- Returns:
- EmSampleSupport
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getEmBuffer
public EmBuffer getEmBuffer()
Description copied from interface:BlockData items in the BUFFER category record details of the sample buffer.- Specified by:
getEmBufferin interfaceBlock- Returns:
- EmBuffer
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getEmVitrification
public EmVitrification getEmVitrification()
Description copied from interface:BlockData items in the EM_VITRIFICATION category record details about the method and cryogen used in rapid freezing of the sample on the grid prior to its insertion in the electron microscope- Specified by:
getEmVitrificationin interfaceBlock- Returns:
- EmVitrification
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getEmImaging
public EmImaging getEmImaging()
Description copied from interface:BlockData items in the EM_IMAGING category record details about the parameters used in imaging the sample in the electron microscope.- Specified by:
getEmImagingin interfaceBlock- Returns:
- EmImaging
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getEmDetector
public EmDetector getEmDetector()
Description copied from interface:BlockData items in the EM_DETECTOR category record details of the image detector type.- Specified by:
getEmDetectorin interfaceBlock- Returns:
- EmDetector
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getEmImageScans
public EmImageScans getEmImageScans()
Description copied from interface:BlockData items in the EM_IMAGE_SCANS category record details of the image scanning device (microdensitometer) and parameters for digitization of the image.- Specified by:
getEmImageScansin interfaceBlock- Returns:
- EmImageScans
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getEm2dProjectionSelection
public Em2dProjectionSelection getEm2dProjectionSelection()
Description copied from interface:BlockData items in the EM_2D_PROJECTION_SELECTION category record details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs.- Specified by:
getEm2dProjectionSelectionin interfaceBlock- Returns:
- Em2dProjectionSelection
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getEm3dReconstruction
public Em3dReconstruction getEm3dReconstruction()
Description copied from interface:BlockData items in the EM_3D_RECONSTRUCTION category record details of the 3D reconstruction procedure from 2D projections.- Specified by:
getEm3dReconstructionin interfaceBlock- Returns:
- Em3dReconstruction
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getEm3dFitting
public Em3dFitting getEm3dFitting()
Description copied from interface:BlockData items in the 3D_FITTING category record details of the method of fitting atomic coordinates from a PDB file into a 3d-em volume map file- Specified by:
getEm3dFittingin interfaceBlock- Returns:
- Em3dFitting
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getEm3dFittingList
public Em3dFittingList getEm3dFittingList()
Description copied from interface:BlockData items in the 3D_FITTING_LIST category lists the methods of fitting atomic coordinates from a PDB file into a 3d-em volume map file- Specified by:
getEm3dFittingListin interfaceBlock- Returns:
- Em3dFittingList
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getEmHelicalEntity
public EmHelicalEntity getEmHelicalEntity()
Description copied from interface:BlockData items in the EM_HELICAL_ENTITY category record details for a helical or filament type of assembly component.- Specified by:
getEmHelicalEntityin interfaceBlock- Returns:
- EmHelicalEntity
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getEmExperiment
public EmExperiment getEmExperiment()
Description copied from interface:BlockData items in the EM_EXPERIMENT category provide high-level classification of the EM experiment.- Specified by:
getEmExperimentin interfaceBlock- Returns:
- EmExperiment
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getEmSingleParticleEntity
public EmSingleParticleEntity getEmSingleParticleEntity()
Description copied from interface:BlockData items in the EM_SINGLE_PARTICLE_ENTITY category provide the details of the symmetry for a single particle entity type.- Specified by:
getEmSingleParticleEntityin interfaceBlock- Returns:
- EmSingleParticleEntity
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getEmAdmin
public EmAdmin getEmAdmin()
Description copied from interface:BlockAdministration-related data items- Specified by:
getEmAdminin interfaceBlock- Returns:
- EmAdmin
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getEmAuthorList
public EmAuthorList getEmAuthorList()
Description copied from interface:BlockCategory to collect the authors of this entry- Specified by:
getEmAuthorListin interfaceBlock- Returns:
- EmAuthorList
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getEmDbReference
public EmDbReference getEmDbReference()
Description copied from interface:BlockCategory holds links to raw data sources for the entry, e.g., held by a remote server.- Specified by:
getEmDbReferencein interfaceBlock- Returns:
- EmDbReference
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getEmDbReferenceAuxiliary
public EmDbReferenceAuxiliary getEmDbReferenceAuxiliary()
Description copied from interface:BlockCategory holds links to raw data sources for the entry, e.g., held by a remote server.- Specified by:
getEmDbReferenceAuxiliaryin interfaceBlock- Returns:
- EmDbReferenceAuxiliary
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getEmDepui
public EmDepui getEmDepui()
Description copied from interface:BlockSome internal items to power the deposition interface- Specified by:
getEmDepuiin interfaceBlock- Returns:
- EmDepui
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getEmObsolete
public EmObsolete getEmObsolete()
Description copied from interface:BlockList of EMD entries made obsolete by this entry.- Specified by:
getEmObsoletein interfaceBlock- Returns:
- EmObsolete
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getEmSupersede
public EmSupersede getEmSupersede()
Description copied from interface:BlockList of newer entries that replace this entry.- Specified by:
getEmSupersedein interfaceBlock- Returns:
- EmSupersede
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getEmEntityAssemblyMolwt
public EmEntityAssemblyMolwt getEmEntityAssemblyMolwt()
Description copied from interface:BlockData items in this category record details about the molecular weight of an assembly component of the sample.- Specified by:
getEmEntityAssemblyMolwtin interfaceBlock- Returns:
- EmEntityAssemblyMolwt
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getEmEntityAssemblyNaturalsource
public EmEntityAssemblyNaturalsource getEmEntityAssemblyNaturalsource()
Description copied from interface:BlockData items in this category record taxonomic details about the natural source for EM assemblies and assembly components.- Specified by:
getEmEntityAssemblyNaturalsourcein interfaceBlock- Returns:
- EmEntityAssemblyNaturalsource
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getEmEntityAssemblyRecombinant
public EmEntityAssemblyRecombinant getEmEntityAssemblyRecombinant()
Description copied from interface:BlockData items in this category record details about recombinant expression of the assembly or assembly component.- Specified by:
getEmEntityAssemblyRecombinantin interfaceBlock- Returns:
- EmEntityAssemblyRecombinant
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getEmVirusNaturalHost
public EmVirusNaturalHost getEmVirusNaturalHost()
Description copied from interface:BlockData items in this category record details of a virus entity.- Specified by:
getEmVirusNaturalHostin interfaceBlock- Returns:
- EmVirusNaturalHost
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getEmVirusShell
public EmVirusShell getEmVirusShell()
Description copied from interface:BlockData items in the EMD_VIRUS_SHELL category record details of the viral shell number, shell diameter, and icosahedral triangulation number.- Specified by:
getEmVirusShellin interfaceBlock- Returns:
- EmVirusShell
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getEmSpecimen
public EmSpecimen getEmSpecimen()
Description copied from interface:BlockData items in the EMD_SPECIMEN category record details about specimens prepared for imaging by electron microscopy.- Specified by:
getEmSpecimenin interfaceBlock- Returns:
- EmSpecimen
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getEmEmbedding
public EmEmbedding getEmEmbedding()
Description copied from interface:BlockSugar embedding category- Specified by:
getEmEmbeddingin interfaceBlock- Returns:
- EmEmbedding
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getEmFiducialMarkers
public EmFiducialMarkers getEmFiducialMarkers()
Description copied from interface:BlockDescription of fiducial markers.- Specified by:
getEmFiducialMarkersin interfaceBlock- Returns:
- EmFiducialMarkers
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getEmFocusedIonBeam
public EmFocusedIonBeam getEmFocusedIonBeam()
Description copied from interface:BlockDescription of sectioning by focused_ion_beam- Specified by:
getEmFocusedIonBeamin interfaceBlock- Returns:
- EmFocusedIonBeam
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getEmGridPretreatment
public EmGridPretreatment getEmGridPretreatment()
Description copied from interface:BlockData items describing glow discharge pretreatment for an EM grid- Specified by:
getEmGridPretreatmentin interfaceBlock- Returns:
- EmGridPretreatment
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getEmUltramicrotomy
public EmUltramicrotomy getEmUltramicrotomy()
Description copied from interface:BlockDescription of sectioning by ultramicrotomy- Specified by:
getEmUltramicrotomyin interfaceBlock- Returns:
- EmUltramicrotomy
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getEmHighPressureFreezing
public EmHighPressureFreezing getEmHighPressureFreezing()
Description copied from interface:BlockDescription of high pressure freezing- Specified by:
getEmHighPressureFreezingin interfaceBlock- Returns:
- EmHighPressureFreezing
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getEmShadowing
public EmShadowing getEmShadowing()
Description copied from interface:BlockData items related to shadowing of an EM specimen- Specified by:
getEmShadowingin interfaceBlock- Returns:
- EmShadowing
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getEmTomographySpecimen
public EmTomographySpecimen getEmTomographySpecimen()
Description copied from interface:BlockDescription specimen preparation for imaging using tomography.- Specified by:
getEmTomographySpecimenin interfaceBlock- Returns:
- EmTomographySpecimen
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getEmCrystalFormation
public EmCrystalFormation getEmCrystalFormation()
Description copied from interface:BlockDescription of growth of a 2D, 3D, or helical crystal array.- Specified by:
getEmCrystalFormationin interfaceBlock- Returns:
- EmCrystalFormation
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getEmStaining
public EmStaining getEmStaining()
Description copied from interface:BlockStaining category- Specified by:
getEmStainingin interfaceBlock- Returns:
- EmStaining
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getEmSupportFilm
public EmSupportFilm getEmSupportFilm()
Description copied from interface:BlockData items to describe films supporting the specimen- Specified by:
getEmSupportFilmin interfaceBlock- Returns:
- EmSupportFilm
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getEmBufferComponent
public EmBufferComponent getEmBufferComponent()
Description copied from interface:BlockBuffer category- Specified by:
getEmBufferComponentin interfaceBlock- Returns:
- EmBufferComponent
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getEmDiffraction
public EmDiffraction getEmDiffraction()
Description copied from interface:BlockMicroscopy parameters relevant only for crystallography- Specified by:
getEmDiffractionin interfaceBlock- Returns:
- EmDiffraction
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getEmDiffractionShell
public EmDiffractionShell getEmDiffractionShell()
Description copied from interface:BlockStatistical parameters for electron diffraction measurements within a resolution shell- Specified by:
getEmDiffractionShellin interfaceBlock- Returns:
- EmDiffractionShell
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getEmDiffractionStats
public EmDiffractionStats getEmDiffractionStats()
Description copied from interface:BlockStatistical parameters for electron diffraction measurements- Specified by:
getEmDiffractionStatsin interfaceBlock- Returns:
- EmDiffractionStats
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getEmTomography
public EmTomography getEmTomography()
Description copied from interface:BlockMicroscopy parameters only relevant for tomography- Specified by:
getEmTomographyin interfaceBlock- Returns:
- EmTomography
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getEmImageRecording
public EmImageRecording getEmImageRecording()
Description copied from interface:BlockData items in the EM_IMAGE_RECORDING category record details of the image recording (either film/microdensitometer or electronic detector) and parameters for image digitization.- Specified by:
getEmImageRecordingin interfaceBlock- Returns:
- EmImageRecording
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getEmImagingOptics
public EmImagingOptics getEmImagingOptics()
Description copied from interface:BlockDescription of a few specialist optics apparatus- Specified by:
getEmImagingOpticsin interfaceBlock- Returns:
- EmImagingOptics
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getEmFinalClassification
public EmFinalClassification getEmFinalClassification()
Description copied from interface:BlockInformation about the final image classification- Specified by:
getEmFinalClassificationin interfaceBlock- Returns:
- EmFinalClassification
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getEmStartModel
public EmStartModel getEmStartModel()
Description copied from interface:BlockThe startup model employed to begin refinement of the parameters for a 3DEM reconstruction- Specified by:
getEmStartModelin interfaceBlock- Returns:
- EmStartModel
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getEmSoftware
public EmSoftware getEmSoftware()
Description copied from interface:BlockDescription of the software that was used for data collection, data processing, data analysis, structure calculations and refinement. The description should include the name of the software, the author of the software and the version used.- Specified by:
getEmSoftwarein interfaceBlock- Returns:
- EmSoftware
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getEmEulerAngleAssignment
public EmEulerAngleAssignment getEmEulerAngleAssignment()
Description copied from interface:BlockCategory to describe the euler angle assignement- Specified by:
getEmEulerAngleAssignmentin interfaceBlock- Returns:
- EmEulerAngleAssignment
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getEmCtfCorrection
public EmCtfCorrection getEmCtfCorrection()
Description copied from interface:BlockDescription of the Contrast Transfer Function (CTF) correction- Specified by:
getEmCtfCorrectionin interfaceBlock- Returns:
- EmCtfCorrection
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getEmVolumeSelection
public EmVolumeSelection getEmVolumeSelection()
Description copied from interface:BlockVolume selection in image processing- Specified by:
getEmVolumeSelectionin interfaceBlock- Returns:
- EmVolumeSelection
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getEm3dCrystalEntity
public Em3dCrystalEntity getEm3dCrystalEntity()
Description copied from interface:BlockData items in the EM_SYMMETRY_3DX category record 3D crystal symmetry parameters utilized in 3DEM reconstruction averaging.- Specified by:
getEm3dCrystalEntityin interfaceBlock- Returns:
- Em3dCrystalEntity
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getEm2dCrystalEntity
public Em2dCrystalEntity getEm2dCrystalEntity()
Description copied from interface:BlockData items in the EM_SYMMETRY_2DX category record 2D crystal symmetry parameters utilized in a 3DEM reconstruction.- Specified by:
getEm2dCrystalEntityin interfaceBlock- Returns:
- Em2dCrystalEntity
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getEmImageProcessing
public EmImageProcessing getEmImageProcessing()
Description copied from interface:BlockData items in the EM_IMAGE_PROCESSING category record details of the EM image processing procedure.- Specified by:
getEmImageProcessingin interfaceBlock- Returns:
- EmImageProcessing
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getEmParticleSelection
public EmParticleSelection getEmParticleSelection()
Description copied from interface:BlockData items in this category record details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs.- Specified by:
getEmParticleSelectionin interfaceBlock- Returns:
- EmParticleSelection
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getEmMap
public EmMap getEmMap()
Description copied from interface:BlockData items in the EMD_MAP category record parameters of the CCP4 binary-format map file header (see ftp://ftp.wwpdb.org/pub/emdb/doc/map_format/EMDB_mapFormat_v1.0.pdf), parameters derived from the map header, pixel size, contour level, and annotation details from the depositor. The map is a three-dimensional array of data-values of the same data-type. Important parameters are data-type and array size in three dimensions (i.e. the number of columns, rows and sections). Columns are the fastest changing, followed by rows and sections.
