Interface Block

    • Method Detail

      • getBlockHeader

        String getBlockHeader()
        The header of this Block.
        Returns:
        String of the header
      • getCategory

        Category getCategory​(String name)
        Retrieve a particular Category by name.
        Parameters:
        name - the category name
        Returns:
        the corresponding Category, if none exists a instance of BaseCategory is returned as proxy
      • getColumn

        Column getColumn​(String name)
        Retrieve a Column by name. This is relevant for CCDC files that identify columns by 'flat' names such as "cell_length_a"
        Parameters:
        name - the category name and column name, joined by an underscore
        Returns:
        the corresponding Column, if none exists a instance of BaseColumn is returned as proxy
      • getCategoryNames

        List<String> getCategoryNames()
        The names of all Category instances which will not return an empty Category when queried.
        Returns:
        collection of all Category names
      • categoryNames

        default Stream<String> categoryNames()
        Convenience method to access all present Category names.
        Returns:
        a stream of all registered categories
      • categories

        default Stream<Category> categories()
        Traverses all present categories.
        Returns:
        a Stream of all Category instances
      • getSaveFrames

        List<Block> getSaveFrames()
        All save frames associated to this Block.
        Returns:
        collection of save frames
      • saveFrames

        default Stream<Block> saveFrames()
        Convenience method to traverse all save frames.
        Returns:
        a Stream of all save frames.
      • getAtomSite

        AtomSite getAtomSite()
        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. 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.
        Returns:
        AtomSite
      • getAtomSiteAnisotrop

        AtomSiteAnisotrop getAtomSiteAnisotrop()
        Data 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.
        Returns:
        AtomSiteAnisotrop
      • getAtomSites

        AtomSites getAtomSites()
        Data items in the ATOM_SITES category record details about the crystallographic cell and cell transformations, which are common to all atom sites.
        Returns:
        AtomSites
      • getAtomSitesAlt

        AtomSitesAlt getAtomSitesAlt()
        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.
        Returns:
        AtomSitesAlt
      • getAtomSitesAltEns

        AtomSitesAltEns getAtomSitesAltEns()
        Data items in the ATOM_SITES_ALT_ENS category record details about the ensemble structure generated from atoms with various alternative conformation IDs.
        Returns:
        AtomSitesAltEns
      • getAtomSitesAltGen

        AtomSitesAltGen getAtomSitesAltGen()
        Data items in the ATOM_SITES_ALT_GEN category record details about the interpretation of multiple conformations in the structure.
        Returns:
        AtomSitesAltGen
      • getAtomSitesFootnote

        AtomSitesFootnote getAtomSitesFootnote()
        Data items in the ATOM_SITES_FOOTNOTE category record detailed comments about an atom site or a group of atom sites.
        Returns:
        AtomSitesFootnote
      • getAtomType

        AtomType getAtomType()
        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.
        Returns:
        AtomType
      • getAudit

        Audit getAudit()
        Data 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.
        Returns:
        Audit
      • getAuditAuthor

        AuditAuthor getAuditAuthor()
        Data items in the AUDIT_AUTHOR category record details about the author(s) of the data block.
        Returns:
        AuditAuthor
      • getAuditConform

        AuditConform getAuditConform()
        Data items in the AUDIT_CONFORM category describe the dictionary versions against which the data names appearing in the current data block are conformant.
        Returns:
        AuditConform
      • getAuditContactAuthor

        AuditContactAuthor getAuditContactAuthor()
        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.
        Returns:
        AuditContactAuthor
      • getCell

        Cell getCell()
        Data items in the CELL category record details about the crystallographic cell parameters.
        Returns:
        Cell
      • getCellMeasurement

        CellMeasurement getCellMeasurement()
        Data items in the CELL_MEASUREMENT category record details about the measurement of the crystallographic cell parameters.
        Returns:
        CellMeasurement
      • getCellMeasurementRefln

        CellMeasurementRefln getCellMeasurementRefln()
        Data 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.
        Returns:
        CellMeasurementRefln
      • getChemComp

        ChemComp getChemComp()
        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. The related categories CHEM_COMP_ATOM, CHEM_COMP_BOND, CHEM_COMP_ANGLE etc. describe the detailed geometry of these chemical components.
        Returns:
        ChemComp
      • getChemCompAngle

        ChemCompAngle getChemCompAngle()
        Data 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.
        Returns:
        ChemCompAngle
      • getChemCompAtom

        ChemCompAtom getChemCompAtom()
        Data 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.
        Returns:
        ChemCompAtom
      • getChemCompBond

        ChemCompBond getChemCompBond()
        Data 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.
        Returns:
        ChemCompBond
      • getChemCompChir

        ChemCompChir getChemCompChir()
        Data 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.
        Returns:
        ChemCompChir
      • getChemCompChirAtom

        ChemCompChirAtom getChemCompChirAtom()
        Data items in the CHEM_COMP_CHIR_ATOM category enumerate the atoms bonded to a chiral atom within a chemical component.
        Returns:
        ChemCompChirAtom
      • getChemCompLink

        ChemCompLink getChemCompLink()
        Data items in the CHEM_COMP_LINK category give details about the links between chemical components.
        Returns:
        ChemCompLink
      • getChemCompPlane