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getEmFscCurve
public EmFscCurve getEmFscCurve()
Description copied from interface:BlockData items in the EMD_VALIDATION_FSC_CURVE category record details of the Fourier Shell Correlation (FSC) curve file.- Specified by:
getEmFscCurvein interfaceBlock- Returns:
- EmFscCurve
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getEmInterpretFigure
public EmInterpretFigure getEmInterpretFigure()
Description copied from interface:BlockListing of all layer line files associated with the EM entry- Specified by:
getEmInterpretFigurein interfaceBlock- Returns:
- EmInterpretFigure
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getEmLayerLines
public EmLayerLines getEmLayerLines()
Description copied from interface:BlockListing of all layer line files associated with the EM entry- Specified by:
getEmLayerLinesin interfaceBlock- Returns:
- EmLayerLines
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getEmStructureFactors
public EmStructureFactors getEmStructureFactors()
Description copied from interface:BlockListing of all structure factor files associated with the EM entry- Specified by:
getEmStructureFactorsin interfaceBlock- Returns:
- EmStructureFactors
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getEmDepositorInfo
public EmDepositorInfo getEmDepositorInfo()
Description copied from interface:BlockData items in the EM_DEPOSITOR INFO category record parameters for EM depositions that are provided by the depositor- Specified by:
getEmDepositorInfoin interfaceBlock- Returns:
- EmDepositorInfo
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getEmMapDepositorInfo
public EmMapDepositorInfo getEmMapDepositorInfo()
Description copied from interface:BlockData items in the EM_MAP_DEPOSITOR INFO category record map parameters that are provided by the depositor- Specified by:
getEmMapDepositorInfoin interfaceBlock- Returns:
- EmMapDepositorInfo
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getEmMaskDepositorInfo
public EmMaskDepositorInfo getEmMaskDepositorInfo()
Description copied from interface:BlockData items in the EM_MASK_DEPOSITOR_INFO category record mask parameters that are provided by the depositor- Specified by:
getEmMaskDepositorInfoin interfaceBlock- Returns:
- EmMaskDepositorInfo
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getEmFigureDepositorInfo
public EmFigureDepositorInfo getEmFigureDepositorInfo()
Description copied from interface:BlockListing of image files (figures) associated with an EMDB entry- Specified by:
getEmFigureDepositorInfoin interfaceBlock- Returns:
- EmFigureDepositorInfo
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getEmLayerLinesDepositorInfo
public EmLayerLinesDepositorInfo getEmLayerLinesDepositorInfo()
Description copied from interface:BlockListing of layer line files associated with the EM entry- Specified by:
getEmLayerLinesDepositorInfoin interfaceBlock- Returns:
- EmLayerLinesDepositorInfo
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getEmStructureFactorsDepositorInfo
public EmStructureFactorsDepositorInfo getEmStructureFactorsDepositorInfo()
Description copied from interface:BlockStructure factor files associated with the EM entry- Specified by:
getEmStructureFactorsDepositorInfoin interfaceBlock- Returns:
- EmStructureFactorsDepositorInfo
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getPdbxSeqMapDepositorInfo
public PdbxSeqMapDepositorInfo getPdbxSeqMapDepositorInfo()
Description copied from interface:BlockData items in the PDBX_SEQ_MAP_DEPOSITOR_INFO record the details about the mapping sample and coordinate sequences.- Specified by:
getPdbxSeqMapDepositorInfoin interfaceBlock- Returns:
- PdbxSeqMapDepositorInfo
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getPdbxChemCompDepositorInfo
public PdbxChemCompDepositorInfo getPdbxChemCompDepositorInfo()
Description copied from interface:BlockData items in the PDBX_CHEM_COMP_DEPOSITOR_INFO category record additional details provided by depositors about deposited chemical components.- Specified by:
getPdbxChemCompDepositorInfoin interfaceBlock- Returns:
- PdbxChemCompDepositorInfo
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getPdbxStructRefSeqDepositorInfo
public PdbxStructRefSeqDepositorInfo getPdbxStructRefSeqDepositorInfo()
Description copied from interface:BlockData items in the PDBX_STRUCT_REF_SEQ_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory STRUCT_REF_SEQ.- Specified by:
getPdbxStructRefSeqDepositorInfoin interfaceBlock- Returns:
- PdbxStructRefSeqDepositorInfo
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getPdbxStructRefSeqDifDepositorInfo
public PdbxStructRefSeqDifDepositorInfo getPdbxStructRefSeqDifDepositorInfo()
Description copied from interface:BlockData items in the PDBX_STRUCT_REF_SEQ_DIF_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory STRUCT_REF_SEQ_DIF.- Specified by:
getPdbxStructRefSeqDifDepositorInfoin interfaceBlock- Returns:
- PdbxStructRefSeqDifDepositorInfo
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getPdbxStructAssemblyPropDepositorInfo
public PdbxStructAssemblyPropDepositorInfo getPdbxStructAssemblyPropDepositorInfo()
Description copied from interface:BlockData items in the PDBX_STRUCT_ASSEMBLY_PROP_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_ASSEMBLY_PROP.- Specified by:
getPdbxStructAssemblyPropDepositorInfoin interfaceBlock- Returns:
- PdbxStructAssemblyPropDepositorInfo
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getPdbxStructAssemblyDepositorInfo
public PdbxStructAssemblyDepositorInfo getPdbxStructAssemblyDepositorInfo()
Description copied from interface:BlockData items in the PDBX_STRUCT_ASSEMBLY_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_ASSEMBLY.- Specified by:
getPdbxStructAssemblyDepositorInfoin interfaceBlock- Returns:
- PdbxStructAssemblyDepositorInfo
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getPdbxStructAssemblyGenDepositorInfo
public PdbxStructAssemblyGenDepositorInfo getPdbxStructAssemblyGenDepositorInfo()
Description copied from interface:BlockData items in the PDBX_STRUCT_ASSEMBLY_GEN_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_ASSEMBLY_GEN.- Specified by:
getPdbxStructAssemblyGenDepositorInfoin interfaceBlock- Returns:
- PdbxStructAssemblyGenDepositorInfo
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getPdbxStructOperListDepositorInfo
public PdbxStructOperListDepositorInfo getPdbxStructOperListDepositorInfo()
Description copied from interface:BlockData items in the PDBX_STRUCT_OPER_LIST_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_OPER_LIST.- Specified by:
getPdbxStructOperListDepositorInfoin interfaceBlock- Returns:
- PdbxStructOperListDepositorInfo
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getPdbxPointSymmetryDepositorInfo
public PdbxPointSymmetryDepositorInfo getPdbxPointSymmetryDepositorInfo()
Description copied from interface:BlockData items in the PDBX_POINT_SYMMETRY_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_POINT_SYMMETRY.- Specified by:
getPdbxPointSymmetryDepositorInfoin interfaceBlock- Returns:
- PdbxPointSymmetryDepositorInfo
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getPdbxHelicalSymmetryDepositorInfo
public PdbxHelicalSymmetryDepositorInfo getPdbxHelicalSymmetryDepositorInfo()
Description copied from interface:BlockData items in the PDBX_HELICAL_SYMMETRY_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_HELICAL_SYMMETRY.- Specified by:
getPdbxHelicalSymmetryDepositorInfoin interfaceBlock- Returns:
- PdbxHelicalSymmetryDepositorInfo
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getPdbxStructAssemblyAuthEvidenceDepositorInfo
public PdbxStructAssemblyAuthEvidenceDepositorInfo getPdbxStructAssemblyAuthEvidenceDepositorInfo()
Description copied from interface:BlockProvides author supplied evidentiary support for assemblies in pdbx_struct_assembly.- Specified by:
getPdbxStructAssemblyAuthEvidenceDepositorInfoin interfaceBlock- Returns:
- PdbxStructAssemblyAuthEvidenceDepositorInfo
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getPdbxSolventAtomSiteMapping
public PdbxSolventAtomSiteMapping getPdbxSolventAtomSiteMapping()
Description copied from interface:BlockData items in the PDBX_SOLVENT_ATOM_SITE_MAPPING category records mapping information between solvent atoms before and after symmetry repositioning.- Specified by:
getPdbxSolventAtomSiteMappingin interfaceBlock- Returns:
- PdbxSolventAtomSiteMapping
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getPdbxMoleculeFeaturesDepositorInfo
public PdbxMoleculeFeaturesDepositorInfo getPdbxMoleculeFeaturesDepositorInfo()
Description copied from interface:BlockData items in the PDBX_MOLECULE_FEATURES_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_MOLECULE_FEATURES.- Specified by:
getPdbxMoleculeFeaturesDepositorInfoin interfaceBlock- Returns:
- PdbxMoleculeFeaturesDepositorInfo
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getPdbxChemCompInstanceDepositorInfo
public PdbxChemCompInstanceDepositorInfo getPdbxChemCompInstanceDepositorInfo()
Description copied from interface:BlockData items in the PDBX_CHEM_COMP_INSTANCE_DEPOSITOR_INFO category records depositor provided information about the chemical context of component instances.- Specified by:
getPdbxChemCompInstanceDepositorInfoin interfaceBlock- Returns:
- PdbxChemCompInstanceDepositorInfo
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getPdbxDepuiStatusFlags
public PdbxDepuiStatusFlags getPdbxDepuiStatusFlags()
Description copied from interface:BlockData items in the PDBX_DEPUI_STATUS_FLAGS category record status details used to maintain state within the wwPDB deposition system.- Specified by:
getPdbxDepuiStatusFlagsin interfaceBlock- Returns:
- PdbxDepuiStatusFlags
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getPdbxDepuiUpload
public PdbxDepuiUpload getPdbxDepuiUpload()
Description copied from interface:BlockData items in the PDBX_DEPUI_UPLOAD category record the details of uploaded data files.- Specified by:
getPdbxDepuiUploadin interfaceBlock- Returns:
- PdbxDepuiUpload
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getPdbxDepuiValidationStatusFlags
public PdbxDepuiValidationStatusFlags getPdbxDepuiValidationStatusFlags()
Description copied from interface:BlockData items in the PDBX_DEPUI_VALIDATION_STATUS_FLAGS category record status details that assess the status of selected validation diagnostics.- Specified by:
getPdbxDepuiValidationStatusFlagsin interfaceBlock- Returns:
- PdbxDepuiValidationStatusFlags
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getPdbxChemCompUploadDepositorInfo