        ChemCompPlane getChemCompPlane()
        Data 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.
        Returns:
        ChemCompPlane
      • getChemCompPlaneAtom

        ChemCompPlaneAtom getChemCompPlaneAtom()
        Data items in the CHEM_COMP_PLANE_ATOM category enumerate the atoms in a plane within a chemical component.
        Returns:
        ChemCompPlaneAtom
      • getChemCompTor

        ChemCompTor getChemCompTor()
        Data 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.
        Returns:
        ChemCompTor
      • getChemCompTorValue

        ChemCompTorValue getChemCompTorValue()
        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. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both.
        Returns:
        ChemCompTorValue
      • getChemLink

        ChemLink getChemLink()
        Data items in the CHEM_LINK category give details about the links between chemical components.
        Returns:
        ChemLink
      • getChemLinkAngle

        ChemLinkAngle getChemLinkAngle()
        Data items in the CHEM_LINK_ANGLE category record details about angles in a link between chemical components.
        Returns:
        ChemLinkAngle
      • getChemLinkBond

        ChemLinkBond getChemLinkBond()
        Data items in the CHEM_LINK_BOND category record details about bonds in a link between components in the chemical structure.
        Returns:
        ChemLinkBond
      • getChemLinkChir

        ChemLinkChir getChemLinkChir()
        Data 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.
        Returns:
        ChemLinkChir
      • getChemLinkChirAtom

        ChemLinkChirAtom getChemLinkChirAtom()
        Data items in the CHEM_LINK_CHIR_ATOM category enumerate the atoms bonded to a chiral atom in a link between two chemical components.
        Returns:
        ChemLinkChirAtom
      • getChemLinkPlane

        ChemLinkPlane getChemLinkPlane()
        Data 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.
        Returns:
        ChemLinkPlane
      • getChemLinkPlaneAtom

        ChemLinkPlaneAtom getChemLinkPlaneAtom()
        Data items in the CHEM_LINK_PLANE_ATOM category enumerate the atoms in a plane in a link between two chemical components.
        Returns:
        ChemLinkPlaneAtom
      • getChemLinkTor

        ChemLinkTor getChemLinkTor()
        Data 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.
        Returns:
        ChemLinkTor
      • getChemLinkTorValue

        ChemLinkTorValue getChemLinkTorValue()
        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. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both.
        Returns:
        ChemLinkTorValue
      • getChemical

        Chemical getChemical()
        Data 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.
        Returns:
        Chemical
      • getChemicalConnAtom

        ChemicalConnAtom getChemicalConnAtom()
        Data 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.
        Returns:
        ChemicalConnAtom
      • getChemicalConnBond

        ChemicalConnBond getChemicalConnBond()
        Data 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.
        Returns:
        ChemicalConnBond
      • getChemicalFormula

        ChemicalFormula getChemicalFormula()
        Data 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.
        Returns:
        ChemicalFormula
      • getCitation

        Citation getCitation()
        Data items in the CITATION category record details about the literature cited as being relevant to the contents of the data block.
        Returns:
        Citation
      • getCitationAuthor

        CitationAuthor getCitationAuthor()
        Data items in the CITATION_AUTHOR category record details about the authors associated with the citations in the CITATION list.
        Returns:
        CitationAuthor
      • getCitationEditor

        CitationEditor getCitationEditor()
        Data items in the CITATION_EDITOR category record details about the editors associated with the books or book chapters cited in the CITATION list.
        Returns:
        CitationEditor
      • getComputing

        Computing getComputing()
        Data 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.
        Returns:
        Computing
      • getDatabase

        Database getDatabase()
        Data 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.
        Returns:
        Database
      • getDatabase2

        Database2 getDatabase2()
        Data 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.
        Returns:
        Database2
      • getDatabasePDBCaveat

        DatabasePDBCaveat getDatabasePDBCaveat()
        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). 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.
        Returns:
        DatabasePDBCaveat
      • getDatabasePDBMatrix

        DatabasePDBMatrix getDatabasePDBMatrix()
        The 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.
        Returns:
        DatabasePDBMatrix
      • getDatabasePDBRemark

        DatabasePDBRemark getDatabasePDBRemark()
        Data 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.
        Returns:
        DatabasePDBRemark
      • getDatabasePDBRev

        DatabasePDBRev getDatabasePDBRev()
        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). These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source.
        Returns:
        DatabasePDBRev
      • getDatabasePDBRevRecord

        DatabasePDBRevRecord getDatabasePDBRevRecord()
        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. These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source.
        Returns:
        DatabasePDBRevRecord
      • getDatabasePDBTvect

        DatabasePDBTvect getDatabasePDBTvect()
        The 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.
        Returns:
        DatabasePDBTvect
      • getDiffrn

        Diffrn getDiffrn()
        Data items in the DIFFRN category record details about the diffraction data and their measurement.
        Returns:
        Diffrn
      • getDiffrnAttenuator

        DiffrnAttenuator getDiffrnAttenuator()
        Data items in the DIFFRN_ATTENUATOR category record details about the diffraction attenuator scales employed.
        Returns:
        DiffrnAttenuator
      • getDiffrnDetector

        DiffrnDetector getDiffrnDetector()
        Data items in the DIFFRN_DETECTOR category describe the detector used to measure the scattered radiation, including any analyser and post-sample collimation.
        Returns:
        DiffrnDetector
      • getDiffrnMeasurement

        DiffrnMeasurement getDiffrnMeasurement()
        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.
        Returns:
        DiffrnMeasurement
      • getDiffrnOrientMatrix

        DiffrnOrientMatrix getDiffrnOrientMatrix()
        Data items in the DIFFRN_ORIENT_MATRIX category record details about the orientation matrix used in the measurement of the diffraction data.
        Returns:
        DiffrnOrientMatrix
      • getDiffrnOrientRefln

        DiffrnOrientRefln getDiffrnOrientRefln()
        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.
        Returns:
        DiffrnOrientRefln
      • getDiffrnRadiation

        DiffrnRadiation getDiffrnRadiation()
        Data 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.
        Returns:
        DiffrnRadiation
      • getDiffrnRadiationWavelength

        DiffrnRadiationWavelength getDiffrnRadiationWavelength()
        Data 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.
        Returns:
        DiffrnRadiationWavelength
      • getDiffrnRefln

        DiffrnRefln getDiffrnRefln()
        Data 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.
        Returns:
        DiffrnRefln
      • getDiffrnReflns

        DiffrnReflns getDiffrnReflns()
        Data 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.
        Returns:
        DiffrnReflns
      • getDiffrnScaleGroup

        DiffrnScaleGroup getDiffrnScaleGroup()
        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. Scaling groups might, for example, correspond to each film in a multi-film data set or each crystal in a multi-crystal data set.
        Returns:
        DiffrnScaleGroup
      • getDiffrnSource

        DiffrnSource getDiffrnSource()
        Data items in the DIFFRN_SOURCE category record details of the source of radiation used in the diffraction experiment.
        Returns:
        DiffrnSource
      • getDiffrnStandardRefln

        DiffrnStandardRefln getDiffrnStandardRefln()
        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. Note that these are the individual standard reflections, not the results of the analysis of the standard reflections.
        Returns:
        DiffrnStandardRefln
      • getDiffrnStandards

        DiffrnStandards getDiffrnStandards()
        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. Note that these records describe properties common to the set of standard reflections, not the standard reflections themselves.
        Returns:
        DiffrnStandards
      • getEntity

        Entity getEntity()
        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. 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.
        Returns:
        Entity
      • getEntityKeywords

        EntityKeywords getEntityKeywords()
        Data 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.
        Returns:
        EntityKeywords
      • getEntityLink

        EntityLink getEntityLink()
        Data items in the ENTITY_LINK category give details about the links between entities.
        Returns:
        EntityLink
      • getEntityNameCom

        EntityNameCom getEntityNameCom()
        Data 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.
        Returns:
        EntityNameCom
      • getEntityNameSys

        EntityNameSys getEntityNameSys()
        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. In some cases, the entity name may not be the same as the name of the biological structure.
        Returns:
        EntityNameSys
      • getEntityPoly

        EntityPoly getEntityPoly()
        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.
        Returns:
        EntityPoly
      • getEntityPolySeq

        EntityPolySeq getEntityPolySeq()
        Data 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.
        Returns:
        EntityPolySeq
      • getEntry

        Entry getEntry()
        There 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.
        Returns:
        Entry
      • getEntryLink

        EntryLink getEntryLink()
        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.
        Returns:
        EntryLink
      • getExptl

        Exptl getExptl()
        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.
        Returns:
        Exptl
      • getExptlCrystal

        ExptlCrystal getExptlCrystal()
        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.
        Returns:
        ExptlCrystal
      • getExptlCrystalFace

        ExptlCrystalFace getExptlCrystalFace()
        Data items in the EXPTL_CRYSTAL_FACE category record details of the crystal faces.
        Returns:
        ExptlCrystalFace
      • getExptlCrystalGrow

        ExptlCrystalGrow getExptlCrystalGrow()
        Data items in the EXPTL_CRYSTAL_GROW category record details about the conditions and methods used to grow the crystal.
        Returns:
        ExptlCrystalGrow
      • getExptlCrystalGrowComp

        ExptlCrystalGrowComp getExptlCrystalGrowComp()
        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. 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.
        Returns:
        ExptlCrystalGrowComp
      • getGeom

        Geom getGeom()
        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. 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.
        Returns:
        Geom
      • getGeomAngle

        GeomAngle getGeomAngle()
        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.
        Returns:
        GeomAngle
      • getGeomBond

        GeomBond getGeomBond()
        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.
        Returns:
        GeomBond
      • getGeomContact

        GeomContact getGeomContact()
        Data items in the GEOM_CONTACT category record details about interatomic contacts as calculated from the contents of the ATOM, CELL and SYMMETRY data.
        Returns:
        GeomContact
      • getGeomHbond

        GeomHbond getGeomHbond()
        Data items in the GEOM_HBOND category record details about hydrogen bonds as calculated from the contents of the ATOM, CELL and SYMMETRY data.
        Returns:
        GeomHbond
      • getGeomTorsion

        GeomTorsion getGeomTorsion()
        Data 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.
        Returns:
        GeomTorsion
      • getJournal

        Journal getJournal()
        Data 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.
        Returns:
        Journal
      • getJournalIndex

        JournalIndex getJournalIndex()
        Data 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.
        Returns:
        JournalIndex
      • getPhasing