public PdbxChemCompUploadDepositorInfo getPdbxChemCompUploadDepositorInfo()
Description copied from interface:BlockData items in the PDBX_CHEM_COMP_UPLOAD_DEPOSITOR_INFO category record details of the uploaded files related to depositor provided chemical assignments.- Specified by:
getPdbxChemCompUploadDepositorInfoin interfaceBlock- Returns:
- PdbxChemCompUploadDepositorInfo
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getPdbxDepuiEntityStatusFlags
public PdbxDepuiEntityStatusFlags getPdbxDepuiEntityStatusFlags()
Description copied from interface:BlockData items in the PDBX_DEPUI_ENTITY_STATUS_FLAGS category record status details related to individual entities.- Specified by:
getPdbxDepuiEntityStatusFlagsin interfaceBlock- Returns:
- PdbxDepuiEntityStatusFlags
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getPdbxDepuiEntityFeatures
public PdbxDepuiEntityFeatures getPdbxDepuiEntityFeatures()
Description copied from interface:BlockData items in the PDBX_DEPUI_ENTITY_FEATURES category record status details related to the features of individual entities.- Specified by:
getPdbxDepuiEntityFeaturesin interfaceBlock- Returns:
- PdbxDepuiEntityFeatures
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getPdbxDepositionMessageInfo
public PdbxDepositionMessageInfo getPdbxDepositionMessageInfo()
Description copied from interface:BlockData items in the PDBX_DEPOSITION_MESSAGE_INFO category record internal messages within the depositon and annotation system.- Specified by:
getPdbxDepositionMessageInfoin interfaceBlock- Returns:
- PdbxDepositionMessageInfo
-
getPdbxDepositionMessageFileReference
public PdbxDepositionMessageFileReference getPdbxDepositionMessageFileReference()
Description copied from interface:BlockData items in the PDBX_DEPOSITION_MESSAGE_FILE_REFERENCE category record details of files references associated with messages defined in the PDBX_DEPOSITION_MESSAGE_INFO data category.- Specified by:
getPdbxDepositionMessageFileReferencein interfaceBlock- Returns:
- PdbxDepositionMessageFileReference
-
getPdbxDepuiEntryDetails
public PdbxDepuiEntryDetails getPdbxDepuiEntryDetails()
Description copied from interface:BlockData items in the PDBX_DEPUI_ENTRY_DETAILS category record information required to identify the depositor and route deposition to an appropriate processing site.- Specified by:
getPdbxDepuiEntryDetailsin interfaceBlock- Returns:
- PdbxDepuiEntryDetails
-
getPdbxDataProcessingStatus
public PdbxDataProcessingStatus getPdbxDataProcessingStatus()
Description copied from interface:BlockData items in the PDBX_DATA_PROCESSING_STATUS category record data processing instructions for workflow processing tasks.- Specified by:
getPdbxDataProcessingStatusin interfaceBlock- Returns:
- PdbxDataProcessingStatus
-
getPdbxEntityInstanceFeature
public PdbxEntityInstanceFeature getPdbxEntityInstanceFeature()
Description copied from interface:BlockData items in the pdbx_entity_instance_feature category records special features of selected entity instances.- Specified by:
getPdbxEntityInstanceFeaturein interfaceBlock- Returns:
- PdbxEntityInstanceFeature
-
getPdbxEntitySrcGenDepositorInfo
public PdbxEntitySrcGenDepositorInfo getPdbxEntitySrcGenDepositorInfo()
Description copied from interface:BlockData items in the PDBX_ENTITY_SRC_GEN_DEPOSITOR_INFO category record details of the source from which the entity was obtained in cases where the source was genetically manipulated. The following are treated separately: items pertaining to the tissue from which the gene was obtained, items pertaining to the host organism for gene expression and items pertaining to the actual producing organism (plasmid).- Specified by:
getPdbxEntitySrcGenDepositorInfoin interfaceBlock- Returns:
- PdbxEntitySrcGenDepositorInfo
-
getPdbxChemCompModel
public PdbxChemCompModel getPdbxChemCompModel()
Description copied from interface:BlockData items in the PDBX_CHEM_COMP_MODEL category give details about each of the chemical component model instances.- Specified by:
getPdbxChemCompModelin interfaceBlock- Returns:
- PdbxChemCompModel
-
getPdbxChemCompModelAtom
public PdbxChemCompModelAtom getPdbxChemCompModelAtom()
Description copied from interface:BlockData items in the PDBX_CHEM_COMP_MODEL_ATOM category record coordinates for the chemical component model instance.- Specified by:
getPdbxChemCompModelAtomin interfaceBlock- Returns:
- PdbxChemCompModelAtom
-
getPdbxChemCompModelBond
public PdbxChemCompModelBond getPdbxChemCompModelBond()
Description copied from interface:BlockData items in the PDBX_CHEM_COMP_MODEL_BOND category record details about the bonds between atoms in a chemical component model instance.- Specified by:
getPdbxChemCompModelBondin interfaceBlock- Returns:
- PdbxChemCompModelBond
-
getPdbxChemCompModelFeature
public PdbxChemCompModelFeature getPdbxChemCompModelFeature()
Description copied from interface:BlockAdditional features associated with the chemical component.- Specified by:
getPdbxChemCompModelFeaturein interfaceBlock- Returns:
- PdbxChemCompModelFeature
-
getPdbxChemCompModelDescriptor
public PdbxChemCompModelDescriptor getPdbxChemCompModelDescriptor()
Description copied from interface:BlockData items in the CHEM_COMP_MODEL_DESCRIPTOR category provide string descriptors for component model structures.- Specified by:
getPdbxChemCompModelDescriptorin interfaceBlock- Returns:
- PdbxChemCompModelDescriptor
-
getPdbxChemCompModelAudit
public PdbxChemCompModelAudit getPdbxChemCompModelAudit()
Description copied from interface:BlockData items in the PDBX_CHEM_COMP_MODEL_AUDIT category records the status and tracking information for this component model instance.- Specified by:
getPdbxChemCompModelAuditin interfaceBlock- Returns:
- PdbxChemCompModelAudit
-
getPdbxChemCompModelReference
public PdbxChemCompModelReference getPdbxChemCompModelReference()
Description copied from interface:BlockAdditional features associated with the chemical component.- Specified by:
getPdbxChemCompModelReferencein interfaceBlock- Returns:
- PdbxChemCompModelReference
-
getPdbxViewCategoryGroup
public PdbxViewCategoryGroup getPdbxViewCategoryGroup()
Description copied from interface:BlockData items in the PDBX_VIEW_CATEGORY_GROUP identify collections of related mmCIF categories. Views provide a vehicle for presenting different logical arrangements of dictionary contents.- Specified by:
getPdbxViewCategoryGroupin interfaceBlock- Returns:
- PdbxViewCategoryGroup
-
getPdbxViewCategory
public PdbxViewCategory getPdbxViewCategory()
Description copied from interface:BlockData items in the PDBX_VIEW_CATEGORY specify the categories belonging to a category view group. An alias name for the the mmCIF category may also be specified for the each category in the view.- Specified by:
getPdbxViewCategoryin interfaceBlock- Returns:
- PdbxViewCategory
-
getPdbxViewItem
public PdbxViewItem getPdbxViewItem()
Description copied from interface:BlockData items in the PDBX_VIEW_ITEM specify the mmCIF data items belonging to a view category. An alias name for the the mmCIF item may be specified for the each item in the view category. The role of the item in the view category can be designated as mandatory, optional, or hidden.- Specified by:
getPdbxViewItemin interfaceBlock- Returns:
- PdbxViewItem
-
getPdbxCoord
public PdbxCoord getPdbxCoord()
Description copied from interface:BlockGives information about what kind of coordinates are available.- Specified by:
getPdbxCoordin interfaceBlock- Returns:
- PdbxCoord
-
getPdbxConnect
public PdbxConnect getPdbxConnect()
Description copied from interface:BlockLocal data items describing ligand and monomer chemical features.- Specified by:
getPdbxConnectin interfaceBlock- Returns:
- PdbxConnect
-
getPdbxConnectType
public PdbxConnectType getPdbxConnectType()
Description copied from interface:BlockLocal data items describing ligand and monomer type information.- Specified by:
getPdbxConnectTypein interfaceBlock- Returns:
- PdbxConnectType
-
getPdbxConnectModification
public PdbxConnectModification getPdbxConnectModification()
Description copied from interface:BlockLocal data items describing ligand and monomer modifications.- Specified by:
getPdbxConnectModificationin interfaceBlock- Returns:
- PdbxConnectModification
-
getPdbxConnectAtom
public PdbxConnectAtom getPdbxConnectAtom()
Description copied from interface:BlockLocal data items describing ligand and monomer atom names and connectivity.- Specified by:
getPdbxConnectAtomin interfaceBlock- Returns:
- PdbxConnectAtom
-
getPdbxDatabasePDBMaster
public PdbxDatabasePDBMaster getPdbxDatabasePDBMaster()
Description copied from interface:BlockThe PDBX_DATABASE_PDB_MASTER category provides placeholders for the count of various PDB record types.- Specified by:
getPdbxDatabasePDBMasterin interfaceBlock- Returns:
- PdbxDatabasePDBMaster
-
getPdbxDatabasePdbOmit
public PdbxDatabasePdbOmit getPdbxDatabasePdbOmit()
Description copied from interface:BlockData items in the PDBX_DATABASE_PDB_OMIT category record list PDB record names that should be omitted in the PDB format file.- Specified by:
getPdbxDatabasePdbOmitin interfaceBlock- Returns:
- PdbxDatabasePdbOmit
-
getPdbxDbref
public PdbxDbref getPdbxDbref()
Description copied from interface:BlockThese records are used in the DBREF record of a PDB file and are used as place holders for NDB ID's in PDB files.- Specified by:
getPdbxDbrefin interfaceBlock- Returns:
- PdbxDbref
-
getPdbxDrugInfo
public PdbxDrugInfo getPdbxDrugInfo()
Description copied from interface:BlockData items in the PDBX_DRUG_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated.- Specified by:
getPdbxDrugInfoin interfaceBlock- Returns:
- PdbxDrugInfo
-
getPdbxInhibitorInfo
public PdbxInhibitorInfo getPdbxInhibitorInfo()
Description copied from interface:BlockData items in the PDBX_INHIBITOR_INFO category are still used until the 'entity' categories are entered into the database, even though the inhibitor is repeated.- Specified by:
getPdbxInhibitorInfoin interfaceBlock- Returns:
- PdbxInhibitorInfo
-
getPdbxIonInfo
public PdbxIonInfo getPdbxIonInfo()
Description copied from interface:BlockData items in the PDBX_ION_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated.- Specified by:
getPdbxIonInfoin interfaceBlock- Returns:
- PdbxIonInfo
-
getPdbxHybrid
public PdbxHybrid getPdbxHybrid()
Description copied from interface:BlockData items in the PDBX_HYBRID category are used to describe the chimeric characteristics of a DNA/RNA structure.- Specified by:
getPdbxHybridin interfaceBlock- Returns:
- PdbxHybrid
-
getPdbxNaStrandInfo