        Phasing getPhasing()
        Data 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.
        Returns:
        Phasing
      • getPhasingAveraging

        PhasingAveraging getPhasingAveraging()
        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.
        Returns:
        PhasingAveraging
      • getPhasingIsomorphous

        PhasingIsomorphous getPhasingIsomorphous()
        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.
        Returns:
        PhasingIsomorphous
      • getPhasingMAD

        PhasingMAD getPhasingMAD()
        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.
        Returns:
        PhasingMAD
      • getPhasingMADClust

        PhasingMADClust getPhasingMADClust()
        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.
        Returns:
        PhasingMADClust
      • getPhasingMADExpt

        PhasingMADExpt getPhasingMADExpt()
        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.
        Returns:
        PhasingMADExpt
      • getPhasingMADRatio

        PhasingMADRatio getPhasingMADRatio()
        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.
        Returns:
        PhasingMADRatio
      • getPhasingMADSet

        PhasingMADSet getPhasingMADSet()
        Data items in the PHASING_MAD_SET category record details about the individual data sets used in a MAD phasing experiment.
        Returns:
        PhasingMADSet
      • getPhasingMIR

        PhasingMIR getPhasingMIR()
        Data 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).
        Returns:
        PhasingMIR
      • getPhasingMIRDer

        PhasingMIRDer getPhasingMIRDer()
        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. 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.
        Returns:
        PhasingMIRDer
      • getPhasingMIRDerRefln

        PhasingMIRDerRefln getPhasingMIRDerRefln()
        Data 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.
        Returns:
        PhasingMIRDerRefln
      • getPhasingMIRDerShell

        PhasingMIRDerShell getPhasingMIRDerShell()
        Data 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.)
        Returns:
        PhasingMIRDerShell
      • getPhasingMIRDerSite

        PhasingMIRDerSite getPhasingMIRDerSite()
        Data 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.)
        Returns:
        PhasingMIRDerSite
      • getPhasingMIRShell

        PhasingMIRShell getPhasingMIRShell()
        Data items in the PHASING_MIR_SHELL category record statistics for an isomorphous replacement phasing experiment.broken down into shells of resolution.
        Returns:
        PhasingMIRShell
      • getPhasingSet

        PhasingSet getPhasingSet()
        Data 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.
        Returns:
        PhasingSet
      • getPhasingSetRefln

        PhasingSetRefln getPhasingSetRefln()
        Data 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.
        Returns:
        PhasingSetRefln
      • getPubl

        Publ getPubl()
        Data items in the PUBL category are used when submitting a manuscript for publication.
        Returns:
        Publ
      • getPublAuthor

        PublAuthor getPublAuthor()
        Data items in the PUBL_AUTHOR category record details of the authors of a manuscript submitted for publication.
        Returns:
        PublAuthor
      • getPublBody

        PublBody getPublBody()
        Data 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.
        Returns:
        PublBody
      • getPublManuscriptIncl

        PublManuscriptIncl getPublManuscriptIncl()
        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.
        Returns:
        PublManuscriptIncl
      • getRefine

        Refine getRefine()
        Data items in the REFINE category record details about the structure-refinement parameters.
        Returns:
        Refine
      • getRefineAnalyze

        RefineAnalyze getRefineAnalyze()
        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. A given computer program may or may not produce values corresponding to these data names.
        Returns:
        RefineAnalyze
      • getRefineBIso

        RefineBIso getRefineBIso()
        Data items in the REFINE_B_ISO category record details about the treatment of isotropic B factors (displacement parameters) during refinement.
        Returns:
        RefineBIso
      • getRefineFunctMinimized

        RefineFunctMinimized getRefineFunctMinimized()
        Data items in the REFINE_FUNCT_MINIMIZED category record details about the individual terms of the function minimized during refinement.
        Returns:
        RefineFunctMinimized
      • getRefineHist

        RefineHist getRefineHist()
        Data 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.
        Returns:
        RefineHist
      • getRefineLsRestr

        RefineLsRestr getRefineLsRestr()
        Data items in the REFINE_LS_RESTR category record details about the restraints applied to various classes of parameters during the least-squares refinement.
        Returns:
        RefineLsRestr
      • getRefineLsRestrNcs

        RefineLsRestrNcs getRefineLsRestrNcs()
        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. It is expected that these values will only be reported once for each set of restrained domains.
        Returns:
        RefineLsRestrNcs
      • getRefineLsRestrType

        RefineLsRestrType getRefineLsRestrType()
        Data items in the REFINE_LS_RESTR_TYPE category record details about the restraint types used in the least-squares refinement.
        Returns:
        RefineLsRestrType
      • getRefineLsShell

        RefineLsShell getRefineLsShell()
        Data items in the REFINE_LS_SHELL category record details about the results of the least-squares refinement broken down into shells of resolution.
        Returns:
        RefineLsShell
      • getRefineOccupancy

        RefineOccupancy getRefineOccupancy()
        Data items in the REFINE_OCCUPANCY category record details about the treatment of atom occupancies during refinement.
        Returns:
        RefineOccupancy
      • getRefln

        Refln getRefln()
        Data 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.
        Returns:
        Refln
      • getReflnSysAbs