public PdbxNaStrandInfo getPdbxNaStrandInfo()
Description copied from interface:BlockData items in the PDBX_NA_STRAND_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated.- Specified by:
getPdbxNaStrandInfoin interfaceBlock- Returns:
- PdbxNaStrandInfo
-
getPdbxNonstandardList
public PdbxNonstandardList getPdbxNonstandardList()
Description copied from interface:BlockThe information in this category is exclusively used to store the HET records of a PDB file. This record will be generated by the PROGRAM.- Specified by:
getPdbxNonstandardListin interfaceBlock- Returns:
- PdbxNonstandardList
-
getPdbxPdbCompnd
public PdbxPdbCompnd getPdbxPdbCompnd()
Description copied from interface:BlockThis is a place holder for the PDB COMPND.- Specified by:
getPdbxPdbCompndin interfaceBlock- Returns:
- PdbxPdbCompnd
-
getPdbxPdbSource
public PdbxPdbSource getPdbxPdbSource()
Description copied from interface:BlockThis is a place holder for the PDB SOURCE.- Specified by:
getPdbxPdbSourcein interfaceBlock- Returns:
- PdbxPdbSource
-
getPdbxProteinInfo
public PdbxProteinInfo getPdbxProteinInfo()
Description copied from interface:BlockData items in the PDBX_PROTEIN_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated.- Specified by:
getPdbxProteinInfoin interfaceBlock- Returns:
- PdbxProteinInfo
-
getPdbxSolventInfo
public PdbxSolventInfo getPdbxSolventInfo()
Description copied from interface:BlockData items in the PDBX_SOLVENT_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated.- Specified by:
getPdbxSolventInfoin interfaceBlock- Returns:
- PdbxSolventInfo
-
getPdbxSource
public PdbxSource getPdbxSource()
Description copied from interface:BlockData item will still be used until the ENTITY category is fully adopted by NDBQuery.- Specified by:
getPdbxSourcein interfaceBlock- Returns:
- PdbxSource
-
getPdbxStructBiolFunc
public PdbxStructBiolFunc getPdbxStructBiolFunc()
Description copied from interface:BlockData items in the PDBX_STRUCT_BIOL_FUNC category record details about the function of a particular biological assembly.- Specified by:
getPdbxStructBiolFuncin interfaceBlock- Returns:
- PdbxStructBiolFunc
-
getPdbxStructPackGen
public PdbxStructPackGen getPdbxStructPackGen()
Description copied from interface:BlockData items in the PDBX_STRUCT_PACK_GEN category record details about the generation of the packing picture(s).- Specified by:
getPdbxStructPackGenin interfaceBlock- Returns:
- PdbxStructPackGen
-
getPdbxTrnaInfo
public PdbxTrnaInfo getPdbxTrnaInfo()
Description copied from interface:BlockData items in the PDBX_TRNA_INFO category are still used until the 'entity' categories are entered into the database, even though the T-RNA is repeated.- Specified by:
getPdbxTrnaInfoin interfaceBlock- Returns:
- PdbxTrnaInfo
-
getPdbxUnpair
public PdbxUnpair getPdbxUnpair()
Description copied from interface:BlockThese records give information about residues which do not pair (h-bond) in the asymmetric unit. The records about Watson-Crick base pairing depend on these records.- Specified by:
getPdbxUnpairin interfaceBlock- Returns:
- PdbxUnpair
-
getPdbxRefineLsRestrNcs
public PdbxRefineLsRestrNcs getPdbxRefineLsRestrNcs()
Description copied from interface:BlockHolds details of NCS restraints in cases where multiple conditions are provided for each domain.- Specified by:
getPdbxRefineLsRestrNcsin interfaceBlock- Returns:
- PdbxRefineLsRestrNcs
-
getPdbxStructNcsVirusGen
public PdbxStructNcsVirusGen getPdbxStructNcsVirusGen()
Description copied from interface:BlockData items in the PDBX_STRUCT_NCS_VIRUS_GEN category record details about the generation of virus structures from NCS matrix operators.- Specified by:
getPdbxStructNcsVirusGenin interfaceBlock- Returns:
- PdbxStructNcsVirusGen
-
getPdbxSequenceAnnotation
public PdbxSequenceAnnotation getPdbxSequenceAnnotation()
Description copied from interface:BlockPDBX_SEQUENCE_ANNOTATION holds internal details about molecular sequences described in the context of PDB chains.- Specified by:
getPdbxSequenceAnnotationin interfaceBlock- Returns:
- PdbxSequenceAnnotation
-
getPdbxPostProcessDetails
public PdbxPostProcessDetails getPdbxPostProcessDetails()
Description copied from interface:BlockData items in the PDBX_POST_PROCESS_DETAILS identify problems or errors encountered in the post-processing of this entry.- Specified by:
getPdbxPostProcessDetailsin interfaceBlock- Returns:
- PdbxPostProcessDetails
-
getPdbxPostProcessStatus
public PdbxPostProcessStatus getPdbxPostProcessStatus()
Description copied from interface:BlockData items in the PDBX_POST_PROCESS_DETAILS record the status of post-processed entries.- Specified by:
getPdbxPostProcessStatusin interfaceBlock- Returns:
- PdbxPostProcessStatus
-
getPdbxStructLink
public PdbxStructLink getPdbxStructLink()
Description copied from interface:BlockData items in the PDBX_STRUCT_LINK category record details about covalent linkages in the structure.- Specified by:
getPdbxStructLinkin interfaceBlock- Returns:
- PdbxStructLink
-
getPdbxMissingResidueList
public PdbxMissingResidueList getPdbxMissingResidueList()
Description copied from interface:BlockProvides a place-holder for PDB REMARK 465 data.- Specified by:
getPdbxMissingResidueListin interfaceBlock- Returns:
- PdbxMissingResidueList
-
getPdbxDataProcessingCell
public PdbxDataProcessingCell getPdbxDataProcessingCell()
Description copied from interface:BlockCrystallographic cell specifications used in data processing.- Specified by:
getPdbxDataProcessingCellin interfaceBlock- Returns:
- PdbxDataProcessingCell
-
getPdbxDataProcessingReflns
public PdbxDataProcessingReflns getPdbxDataProcessingReflns()
Description copied from interface:BlockDetails of reflections used in data processing.- Specified by:
getPdbxDataProcessingReflnsin interfaceBlock- Returns:
- PdbxDataProcessingReflns
-
getPdbxDataProcessingDetector
public PdbxDataProcessingDetector getPdbxDataProcessingDetector()
Description copied from interface:BlockDetails of the detector used at data collection site.- Specified by:
getPdbxDataProcessingDetectorin interfaceBlock- Returns:
- PdbxDataProcessingDetector
-
getPdbxChemCompNonstandard
public PdbxChemCompNonstandard getPdbxChemCompNonstandard()
Description copied from interface:BlockData items in the PDBX_CHEM_COMP_NONSTANDARD category describes common nucleotide modifications and nonstandard features.- Specified by:
getPdbxChemCompNonstandardin interfaceBlock- Returns:
- PdbxChemCompNonstandard
-
getPdbxEntityPolyProteinClass
public PdbxEntityPolyProteinClass getPdbxEntityPolyProteinClass()
Description copied from interface:BlockData items in the PDBX_ENTITY_POLY_PROTEIN_CLASS category provides a top-level protein classification.- Specified by:
getPdbxEntityPolyProteinClassin interfaceBlock- Returns:
- PdbxEntityPolyProteinClass
-
getPdbxEntityNameTaxonomyTree
public PdbxEntityNameTaxonomyTree getPdbxEntityNameTaxonomyTree()
Description copied from interface:BlockData items in the PDBX_ENTITY_NAME_TAXONOMY_TREE category define the tree structure of the entity name taxonomy.- Specified by:
getPdbxEntityNameTaxonomyTreein interfaceBlock- Returns:
- PdbxEntityNameTaxonomyTree
-
getPdbxEntityNameTaxonomy
public PdbxEntityNameTaxonomy getPdbxEntityNameTaxonomy()
Description copied from interface:BlockData items in the PDBX_ENTITY_NAME_TAXONOMY category define the names and synonyms of the entity name taxonomy.- Specified by:
getPdbxEntityNameTaxonomyin interfaceBlock- Returns:
- PdbxEntityNameTaxonomy
-
getPdbxEntityNameInstance
public PdbxEntityNameInstance getPdbxEntityNameInstance()
Description copied from interface:BlockData items in the PDBX_ENTITY_NAME_INSTANCE category list names used to define entities with their associated database, entity, chain, and molecule identifiers.- Specified by:
getPdbxEntityNameInstancein interfaceBlock- Returns:
- PdbxEntityNameInstance
-
getPdbxTableinfo
public PdbxTableinfo getPdbxTableinfo()
- Specified by:
getPdbxTableinfoin interfaceBlock- Returns:
- PdbxTableinfo
-
getPdbxColumninfo
public PdbxColumninfo getPdbxColumninfo()
- Specified by:
getPdbxColumninfoin interfaceBlock- Returns:
- PdbxColumninfo
-
getPdbxValAngle
public PdbxValAngle getPdbxValAngle()
Description copied from interface:BlockThe PDBX_VAL_ANGLE category lists the covalent bond angles in this entry deviating by greater than 6*sigma from standard values. This is a completely derived category. Do not edit.- Specified by:
getPdbxValAnglein interfaceBlock- Returns:
- PdbxValAngle
-
getPdbxValBond
public PdbxValBond getPdbxValBond()
Description copied from interface:BlockThe PDBX_VAL_BOND category lists the covalent bond angles in this entry deviating by greater than 6*sigma from standard values. This is a completely derived category. Do not edit.- Specified by:
getPdbxValBondin interfaceBlock- Returns:
- PdbxValBond
-
getPdbxValContact
public PdbxValContact getPdbxValContact()
Description copied from interface:BlockThe PDBX_VAL_CONTACT category lists non-bonded atoms within the assymetric unit of the entry that are in close contact. For those contacts not involving hydrogen a limit of 2.2 Angstroms is used. For contacts involving a hydrogen atom a cutoff of 1.6 Angstrom is used. This is a completely derived category. Do not edit.- Specified by:
getPdbxValContactin interfaceBlock- Returns:
- PdbxValContact
-
getPdbxValSymContact
public PdbxValSymContact getPdbxValSymContact()
Description copied from interface:BlockThe PDBX_VAL_SYM_CONTACT category lists symmetry related contacts amoung non-bonded atoms. For those contacts not involving hydrogen a limit of 2.2 Angstroms is used. For contacts involving a hydrogen atom a cutoff of 1.6 Angstrom is used. This is a completely derived category. Do not edit.- Specified by:
getPdbxValSymContactin interfaceBlock- Returns:
- PdbxValSymContact
-
getPdbxRmchOutlier
public PdbxRmchOutlier getPdbxRmchOutlier()
Description copied from interface:BlockData items in the PDBX_RMCH_OUTLIER category list the residues with torsion angles outside the expected Ramachandran regions. This is a completely derived category. Do not edit.- Specified by:
getPdbxRmchOutlierin interfaceBlock- Returns:
- PdbxRmchOutlier
-
getPdbxMissingAtomPoly
public PdbxMissingAtomPoly getPdbxMissingAtomPoly()
Description copied from interface:BlockData items in the PDBX_MISSING_ATOM_POLY category lists atoms missing in polymer residues. This is a completely derived category. Do not edit.- Specified by:
getPdbxMissingAtomPolyin interfaceBlock- Returns:
- PdbxMissingAtomPoly
-
getPdbxMissingAtomNonpoly
public PdbxMissingAtomNonpoly getPdbxMissingAtomNonpoly()
Description copied from interface:BlockData items in the PDBX_MISSING_ATOM_NONPOLY category list the atoms missing in nonpolymer residues. This is a completely derived category. Do not edit.- Specified by:
getPdbxMissingAtomNonpolyin interfaceBlock- Returns:
- PdbxMissingAtomNonpoly
-
getPdbxValChiral
public PdbxValChiral getPdbxValChiral()
Description copied from interface:BlockData items in the PDBX_VAL_CHIRAL category list the atoms with nonstandard chiralities. This is a completely derived category. Do not edit.- Specified by:
getPdbxValChiralin interfaceBlock- Returns:
- PdbxValChiral
-
getPdbxAtlas
public PdbxAtlas getPdbxAtlas()
Description copied from interface:BlockGives information about the organization of the NDB Structural Atlas.- Specified by:
getPdbxAtlasin interfaceBlock- Returns:
- PdbxAtlas
-
getPdbxSummaryFlags
public PdbxSummaryFlags getPdbxSummaryFlags()
Description copied from interface:BlockContainer category for a list of feature flags associated with each structure entry.- Specified by:
getPdbxSummaryFlagsin interfaceBlock- Returns:
- PdbxSummaryFlags
-
getPdbxEntityFuncBindMode
public PdbxEntityFuncBindMode getPdbxEntityFuncBindMode()
Description copied from interface:BlockData items in the PDBX_ENTITY_FUNC_BIND_MODE category describe characteristics of protein oligonucleotide binding.- Specified by:
getPdbxEntityFuncBindModein interfaceBlock- Returns:
- PdbxEntityFuncBindMode
-
getPdbxEntityFuncEnzyme
public PdbxEntityFuncEnzyme getPdbxEntityFuncEnzyme()
Description copied from interface:BlockData items in the PDBX_ENTITY_FUNC_ENZYME category describe characteristics of protein oligonucleotide binding in which the binding mode is enzymatic.- Specified by:
getPdbxEntityFuncEnzymein interfaceBlock- Returns:
- PdbxEntityFuncEnzyme
-
getPdbxEntityFuncRegulatory
public PdbxEntityFuncRegulatory getPdbxEntityFuncRegulatory()
Description copied from interface:BlockData items in the PDBX_ENTITY_FUNC_REGULATORY category describe characteristics of protein oligonucleotide binding in which the binding mode is regulatory.- Specified by:
getPdbxEntityFuncRegulatoryin interfaceBlock- Returns:
- PdbxEntityFuncRegulatory
-
getPdbxEntityFuncStructural
public PdbxEntityFuncStructural getPdbxEntityFuncStructural()
Description copied from interface:BlockData items in the PDBX_ENTITY_FUNC_STRUCTURAL category describe characteristics of protein oligonucleotide binding in which the binding mode is structural.- Specified by:
getPdbxEntityFuncStructuralin interfaceBlock- Returns:
- PdbxEntityFuncStructural
-
getPdbxEntityFuncOther
public PdbxEntityFuncOther getPdbxEntityFuncOther()
Description copied from interface:BlockData items in the PDBX_ENTITY_FUNC_OTHER category describe characteristics of protein oligonucleotide binding in which the binding mode is not classified.- Specified by:
getPdbxEntityFuncOtherin interfaceBlock- Returns:
- PdbxEntityFuncOther
-
getPdbxEntityPolyDomain
public PdbxEntityPolyDomain getPdbxEntityPolyDomain()
Description copied from interface:BlockData items in the PDBX_ENTITY_POLY_DOMAIN category specify domains of monomers within a polymer.- Specified by:
getPdbxEntityPolyDomainin interfaceBlock- Returns:
- PdbxEntityPolyDomain
-
getPdbxNaStructKeywds
public PdbxNaStructKeywds getPdbxNaStructKeywds()
Description copied from interface:BlockData items in the PDBX_NA_STRUCT_KEYWDS category record give details about structural features of the NA.- Specified by:
getPdbxNaStructKeywdsin interfaceBlock- Returns:
- PdbxNaStructKeywds
-
getPdbxEntityPolyNaType
public PdbxEntityPolyNaType getPdbxEntityPolyNaType()
Description copied from interface:BlockData items in the PDBX_ENTITY_POLY_NA_TYPE category describe type of nucleic acid polymer entities.- Specified by:
getPdbxEntityPolyNaTypein interfaceBlock- Returns:
- PdbxEntityPolyNaType
-
getPdbxEntityPolyNaNonstandard
public PdbxEntityPolyNaNonstandard getPdbxEntityPolyNaNonstandard()
Description copied from interface:BlockData items in the PDBX_ENTITY_POLY_NA_NONSTANDARD category describe the nonstandard features of the nucleic acid polymer entities.- Specified by:
getPdbxEntityPolyNaNonstandardin interfaceBlock- Returns:
- PdbxEntityPolyNaNonstandard
-
getPdbxVirtualAngle
public PdbxVirtualAngle getPdbxVirtualAngle()
Description copied from interface:BlockData items in the PDBX_VIRTUAL_ANGLE category record details about the molecular virtual angles, as calculated from the contents of the ATOM, CELL, and SYMMETRY data.- Specified by:
getPdbxVirtualAnglein interfaceBlock- Returns:
- PdbxVirtualAngle
-
getPdbxVirtualBond
public PdbxVirtualBond getPdbxVirtualBond()
Description copied from interface:BlockData items in the PDBX_VIRTUAL_BOND category record details about virtual bonds, as calculated from the contents of the ATOM, CELL, and SYMMETRY data.- Specified by:
getPdbxVirtualBondin interfaceBlock- Returns:
- PdbxVirtualBond
-
getPdbxVirtualTorsion
public PdbxVirtualTorsion getPdbxVirtualTorsion()
Description copied from interface:BlockData items in the PDBX_VIRTUAL_TORSION category record details about virtual torsion angles, as calculated from the contents of the ATOM, CELL, and SYMMETRY data.- Specified by:
getPdbxVirtualTorsionin interfaceBlock- Returns:
- PdbxVirtualTorsion
-
getPdbxSequencePattern
public PdbxSequencePattern getPdbxSequencePattern()
Description copied from interface:BlockData items in the PDBX_SEQUENCE_PATTERN category record the number of occurences of common step sequence patterns (e.g. AA, CG, AT).- Specified by:
getPdbxSequencePatternin interfaceBlock- Returns:
- PdbxSequencePattern
-
getPdbxStereochemistry
public PdbxStereochemistry getPdbxStereochemistry()
Description copied from interface:BlockData items in the PDBX_STEREOCHEMISTRY identify chiral centers and associated chiral volumes.- Specified by:
getPdbxStereochemistryin interfaceBlock- Returns:
- PdbxStereochemistry
-
getPdbxRmsDevsCovalent
public PdbxRmsDevsCovalent getPdbxRmsDevsCovalent()
Description copied from interface:BlockData items in the PDBX_RMS_DEVS_COVALENT record the summary RMS deviations for nucleic acid covalent geometry relative to small molecule crystal standards.- Specified by:
getPdbxRmsDevsCovalentin interfaceBlock- Returns:
- PdbxRmsDevsCovalent
-
getPdbxRmsDevsCovByMonomer
public PdbxRmsDevsCovByMonomer getPdbxRmsDevsCovByMonomer()
Description copied from interface:BlockData items in the PDBX_RMS_DEVS_COV_BY_MONOMER record the RMS deviations covalent geometry for each momoner relative to small molecule crystal standards.- Specified by:
getPdbxRmsDevsCovByMonomerin interfaceBlock- Returns:
- PdbxRmsDevsCovByMonomer
-
getPdbxSugarPhosphateGeometry
public PdbxSugarPhosphateGeometry getPdbxSugarPhosphateGeometry()
Description copied from interface:BlockData items in the PDBX_SUGAR_PHOSPHATE_GEOMETRY record the RMS deviations covalent geometry for each momoner relative to small molecule crystal standards.- Specified by:
getPdbxSugarPhosphateGeometryin interfaceBlock- Returns:
- PdbxSugarPhosphateGeometry
-
getPdbxNmrComputing
public PdbxNmrComputing getPdbxNmrComputing()
Description copied from interface:BlockThe table in this section is used to describe the software that was used for data collection, data processing, data analysis, structure calculations and refinement. The description should include both the name of the software and the version used.- Specified by:
getPdbxNmrComputingin interfaceBlock- Returns:
- PdbxNmrComputing
-
getPdbxAuditConformExtension
public PdbxAuditConformExtension getPdbxAuditConformExtension()
Description copied from interface:BlockData items in the PDBX_AUDIT_CONFORM_EXTENSION category describe extension dictionary versions against which the data names appearing the current data block are conformant.- Specified by:
getPdbxAuditConformExtensionin interfaceBlock- Returns:
- PdbxAuditConformExtension
-
getPdbxDccMapman
public PdbxDccMapman getPdbxDccMapman()
Description copied from interface:BlockData items in the category record details from the output of mapman used by the DCC program.- Specified by:
getPdbxDccMapmanin interfaceBlock- Returns:
- PdbxDccMapman
-
getPdbxDccRsccMapman
public PdbxDccRsccMapman getPdbxDccRsccMapman()
Description copied from interface:BlockData items in this category record residual map properties such as correlation, real space Rfactors and the Zscore calculated from refmac and mapman.- Specified by:
getPdbxDccRsccMapmanin interfaceBlock- Returns:
- PdbxDccRsccMapman
-
getPdbxDccRsccMapmanOverall
public PdbxDccRsccMapmanOverall getPdbxDccRsccMapmanOverall()
Description copied from interface:BlockData items in the category record overall map properties such as correlation, real space Rfactors and the Zscore calculated from refmac and mapman.- Specified by:
getPdbxDccRsccMapmanOverallin interfaceBlock- Returns:
- PdbxDccRsccMapmanOverall
-
getPdbxDccDensity
public PdbxDccDensity getPdbxDccDensity()
Description copied from interface:BlockData items in the category record various overall metrics calculated by DCC and various wrapped programs (such as Xtriage, pointless, REFMAC ...).- Specified by:
getPdbxDccDensityin interfaceBlock- Returns:
- PdbxDccDensity
-
getPdbxDccGeometry
public PdbxDccGeometry getPdbxDccGeometry()
Description copied from interface:BlockData items in the category record the overall deviations about geometry (such as bond length, angle, dihedral, chirality, planarity). These data are calculated with the phenix module model_vs_data.- Specified by:
getPdbxDccGeometryin interfaceBlock- Returns:
- PdbxDccGeometry
-
getPdbxDccDensityCorr
public PdbxDccDensityCorr getPdbxDccDensityCorr()
Description copied from interface:BlockData items in the category record calculated metrics from various programs (such as phenix, refmac, cns, sfcheck).- Specified by:
getPdbxDccDensityCorrin interfaceBlock- Returns:
- PdbxDccDensityCorr
-
getPdbxDccMap
public PdbxDccMap getPdbxDccMap()
Description copied from interface:BlockData items in the category record residual map properties such as Real Space electron density Correlation Coefficient (RSCC), real space R factors (RSR) and the Zscores for each residue, the main/side chains.- Specified by:
getPdbxDccMapin interfaceBlock- Returns:
- PdbxDccMap
-
getPdbxDepositGroup
public PdbxDepositGroup getPdbxDepositGroup()
Description copied from interface:BlockData items in the pdbx_deposit_group category provide identifiers and related information for groups of entries deposited in a collection.- Specified by:
getPdbxDepositGroupin interfaceBlock- Returns:
- PdbxDepositGroup
-
getPdbxDepositGroupIndex
public PdbxDepositGroupIndex getPdbxDepositGroupIndex()