        ReflnSysAbs getReflnSysAbs()
        Data items in the REFLN_SYS_ABS category record details about the reflection data that should be systematically absent, given the designated space group.
        Returns:
        ReflnSysAbs
      • getReflns

        Reflns getReflns()
        Data 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.
        Returns:
        Reflns
      • getReflnsScale

        ReflnsScale getReflnsScale()
        Data 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.
        Returns:
        ReflnsScale
      • getReflnsShell

        ReflnsShell getReflnsShell()
        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.
        Returns:
        ReflnsShell
      • getSoftware

        Software getSoftware()
        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. These data items allow computer programs to be referenced in more detail than data items in the COMPUTING category do.
        Returns:
        Software
      • getStruct

        Struct getStruct()
        Data items in the STRUCT category record details about the description of the crystallographic structure.
        Returns:
        Struct
      • getStructAsym

        StructAsym getStructAsym()
        Data items in the STRUCT_ASYM category record details about the structural elements in the asymmetric unit.
        Returns:
        StructAsym
      • getStructBiol

        StructBiol getStructBiol()
        Data 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.
        Returns:
        StructBiol
      • getStructBiolGen

        StructBiolGen getStructBiolGen()
        Data 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.
        Returns:
        StructBiolGen
      • getStructBiolKeywords

        StructBiolKeywords getStructBiolKeywords()
        Data items in the STRUCT_BIOL_KEYWORDS category record keywords that describe each biological unit.
        Returns:
        StructBiolKeywords
      • getStructBiolView

        StructBiolView getStructBiolView()
        Data items in the STRUCT_BIOL_VIEW category record details about how to draw and annotate an informative view of the biological structure.
        Returns:
        StructBiolView
      • getStructConf

        StructConf getStructConf()
        Data 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.
        Returns:
        StructConf
      • getStructConfType

        StructConfType getStructConfType()
        Data items in the STRUCT_CONF_TYPE category record details about the criteria used to identify backbone conformations of a segment of polymer.
        Returns:
        StructConfType
      • getStructConn

        StructConn getStructConn()
        Data 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.
        Returns:
        StructConn
      • getStructConnType

        StructConnType getStructConnType()
        Data items in the STRUCT_CONN_TYPE category record details about the criteria used to identify interactions between portions of the structure.
        Returns:
        StructConnType
      • getStructKeywords

        StructKeywords getStructKeywords()
        Data items in the STRUCT_KEYWORDS category specify keywords that describe the chemical structure in this entry.
        Returns:
        StructKeywords
      • getStructMonDetails

        StructMonDetails getStructMonDetails()
        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. These can include the coefficients used in map calculations, the radii used for including points in a calculation and so on.
        Returns:
        StructMonDetails
      • getStructMonNucl

        StructMonNucl getStructMonNucl()
        Data 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.
        Returns:
        StructMonNucl
      • getStructMonProt

        StructMonProt getStructMonProt()
        Data 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.
        Returns:
        StructMonProt
      • getStructMonProtCis

        StructMonProtCis getStructMonProtCis()
        Data 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.
        Returns:
        StructMonProtCis
      • getStructNcsDom

        StructNcsDom getStructNcsDom()
        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. 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.
        Returns:
        StructNcsDom
      • getStructNcsDomLim

        StructNcsDomLim getStructNcsDomLim()
        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.
        Returns:
        StructNcsDomLim
      • getStructNcsEns

        StructNcsEns getStructNcsEns()
        Data 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.
        Returns:
        StructNcsEns
      • getStructNcsEnsGen

        StructNcsEnsGen getStructNcsEnsGen()
        Data items in the STRUCT_NCS_ENS_GEN category list domains related by a noncrystallographic symmetry operation and identify the operator.
        Returns:
        StructNcsEnsGen
      • getStructNcsOper

        StructNcsOper getStructNcsOper()
        Data 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.
        Returns:
        StructNcsOper
      • getStructRef

        StructRef getStructRef()
        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. 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.
        Returns:
        StructRef
      • getStructRefSeq

        StructRefSeq getStructRefSeq()
        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.
        Returns:
        StructRefSeq
      • getStructRefSeqDif

        StructRefSeqDif getStructRefSeqDif()
        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.
        Returns:
        StructRefSeqDif
      • getStructSheet

        StructSheet getStructSheet()
        Data items in the STRUCT_SHEET category record details about the beta-sheets.
        Returns:
        StructSheet
      • getStructSheetHbond

        StructSheetHbond getStructSheetHbond()
        Data 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.
        Returns:
        StructSheetHbond
      • getStructSheetOrder

        StructSheetOrder getStructSheetOrder()
        Data 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.
        Returns:
        StructSheetOrder
      • getStructSheetRange

        StructSheetRange getStructSheetRange()
        Data 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.
        Returns:
        StructSheetRange
      • getStructSheetTopology

        StructSheetTopology getStructSheetTopology()
        Data 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.
        Returns:
        StructSheetTopology
      • getStructSite

        StructSite getStructSite()
        Data 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).
        Returns:
        StructSite
      • getStructSiteGen

        StructSiteGen getStructSiteGen()
        Data items in the STRUCT_SITE_GEN category record details about the generation of portions of the structure that contribute to structurally relevant sites.
        Returns:
        StructSiteGen
      • getStructSiteKeywords