Description copied from interface:BlockData items in the pdbx_deposit_group_index category provides details about the individual data files in the collection of deposited entries.- Specified by:
getPdbxDepositGroupIndexin interfaceBlock- Returns:
- PdbxDepositGroupIndex
-
getPdbxStructAssemblyAuthEvidence
public PdbxStructAssemblyAuthEvidence getPdbxStructAssemblyAuthEvidence()
Description copied from interface:BlockProvides author supplied evidentiary support for assemblies in pdbx_struct_assembly.- Specified by:
getPdbxStructAssemblyAuthEvidencein interfaceBlock- Returns:
- PdbxStructAssemblyAuthEvidence
-
getPdbxStructAssemblyAuthClassification
public PdbxStructAssemblyAuthClassification getPdbxStructAssemblyAuthClassification()
Description copied from interface:BlockProvides reason a particular assembly in pdbx_struct_assembly is of interest.- Specified by:
getPdbxStructAssemblyAuthClassificationin interfaceBlock- Returns:
- PdbxStructAssemblyAuthClassification
-
getPdbxCrystalAlignment
public PdbxCrystalAlignment getPdbxCrystalAlignment()
Description copied from interface:BlockData in the PDBX_CRYSTAL_ALIGNMENT are produced by log files from programs during indexing- Specified by:
getPdbxCrystalAlignmentin interfaceBlock- Returns:
- PdbxCrystalAlignment
-
getPdbxAuditRevisionHistory
public PdbxAuditRevisionHistory getPdbxAuditRevisionHistory()
Description copied from interface:BlockData items in the PDBX_AUDIT_REVISION_HISTORY category record the revision history for a data entry.- Specified by:
getPdbxAuditRevisionHistoryin interfaceBlock- Returns:
- PdbxAuditRevisionHistory
-
getPdbxAuditRevisionGroup
public PdbxAuditRevisionGroup getPdbxAuditRevisionGroup()
Description copied from interface:BlockData items in the PDBX_AUDIT_revision_group category report the content groups associated with a PDBX_AUDIT_REVISION_HISTORY record.- Specified by:
getPdbxAuditRevisionGroupin interfaceBlock- Returns:
- PdbxAuditRevisionGroup
-
getPdbxAuditRevisionCategory
public PdbxAuditRevisionCategory getPdbxAuditRevisionCategory()
Description copied from interface:BlockData items in the PDBX_AUDIT_REVISION_CATEGORY category report the data categories associated with a PDBX_AUDIT_REVISION_HISTORY record.- Specified by:
getPdbxAuditRevisionCategoryin interfaceBlock- Returns:
- PdbxAuditRevisionCategory
-
getPdbxAuditRevisionDetails
public PdbxAuditRevisionDetails getPdbxAuditRevisionDetails()
Description copied from interface:BlockData items in the PDBX_audit_revision_details category record descriptions of changes associated with PDBX_AUDIT_REVISION_HISTORY records.- Specified by:
getPdbxAuditRevisionDetailsin interfaceBlock- Returns:
- PdbxAuditRevisionDetails
-
getPdbxAuditRevisionItem
public PdbxAuditRevisionItem getPdbxAuditRevisionItem()
Description copied from interface:BlockData items in the PDBX_AUDIT_REVISION_ITEM category report the data items associated with a PDBX_AUDIT_REVISION_HISTORY record.- Specified by:
getPdbxAuditRevisionItemin interfaceBlock- Returns:
- PdbxAuditRevisionItem
-
getPdbxSupportingExpDataSet
public PdbxSupportingExpDataSet getPdbxSupportingExpDataSet()
Description copied from interface:BlockData items in the PDBX_SUPPORTING_EXP_DATA_SET category record to experimental data set dependencies for this entry.- Specified by:
getPdbxSupportingExpDataSetin interfaceBlock- Returns:
- PdbxSupportingExpDataSet
-
getPdbxSerialCrystallographyMeasurement
public PdbxSerialCrystallographyMeasurement getPdbxSerialCrystallographyMeasurement()
Description copied from interface:BlockData items in the PDBX_SERIAL_CRYSTALLOGRAPHY_MEASUREMENT category record details the beam that is impinging on the sample- Specified by:
getPdbxSerialCrystallographyMeasurementin interfaceBlock- Returns:
- PdbxSerialCrystallographyMeasurement
-
getPdbxSerialCrystallographySampleDelivery
public PdbxSerialCrystallographySampleDelivery getPdbxSerialCrystallographySampleDelivery()
Description copied from interface:BlockData items in the PDBX_SERIAL_CRYSTALLOGRAPHY_SAMPLE_DELIVERY category record general details about the sample delivery- Specified by:
getPdbxSerialCrystallographySampleDeliveryin interfaceBlock- Returns:
- PdbxSerialCrystallographySampleDelivery
-
getPdbxSerialCrystallographySampleDeliveryInjection
public PdbxSerialCrystallographySampleDeliveryInjection getPdbxSerialCrystallographySampleDeliveryInjection()
Description copied from interface:BlockData items in the PDBX_SERIAL_CRYSTALLOGRAPHY_SAMPLE_DELIVERY_INJECTION category record details about sample delivery by injection- Specified by:
getPdbxSerialCrystallographySampleDeliveryInjectionin interfaceBlock- Returns:
- PdbxSerialCrystallographySampleDeliveryInjection
-
getPdbxSerialCrystallographySampleDeliveryFixedTarget
public PdbxSerialCrystallographySampleDeliveryFixedTarget getPdbxSerialCrystallographySampleDeliveryFixedTarget()
Description copied from interface:BlockData items in the PDBX_SERIAL_CRYSTALLOGRAPHY_SAMPLE_DELIVERY_FIXED_TARGET category record details about sample delivery using a fixed taget.- Specified by:
getPdbxSerialCrystallographySampleDeliveryFixedTargetin interfaceBlock- Returns:
- PdbxSerialCrystallographySampleDeliveryFixedTarget
-
getPdbxSerialCrystallographyDataReduction
public PdbxSerialCrystallographyDataReduction getPdbxSerialCrystallographyDataReduction()
Description copied from interface:BlockData items in the PDBX_SERIAL_CRYSTALLOGRAPHY_DATA_REDUCTION category record details about data processing that are unique to XFEL experiments. These will compliment data recorded in category pdbx_diffrn_merge_stat.- Specified by:
getPdbxSerialCrystallographyDataReductionin interfaceBlock- Returns:
- PdbxSerialCrystallographyDataReduction
-
getPdbxChemCompSynonyms
public PdbxChemCompSynonyms getPdbxChemCompSynonyms()
Description copied from interface:BlockPDBX_CHEM_COMP_SYNONYMS holds chemical name and synonym correspondences.- Specified by:
getPdbxChemCompSynonymsin interfaceBlock- Returns:
- PdbxChemCompSynonyms
-
getPdbxChemCompRelated
public PdbxChemCompRelated getPdbxChemCompRelated()
Description copied from interface:BlockPDBX_CHEM_COMP_RELATED describes the relationship between two chemical components.- Specified by:
getPdbxChemCompRelatedin interfaceBlock- Returns:
- PdbxChemCompRelated
-
getPdbxChemCompAtomRelated
public PdbxChemCompAtomRelated getPdbxChemCompAtomRelated()
Description copied from interface:BlockPDBX_CHEM_COMP_ATOM_RELATED provides atom level nomenclature mapping between two related chemical components.- Specified by:
getPdbxChemCompAtomRelatedin interfaceBlock- Returns:
- PdbxChemCompAtomRelated
-
getPdbxEntityBranchList
public PdbxEntityBranchList getPdbxEntityBranchList()
Description copied from interface:BlockData items in the PDBX_ENTITY_BRANCH_LIST category specify the list of monomers in a branched entity. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID. The corresponding ATOM_SITE entries should reflect this heterogeneity.- Specified by:
getPdbxEntityBranchListin interfaceBlock- Returns:
- PdbxEntityBranchList
-
getPdbxEntityBranchLink
public PdbxEntityBranchLink getPdbxEntityBranchLink()
Description copied from interface:BlockData items in the PDBX_ENTITY_BRANCH_LINK category give details about the linkages between components within a branched entity.- Specified by:
getPdbxEntityBranchLinkin interfaceBlock- Returns:
- PdbxEntityBranchLink
-
getPdbxEntityBranch
public PdbxEntityBranch getPdbxEntityBranch()
Description copied from interface:BlockData items in the PDBX_ENTITY_BRANCH category specify the list of branched entities and the type.- Specified by:
getPdbxEntityBranchin interfaceBlock- Returns:
- PdbxEntityBranch
-
getPdbxBranchScheme
public PdbxBranchScheme getPdbxBranchScheme()
Description copied from interface:BlockThe PDBX_BRANCH_SCHEME category provides residue level nomenclature mapping for branch chain entities.- Specified by:
getPdbxBranchSchemein interfaceBlock- Returns:
- PdbxBranchScheme
-
getIhmStartingModelDetails
public IhmStartingModelDetails getIhmStartingModelDetails()
Description copied from interface:BlockData items in the IHM_STARTING_MODEL_DETAILS category records the details about structural models used as starting inputs in the integrative model building process.- Specified by:
getIhmStartingModelDetailsin interfaceBlock- Returns:
- IhmStartingModelDetails
-
getIhmStartingComparativeModels
public IhmStartingComparativeModels getIhmStartingComparativeModels()
Description copied from interface:BlockData items in the IHM_STARTING_COMPARATIVE_MODELS category records additional details about comparative models used as starting inputs in the integrative model building process.- Specified by:
getIhmStartingComparativeModelsin interfaceBlock- Returns:
- IhmStartingComparativeModels
-
getIhmStartingComputationalModels
public IhmStartingComputationalModels getIhmStartingComputationalModels()
Description copied from interface:BlockData items in the IHM_STARTING_COMPUTATIONAL_MODELS category records additional details about computational models used as starting inputs in the integrative model building process.- Specified by:
getIhmStartingComputationalModelsin interfaceBlock- Returns:
- IhmStartingComputationalModels
-
getIhmStartingModelSeqDif
public IhmStartingModelSeqDif getIhmStartingModelSeqDif()
Description copied from interface:BlockData items in the IHM_STARTING_MODEL_SEQ_DIF category provide a mechanism for indicating and annotating point differences between the sequence of the entity or biological unit described in the data block and the sequence of the starting model used in the integrative modeling referenced from a database. The point differences may be due to point mutations introduced in the starting model or the presence of modified amino acid residues.- Specified by:
getIhmStartingModelSeqDifin interfaceBlock- Returns:
- IhmStartingModelSeqDif
-
getIhmModelRepresentation
public IhmModelRepresentation getIhmModelRepresentation()
Description copied from interface:BlockData items in the IHM_MODEL_REPRESENTATION category records the details about the architecture and representation of structural models created by the integrative model building tasks. This category handles the multi-scale model representation, if employed.- Specified by:
getIhmModelRepresentationin interfaceBlock- Returns:
- IhmModelRepresentation
-
getIhmStructAssembly
public IhmStructAssembly getIhmStructAssembly()
Description copied from interface:BlockData items in the IHM_STRUCT_ASSEMBLY category records the details of the structural assemblies and used in the IHM modeling.- Specified by:
getIhmStructAssemblyin interfaceBlock- Returns:
- IhmStructAssembly
-
getIhmStructAssemblyDetails
public IhmStructAssemblyDetails getIhmStructAssemblyDetails()
Description copied from interface:BlockData items in the IHM_STRUCT_ASSEMBLY_DETAILS category provides additional details regarding the structure assembly.- Specified by:
getIhmStructAssemblyDetailsin interfaceBlock- Returns:
- IhmStructAssemblyDetails
-
getIhmStructAssemblyClassList
public IhmStructAssemblyClassList getIhmStructAssemblyClassList()
Description copied from interface:BlockData items in the IHM_STRUCT_ASSEMBLY_CLASS_LIST category lists all the structural assembly classes relevant to the entry. This category provides a mechanism to define classes of the structural assemblies.- Specified by:
getIhmStructAssemblyClassListin interfaceBlock- Returns:
- IhmStructAssemblyClassList
-
getIhmStructAssemblyClass
public IhmStructAssemblyClass getIhmStructAssemblyClass()
Description copied from interface:BlockData items in the IHM_STRUCT_ASSEMBLY_CLASS category provides details regarding the structural assembly classes. This category provides a mechanism to identify the classes to which structural assemblies belong.- Specified by:
getIhmStructAssemblyClassin interfaceBlock- Returns:
- IhmStructAssemblyClass
-
getIhmModelingProtocol
public IhmModelingProtocol getIhmModelingProtocol()
Description copied from interface:BlockData items in the IHM_MODELING_PROTOCOL category records the step-wise details of the integrative modeling workflow.- Specified by:
getIhmModelingProtocolin interfaceBlock- Returns:
- IhmModelingProtocol
-
getIhmMultiStateModeling
public IhmMultiStateModeling getIhmMultiStateModeling()
Description copied from interface:BlockData items in the IHM_MULTI_STATE_MODELING category records the details of the multi-state modeling protocol, if applicable.- Specified by:
getIhmMultiStateModelingin interfaceBlock- Returns:
- IhmMultiStateModeling
-
getIhmOrderedEnsemble
public IhmOrderedEnsemble getIhmOrderedEnsemble()
Description copied from interface:BlockData items in the IHM_ORDERED_ENSEMBLE category records the details of the ensembles ordered by time or other order. Ordered ensembles are described as directed graphs with edges between nodes representing models or model groups.- Specified by:
getIhmOrderedEnsemblein interfaceBlock- Returns:
- IhmOrderedEnsemble
-
getIhmModelingPostProcess
public IhmModelingPostProcess getIhmModelingPostProcess()
Description copied from interface:BlockData items in the IHM_MODELING_POST_PROCESS category records the details of the post processing of the models/results of the modeling protocol.- Specified by:
getIhmModelingPostProcessin interfaceBlock- Returns:
- IhmModelingPostProcess
-
getIhmEnsembleInfo
public IhmEnsembleInfo getIhmEnsembleInfo()
Description copied from interface:BlockData items in the IHM_ENSEMBLE_INFO category records the details of the model clusters or ensembles obtained after sampling.- Specified by:
getIhmEnsembleInfoin interfaceBlock- Returns:
- IhmEnsembleInfo
-
getIhmModelList
public IhmModelList getIhmModelList()
Description copied from interface:BlockData items in the IHM_MODEL_LIST category record the details of the models being deposited.- Specified by:
getIhmModelListin interfaceBlock- Returns:
- IhmModelList
-
getIhmModelRepresentative
public IhmModelRepresentative getIhmModelRepresentative()
Description copied from interface:BlockData items in the IHM_MODEL_REPRESENTATIVE category record the details of the representative model in an ensemble or cluster.- Specified by:
getIhmModelRepresentativein interfaceBlock- Returns:
- IhmModelRepresentative
-
getIhmDatasetList
public IhmDatasetList getIhmDatasetList()
Description copied from interface:BlockCategory holds the list of all datasets used in the IHM modeling. These can be datasets archived in other related databases such as BMRB, EMDB, EMPIAR, SASBDB, PRIDE etc., or can be hosted in other places such as the authors website, github etc. These datasets are elaborated in detail in the IHM_DATASET_RELATED_DB_REFERENCE and/or the IHM_DATASET_EXTERNAL_REFERENCE categories. This category holds the list of all datasets used.- Specified by:
getIhmDatasetListin interfaceBlock- Returns:
- IhmDatasetList
-
getIhmDatasetGroup
public IhmDatasetGroup getIhmDatasetGroup()
Description copied from interface:BlockCategory provides a mechanism to group datasets.- Specified by:
getIhmDatasetGroupin interfaceBlock- Returns:
- IhmDatasetGroup
-
getIhmRelatedDatasets
public IhmRelatedDatasets getIhmRelatedDatasets()
Description copied from interface:BlockCategory holds information about related datasets, where one is derived from the other.- Specified by:
getIhmRelatedDatasetsin interfaceBlock- Returns:
- IhmRelatedDatasets
-
getIhmDatasetRelatedDbReference
public IhmDatasetRelatedDbReference getIhmDatasetRelatedDbReference()
Description copied from interface:BlockCategory holds information related to data sources for the entry. These can be datasets archived in other related databases such as BMRB, EMDB, EMPIAR, SASBDB, PRIDE etc.- Specified by:
getIhmDatasetRelatedDbReferencein interfaceBlock- Returns:
- IhmDatasetRelatedDbReference
-
getIhmExternalReferenceInfo
public IhmExternalReferenceInfo getIhmExternalReferenceInfo()
Description copied from interface:BlockCategory holds links to other external data sources for the I/H model entry. Input datasets held in other databases such as EMDB, BMRB, SASBDB etc. are referenced in the IHM_DATASET_RELATED_DB_REFERENCE category. This data category, along with IHM_EXTERNAL_FILES category, holds information regarding other non-database external data sources, such as DOIs (digital object identifiers) or supplementary files stored locally. The DOIs can either lead to the external data file(s) directly (as in case of DOIs provided by the PDB) or might lead to an HTML landing page (as provided by Zenodo). In the latter case, additional URL (Uniform Resource Locator) information is required to retrieve the external data file(s).- Specified by:
getIhmExternalReferenceInfoin interfaceBlock- Returns:
- IhmExternalReferenceInfo
-
getIhmExternalFiles
public IhmExternalFiles getIhmExternalFiles()
Description copied from interface:BlockCategory provides details regarding external files. The IHM_EXTERNAL_REFERENCE_INFO category captures the top-level details regarding external data sources. This category captures the specific details regarding externally stored files related to the particular I/H model entry.- Specified by:
getIhmExternalFilesin interfaceBlock- Returns:
- IhmExternalFiles
-
getIhmDatasetExternalReference
public IhmDatasetExternalReference getIhmDatasetExternalReference()
Description copied from interface:BlockCategory provides additional details regarding input data hosted externally at other resources.- Specified by:
getIhmDatasetExternalReferencein interfaceBlock- Returns:
- IhmDatasetExternalReference
-
getIhmLocalizationDensityFiles
public IhmLocalizationDensityFiles getIhmLocalizationDensityFiles()
Description copied from interface:BlockData items in the IHM_LOCALIZATION_DENSITY_FILES category records the details of files that provide information regarding localization densities of ensembles. These may be stored externally as local files or linked via DOI and can be in any accepted format that provides volume information (CCP4, MRC, etc.).- Specified by:
getIhmLocalizationDensityFilesin interfaceBlock- Returns:
- IhmLocalizationDensityFiles
-
getIhmPredictedContactRestraint
public IhmPredictedContactRestraint getIhmPredictedContactRestraint()
Description copied from interface:BlockData items in the IHM_PREDICTED_CONTACT_RESTRAINT category records the list of predicted contacts used in the integrative modeling experiment. This has been adapted from the widely used CASP RR format (http://www.predictioncenter.org/casp8/index.cgi?page=format#RR). These contacts may be derived from various computational tools. The software information can be provided in the SOFTWARE category.- Specified by:
getIhmPredictedContactRestraintin interfaceBlock- Returns:
- IhmPredictedContactRestraint
-
getIhmHydroxylRadicalFpRestraint
public IhmHydroxylRadicalFpRestraint getIhmHydroxylRadicalFpRestraint()
Description copied from interface:BlockData items in the IHM_HYDROXYL_RADICAL_FP_RESTRAINT category records the restraints derived from hydroxyl radical footprinting experiment. These restraints provide information regarding solvent accessible surface area of residues.- Specified by:
getIhmHydroxylRadicalFpRestraintin interfaceBlock- Returns:
- IhmHydroxylRadicalFpRestraint
-
getIhmCrossLinkList
public IhmCrossLinkList getIhmCrossLinkList()
Description copied from interface:BlockData items in the IHM_CROSS_LINK_LIST category records the list of spatial restraints derived from chemical crosslinking experiment.- Specified by:
getIhmCrossLinkListin interfaceBlock- Returns:
- IhmCrossLinkList
-
getIhmCrossLinkRestraint
public IhmCrossLinkRestraint getIhmCrossLinkRestraint()
Description copied from interface:BlockData items in the IHM_CROSS_LINK_RESTRAINT category enumerates the implementation details of the chemical crosslinking restraints in the integrative modeling. This category holds the details of how the experimentally derived crosslinks are applied in the modeling.- Specified by:
getIhmCrossLinkRestraintin interfaceBlock- Returns:
- IhmCrossLinkRestraint
-
getIhmCrossLinkResult
public IhmCrossLinkResult getIhmCrossLinkResult()
Description copied from interface:BlockData items in the IHM_CROSS_LINK_RESULT category records the results of the crosslinking restraints in the IHM modeling.- Specified by:
getIhmCrossLinkResultin interfaceBlock- Returns:
- IhmCrossLinkResult
-
getIhmCrossLinkResultParameters
public IhmCrossLinkResultParameters getIhmCrossLinkResultParameters()
Description copied from interface:BlockData items in the IHM_CROSS_LINK_RESULT_PARAMETERS category records the results of the crosslinking restraint parameters in the IHM modeling.- Specified by:
getIhmCrossLinkResultParametersin interfaceBlock- Returns:
- IhmCrossLinkResultParameters
-
getIhm2demClassAverageRestraint
public Ihm2demClassAverageRestraint getIhm2demClassAverageRestraint()
Description copied from interface:BlockData items in the IHM_2DEM_CLASS_AVERAGE_RESTRAINT category records the details of the 2DEM class averages used in the IHM modeling.- Specified by:
getIhm2demClassAverageRestraintin interfaceBlock- Returns:
- Ihm2demClassAverageRestraint
-
getIhm2demClassAverageFitting
public Ihm2demClassAverageFitting getIhm2demClassAverageFitting()