        StructSiteKeywords getStructSiteKeywords()
        Data items in the STRUCT_SITE_KEYWORDS category record keywords describing the site.
        Returns:
        StructSiteKeywords
      • getStructSiteView

        StructSiteView getStructSiteView()
        Data items in the STRUCT_SITE_VIEW category record details about how to draw and annotate an informative view of the site.
        Returns:
        StructSiteView
      • getSymmetry

        Symmetry getSymmetry()
        Data items in the SYMMETRY category record details about the space-group symmetry.
        Returns:
        Symmetry
      • getSymmetryEquiv

        SymmetryEquiv getSymmetryEquiv()
        Data items in the SYMMETRY_EQUIV category list the symmetry-equivalent positions for the space group.
        Returns:
        SymmetryEquiv
      • getAuditLink

        AuditLink getAuditLink()
        Data items in the AUDIT_LINK category record details about the relationships between data blocks in the current CIF.
        Returns:
        AuditLink
      • getDiffrnReflnsClass

        DiffrnReflnsClass getDiffrnReflnsClass()
        Data items in the DIFFRN_REFLNS_CLASS category record details about the classes of reflections measured in the diffraction experiment.
        Returns:
        DiffrnReflnsClass
      • getRefineLsClass

        RefineLsClass getRefineLsClass()
        Data items in the REFINE_LS_CLASS category record details about the reflections used for the structure refinement for each reflection class separately.
        Returns:
        RefineLsClass
      • getReflnsClass

        ReflnsClass getReflnsClass()
        Data items in the REFLNS_CLASS category record details of the reflections used to determine the structural parameters for each reflection class.
        Returns:
        ReflnsClass
      • getSpaceGroup

        SpaceGroup getSpaceGroup()
        Contains 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.
        Returns:
        SpaceGroup
      • getSpaceGroupSymop

        SpaceGroupSymop getSpaceGroupSymop()
        Contains information about the symmetry operations of the space group.
        Returns:
        SpaceGroupSymop
      • getValenceParam

        ValenceParam getValenceParam()
        Data 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.
        Returns:
        ValenceParam
      • getValenceRef

        ValenceRef getValenceRef()
        Data items in the VALENCE_REF category list the references from which the bond-valence parameters have been taken.
        Returns:
        ValenceRef
      • getPdbxAudit

        PdbxAudit getPdbxAudit()
        The PDBX_AUDIT holds current version information.
        Returns:
        PdbxAudit
      • getPdbxVersion

        PdbxVersion getPdbxVersion()
        Data items in the PDBX_VERSION category record details about the version of this entry.
        Returns:
        PdbxVersion
      • getPdbxAuditAuthor

        PdbxAuditAuthor getPdbxAuditAuthor()
        Data items in the PDBX_AUDIT_AUTHOR category record details about the author(s) of the data block.
        Returns:
        PdbxAuditAuthor
      • getPdbxDatabaseMessage

        PdbxDatabaseMessage getPdbxDatabaseMessage()
        The PDBX_DATABASE_MESSAGE category provides information about correspondance related to a structure deposition.
        Returns:
        PdbxDatabaseMessage
      • getPdbxDatabasePDBObsSpr

        PdbxDatabasePDBObsSpr getPdbxDatabasePDBObsSpr()
        The PDBX_DATABASE_PDB_OBS_SPR category provides placeholders for information on obsolete/superseded PDB entries
        Returns:
        PdbxDatabasePDBObsSpr
      • getPdbxDatabaseProc

        PdbxDatabaseProc getPdbxDatabaseProc()
        Internal records to track the data processing cycle.
        Returns:
        PdbxDatabaseProc
      • getPdbxDatabaseRemark

        PdbxDatabaseRemark getPdbxDatabaseRemark()
        Data 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).
        Returns:
        PdbxDatabaseRemark
      • getPdbxDatabaseStatus

        PdbxDatabaseStatus getPdbxDatabaseStatus()
        These are internal RCSB records to keep track of data processing and status of the entry.
        Returns:
        PdbxDatabaseStatus
      • getPdbxEntityName

        PdbxEntityName getPdbxEntityName()
        The PDBX_ENTITY_NAME records additional name information for each entity.
        Returns:
        PdbxEntityName
      • getPdbxPrereleaseSeq

        PdbxPrereleaseSeq getPdbxPrereleaseSeq()
        This category provides a placeholder for pre-release sequence information. After release this category should be discarded.
        Returns:
        PdbxPrereleaseSeq
      • getPdbxPolySeqScheme

        PdbxPolySeqScheme getPdbxPolySeqScheme()
        The PDBX_POLY_SEQ_SCHEME category provides residue level nomenclature mapping for polymer entities.
        Returns:
        PdbxPolySeqScheme
      • getPdbxNonpolyScheme

        PdbxNonpolyScheme getPdbxNonpolyScheme()
        The PDBX_NONPOLY_SCHEME category provides residue level nomenclature mapping for non-polymer entities.
        Returns:
        PdbxNonpolyScheme
      • getPdbxRefine

        PdbxRefine getPdbxRefine()
        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.
        Returns:
        PdbxRefine
      • getPdbxStructSheetHbond

        PdbxStructSheetHbond getPdbxStructSheetHbond()
        Data 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.
        Returns:
        PdbxStructSheetHbond
      • getPdbxXplorFile