Description copied from interface:BlockData items in the IHM_2DEM_CLASS_AVERAGE_FITTING category records the details of the fitting of the model to the 2DEM class averages used in the IHM modeling. The following conventions are recommended while generating the rotation matrix and translation vector for transformation. - The model is rotated and translated to fit to the 2DEM image. - The 2DEM image should be in the XY plane. - The lower left image corner (image pixel index 0,0) should be at x,y,z = (0,0,0). - The 2D image is scaled by the _ihm_2dem_class_average_restraint.pixel_size_width and _ihm_2dem_class_average_restraint.pixel_size_height from the IHM_2DEM_CLASS_AVERAGE_RESTRAINT table. - The transformation is applied after the scaling and hence the translation vector should account for the scaling. - There are no specifications for Z translations i.e., how far the image should be from the model while projecting. It may be set to zero.- Specified by:
getIhm2demClassAverageFittingin interfaceBlock- Returns:
- Ihm2demClassAverageFitting
-
getIhm3demRestraint
public Ihm3demRestraint getIhm3demRestraint()
Description copied from interface:BlockData items in the IHM_3DEM_RESTRAINT category records the details of the 3DEM maps used as restraints in the IHM modeling.- Specified by:
getIhm3demRestraintin interfaceBlock- Returns:
- Ihm3demRestraint
-
getIhmSasRestraint
public IhmSasRestraint getIhmSasRestraint()
Description copied from interface:BlockData items in the IHM_SAS_RESTRAINT category records the details of the SAS data used as restraints in the IHM modeling.- Specified by:
getIhmSasRestraintin interfaceBlock- Returns:
- IhmSasRestraint
-
getIhmStartingModelCoord
public IhmStartingModelCoord getIhmStartingModelCoord()
Description copied from interface:BlockData items in the IHM_STARTING_MODEL_COORD category records the coordinates for structural templates used as starting inputs in the integrative model building tasks.- Specified by:
getIhmStartingModelCoordin interfaceBlock- Returns:
- IhmStartingModelCoord
-
getIhmSphereObjSite
public IhmSphereObjSite getIhmSphereObjSite()
Description copied from interface:BlockData items in the IHM_SPHERE_OBJ_SITE category records the details of the spherical objects modeled in the integrative structural model.- Specified by:
getIhmSphereObjSitein interfaceBlock- Returns:
- IhmSphereObjSite
-
getIhmGaussianObjSite
public IhmGaussianObjSite getIhmGaussianObjSite()
Description copied from interface:BlockData items in the IHM_GAUSSIAN_OBJ_SITE category records the details of the gaussian objects modeled in the integrative structural model.- Specified by:
getIhmGaussianObjSitein interfaceBlock- Returns:
- IhmGaussianObjSite
-
getIhmGaussianObjEnsemble
public IhmGaussianObjEnsemble getIhmGaussianObjEnsemble()
Description copied from interface:BlockData items in the IHM_GAUSSIAN_OBJ_ENSEMBLE category records the details of the gaussian objects representing an ensemble or cluster of models.- Specified by:
getIhmGaussianObjEnsemblein interfaceBlock- Returns:
- IhmGaussianObjEnsemble
-
getIhmResiduesNotModeled
public IhmResiduesNotModeled getIhmResiduesNotModeled()
Description copied from interface:BlockData items in the IHM_RESIDUES_NOT_MODELED category record the details of the residues that are defined in the IHM_STRUCT_ASSEMBLY category but are missing in the three-dimensional model (ATOM_SITE, IHM_SPHERE_OBJ_SITE, IHM_GAUSSIAN_OBJ_SITE categories) i.e., residues in the assembly that are not modeled.- Specified by:
getIhmResiduesNotModeledin interfaceBlock- Returns:
- IhmResiduesNotModeled
-
getIhmFeatureList
public IhmFeatureList getIhmFeatureList()
Description copied from interface:BlockIHM_FEATURE_LIST is the high level category that provides defintions to select atoms/residues from polymeric and non-polymeric entities.- Specified by:
getIhmFeatureListin interfaceBlock- Returns:
- IhmFeatureList
-
getIhmPseudoSiteFeature
public IhmPseudoSiteFeature getIhmPseudoSiteFeature()
Description copied from interface:BlockData items in the IHM_PSEUDO_SITE_FEATURE category records the details of pseudo positions for the features listed in IHM_FEATURE_LIST.- Specified by:
getIhmPseudoSiteFeaturein interfaceBlock- Returns:
- IhmPseudoSiteFeature
-
getIhmPolyAtomFeature
public IhmPolyAtomFeature getIhmPolyAtomFeature()
Description copied from interface:BlockData items in the IHM_POLY_ATOM_FEATURE category provides the defintions required to select specific atoms.- Specified by:
getIhmPolyAtomFeaturein interfaceBlock- Returns:
- IhmPolyAtomFeature
-
getIhmPolyResidueFeature
public IhmPolyResidueFeature getIhmPolyResidueFeature()
Description copied from interface:BlockData items in the IHM_POLY_RESIDUE_FEATURE category provides the defintions required to select a specific residue or a set of residues that may or may not be in a contiguous range.- Specified by:
getIhmPolyResidueFeaturein interfaceBlock- Returns:
- IhmPolyResidueFeature
-
getIhmNonPolyFeature
public IhmNonPolyFeature getIhmNonPolyFeature()
Description copied from interface:BlockData items in the IHM_NON_POLY_FEATURE category provides the defintions required to select a non-polymeric (ligand) feature.- Specified by:
getIhmNonPolyFeaturein interfaceBlock- Returns:
- IhmNonPolyFeature
-
getIhmInterfaceResidueFeature
public IhmInterfaceResidueFeature getIhmInterfaceResidueFeature()
Description copied from interface:BlockData items in the IHM_INTERFACE_RESIDUE_FEATURE category captures the details of residues that are identified to be at the binding interface from experiments. This information is used by modeling software such as HADDOCK to create a set of ambiguous distance restraints at the binding interface between the molecular entities involved.- Specified by:
getIhmInterfaceResidueFeaturein interfaceBlock- Returns:
- IhmInterfaceResidueFeature
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getIhmDerivedDistanceRestraint
public IhmDerivedDistanceRestraint getIhmDerivedDistanceRestraint()
Description copied from interface:BlockData items in the IHM_DERIVED_DISTANCE_RESTRAINT category records the list of distance restraints used in the integrative modeling experiment. These distance redistance restraints may be derived from various kinds of experiments.- Specified by:
getIhmDerivedDistanceRestraintin interfaceBlock- Returns:
- IhmDerivedDistanceRestraint
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getIhmGeometricObjectList
public IhmGeometricObjectList getIhmGeometricObjectList()
Description copied from interface:BlockData items in the IHM_GEOMETRIC_OBJECT_LIST category records the list of geometric objects used as restraints in the integrative modeling study.- Specified by:
getIhmGeometricObjectListin interfaceBlock- Returns:
- IhmGeometricObjectList
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getIhmGeometricObjectCenter
public IhmGeometricObjectCenter getIhmGeometricObjectCenter()
Description copied from interface:BlockData items in the IHM_GEOMETRIC_OBJECT_CENTER category records the center of geometric objects used as restraints in the integrative modeling study.- Specified by:
getIhmGeometricObjectCenterin interfaceBlock- Returns:
- IhmGeometricObjectCenter
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getIhmGeometricObjectTransformation
public IhmGeometricObjectTransformation getIhmGeometricObjectTransformation()
Description copied from interface:BlockData items in the IHM_GEOMETRIC_OBJECT_TRANSFORMATION category records the details of the rotation matrix and translation vector applied for transforming the geometric object. If no transformation is provide, identity transformation is assumed.- Specified by:
getIhmGeometricObjectTransformationin interfaceBlock- Returns:
- IhmGeometricObjectTransformation
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getIhmGeometricObjectSphere
public IhmGeometricObjectSphere getIhmGeometricObjectSphere()
Description copied from interface:BlockData items in the IHM_GEOMETRIC_OBJECT_SPHERE category records the parameters of a sphere.- Specified by:
getIhmGeometricObjectSpherein interfaceBlock- Returns:
- IhmGeometricObjectSphere
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getIhmGeometricObjectTorus
public IhmGeometricObjectTorus getIhmGeometricObjectTorus()
Description copied from interface:BlockData items in the IHM_GEOMETRIC_OBJECT_TORUS category records the parameters of a torus. By definition, the base plane of the torus is the XY plane. The `ihm_geometric_object_transformation` category can be used to generate transformations to any other plane.- Specified by:
getIhmGeometricObjectTorusin interfaceBlock- Returns:
- IhmGeometricObjectTorus
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getIhmGeometricObjectHalfTorus
public IhmGeometricObjectHalfTorus getIhmGeometricObjectHalfTorus()
Description copied from interface:BlockData items in the IHM_GEOMETRIC_OBJECT_HALF_TORUS category records the parameters of half-torus that represents a membrane.- Specified by:
getIhmGeometricObjectHalfTorusin interfaceBlock- Returns:
- IhmGeometricObjectHalfTorus
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getIhmGeometricObjectAxis
public IhmGeometricObjectAxis getIhmGeometricObjectAxis()
Description copied from interface:BlockData items in the IHM_GEOMETRIC_OBJECT_AXIS category records the details of an axis used in a spatial restraint.- Specified by:
getIhmGeometricObjectAxisin interfaceBlock- Returns:
- IhmGeometricObjectAxis
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getIhmGeometricObjectPlane
public IhmGeometricObjectPlane getIhmGeometricObjectPlane()
Description copied from interface:BlockData items in the IHM_GEOMETRIC_OBJECT_PLANE category records the details of a plane used in a spatial restraint.- Specified by:
getIhmGeometricObjectPlanein interfaceBlock- Returns:
- IhmGeometricObjectPlane
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getIhmGeometricObjectDistanceRestraint
public IhmGeometricObjectDistanceRestraint getIhmGeometricObjectDistanceRestraint()
Description copied from interface:BlockData items in the IHM_GEOMETRIC_OBJECT_DISTANCE_RESTRAINT category records the details of distance restraints involving geometric objects. If the geometric object involved is a plane, then the distance is along the normal following the right-hand rule. So for the xy plane, distance is along the z axis in the positive direction, 'above' the plane such that negative distances corresponded to positions below the plane.- Specified by:
getIhmGeometricObjectDistanceRestraintin interfaceBlock- Returns:
- IhmGeometricObjectDistanceRestraint
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