        PdbxXplorFile getPdbxXplorFile()
        Parameter and topology files used in X-PLOR/CNS refinement.
        Returns:
        PdbxXplorFile
      • getPdbxRefineAuxFile

        PdbxRefineAuxFile getPdbxRefineAuxFile()
        Auxilary parameter and topology files used in refinement.
        Returns:
        PdbxRefineAuxFile
      • getPdbxDatabaseRelated

        PdbxDatabaseRelated getPdbxDatabaseRelated()
        Data items in PDBX_DATABASE_RELATED contain references to entries that are related to the this entry.
        Returns:
        PdbxDatabaseRelated
      • getPdbxEntityAssembly

        PdbxEntityAssembly getPdbxEntityAssembly()
        The PDBX_ENTITY_ASSEMBLY category provides a chemical description of the biological assembly studied in terms of its constituent entities.
        Returns:
        PdbxEntityAssembly
      • getPdbxExptlCrystalGrowComp

        PdbxExptlCrystalGrowComp getPdbxExptlCrystalGrowComp()
        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.
        Returns:
        PdbxExptlCrystalGrowComp
      • getPdbxExptlCrystalGrowSol

        PdbxExptlCrystalGrowSol getPdbxExptlCrystalGrowSol()
        Data items in the PDBX_EXPTL_CRYSTAL_GROW_SOL category record details about the solutions that were 'mixed' to produce the crystal.
        Returns:
        PdbxExptlCrystalGrowSol
      • getPdbxExptlCrystalCryoTreatment

        PdbxExptlCrystalCryoTreatment getPdbxExptlCrystalCryoTreatment()
        Data items in the PDBX_EXPTL_CRYSTAL_CRYO_TREATMENT category record details cryogenic treatments applied to this crystal.
        Returns:
        PdbxExptlCrystalCryoTreatment
      • getPdbxRefineTls

        PdbxRefineTls getPdbxRefineTls()
        Data 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
        Returns:
        PdbxRefineTls
      • getPdbxRefineTlsGroup

        PdbxRefineTlsGroup getPdbxRefineTlsGroup()
        Data 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
        Returns:
        PdbxRefineTlsGroup
      • getPdbxContactAuthor

        PdbxContactAuthor getPdbxContactAuthor()
        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. This category atomizes information to a greater degree than the standard AUDIT_CONTACT_AUTHOR category.
        Returns:
        PdbxContactAuthor
      • getPdbxSGProject

        PdbxSGProject getPdbxSGProject()
        Data items in the PDBX_CONTACT_AUTHOR category record details about the Structural Genomics Project and name and initials for each Center.
        Returns:
        PdbxSGProject
      • getPdbxAtomSiteAnisoTls

        PdbxAtomSiteAnisoTls getPdbxAtomSiteAnisoTls()
        Data items in the PDBX_ATOM_SITE_ANISO_TLS category record details about the TLS contribution to anisotropic displacement parameters.
        Returns:
        PdbxAtomSiteAnisoTls
      • getPdbxNmrDetails

        PdbxNmrDetails getPdbxNmrDetails()
        Experimental details of the NMR study that have not been described elsewhere in this deposition.
        Returns:
        PdbxNmrDetails
      • getPdbxNmrSampleDetails

        PdbxNmrSampleDetails getPdbxNmrSampleDetails()
        Complete description of each NMR sample, including the solvent system used.
        Returns:
        PdbxNmrSampleDetails
      • getPdbxNmrExptlSample

        PdbxNmrExptlSample getPdbxNmrExptlSample()
        The chemical constituents of each NMR sample. Each sample is identified by a number and each component in the sample is identified by name.
        Returns:
        PdbxNmrExptlSample
      • getPdbxNmrExptlSampleConditions

        PdbxNmrExptlSampleConditions getPdbxNmrExptlSampleConditions()
        The experimental conditions used to for each sample. Each set of conditions is identified by a numerical code.
        Returns:
        PdbxNmrExptlSampleConditions
      • getPdbxNmrSpectrometer

        PdbxNmrSpectrometer getPdbxNmrSpectrometer()
        The details about each spectrometer used to collect data for this deposition.
        Returns:
        PdbxNmrSpectrometer
      • getPdbxNmrExptl

        PdbxNmrExptl getPdbxNmrExptl()
        In 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.
        Returns:
        PdbxNmrExptl
      • getPdbxNmrSoftware

        PdbxNmrSoftware getPdbxNmrSoftware()
        Description 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.
        Returns:
        PdbxNmrSoftware
      • getPdbxNmrConstraints

        PdbxNmrConstraints getPdbxNmrConstraints()
        This section provides a tabulation of constraint data.
        Returns:
        PdbxNmrConstraints
      • getPdbxNmrEnsemble

        PdbxNmrEnsemble getPdbxNmrEnsemble()
        This category contains the information that describes the ensemble of deposited structures. If only an average structure has been deposited skip this section.
        Returns:
        PdbxNmrEnsemble
      • getPdbxNmrEnsembleRms

        PdbxNmrEnsembleRms getPdbxNmrEnsembleRms()
        Structural statistics are derived from molecular dynamics and simulated annealing programs.
        Returns:
        PdbxNmrEnsembleRms
      • getPdbxNmrRepresentative

        PdbxNmrRepresentative getPdbxNmrRepresentative()
        An 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.
        Returns:
        PdbxNmrRepresentative
      • getPdbxNmrRefine

        PdbxNmrRefine getPdbxNmrRefine()
        Describe the method and details of the refinement of the deposited structure.
        Returns:
        PdbxNmrRefine
      • getPdbxNmrForceConstants

        PdbxNmrForceConstants getPdbxNmrForceConstants()
        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.
        Returns:
        PdbxNmrForceConstants
      • getNdbStructConfNa

        NdbStructConfNa getNdbStructConfNa()
        Data items in the NDB_STRUCT_CONF_NA category describes secondary structure features in this entry.
        Returns:
        NdbStructConfNa
      • getNdbStructFeatureNa

        NdbStructFeatureNa getNdbStructFeatureNa()
        Data items in the NDB_STRUCT_FEATURE_NA category describes tertiary and other special structural features in this entry.
        Returns:
        NdbStructFeatureNa
      • getNdbStructNaBasePair

        NdbStructNaBasePair getNdbStructNaBasePair()
        Data items in the NDB_STRUCT_NA_BASE_PAIR category record details of base pairing interactions.
        Returns:
        NdbStructNaBasePair
      • getNdbStructNaBasePairStep

        NdbStructNaBasePairStep getNdbStructNaBasePairStep()
        Data items in the NDB_STRUCT_NA_BASE_PAIR_STEP category record details of base pair step interactions.
        Returns:
        NdbStructNaBasePairStep
      • getNdbOriginalNdbCoordinates

        NdbOriginalNdbCoordinates getNdbOriginalNdbCoordinates()
        Placeholder category for PDB coordinate data.
        Returns:
        NdbOriginalNdbCoordinates
      • getPdbxEntityNonpoly

        PdbxEntityNonpoly getPdbxEntityNonpoly()
        Returns:
        PdbxEntityNonpoly
      • getPdbxPhasingDm

        PdbxPhasingDm getPdbxPhasingDm()
        Data items in the PDBX_PHASING_DM category record details about density modification
        Returns:
        PdbxPhasingDm
      • getPdbxPhasingDmShell

        PdbxPhasingDmShell getPdbxPhasingDmShell()
        Data items in the PDBX_PHASING_DM_SHELL category record details about density modification in resolution shell.
        Returns:
        PdbxPhasingDmShell
      • getPdbxPhasingMADShell

        PdbxPhasingMADShell getPdbxPhasingMADShell()
        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)
        Returns:
        PdbxPhasingMADShell
      • getPdbxPhasingMADSet

        PdbxPhasingMADSet getPdbxPhasingMADSet()
        Record 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.
        Returns:
        PdbxPhasingMADSet
      • getPdbxPhasingMADSetShell

        PdbxPhasingMADSetShell getPdbxPhasingMADSetShell()
        The same as category pdbx_phasing_MAD_set, but broken into shells.
        Returns:
        PdbxPhasingMADSetShell
      • getPdbxPhasingMADSetSite

        PdbxPhasingMADSetSite getPdbxPhasingMADSetSite()
        record the details (coordinates etc.) of anomalous scatters.
        Returns:
        PdbxPhasingMADSetSite
      • getPdbxPhasingMR

        PdbxPhasingMR getPdbxPhasingMR()
        Data items in the PDBX_PHASING_MR category record details about molecular replacement.
        Returns:
        PdbxPhasingMR
      • getPdbxRefineComponent

        PdbxRefineComponent getPdbxRefineComponent()
        Data items in the PDBX_REFINE_COMPONENT category record statistics of the final model relative to the density map.
        Returns:
        PdbxRefineComponent
      • getPdbxEntityProdProtocol

        PdbxEntityProdProtocol getPdbxEntityProdProtocol()
        This category contains descriptive protocols for the production of this entity.
        Returns:
        PdbxEntityProdProtocol
      • getPdbxEntitySrcGenProdOther

        PdbxEntitySrcGenProdOther getPdbxEntitySrcGenProdOther()
        This 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.
        Returns:
        PdbxEntitySrcGenProdOther
      • getPdbxEntitySrcGenProdOtherParameter

        PdbxEntitySrcGenProdOtherParameter getPdbxEntitySrcGenProdOtherParameter()
        This category contains parameters and values required to capture information about a particular process step
        Returns:
        PdbxEntitySrcGenProdOtherParameter
      • getPdbxEntitySrcGenProdPcr

        PdbxEntitySrcGenProdPcr getPdbxEntitySrcGenProdPcr()
        This 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.
        Returns:
        PdbxEntitySrcGenProdPcr
      • getPdbxEntitySrcGenProdDigest

        PdbxEntitySrcGenProdDigest getPdbxEntitySrcGenProdDigest()
        This 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.
        Returns:
        PdbxEntitySrcGenProdDigest
      • getPdbxEntitySrcGenClone

        PdbxEntitySrcGenClone getPdbxEntitySrcGenClone()
        This 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.
        Returns:
        PdbxEntitySrcGenClone
      • getPdbxEntitySrcGenCloneLigation

        PdbxEntitySrcGenCloneLigation getPdbxEntitySrcGenCloneLigation()
        This 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.
        Returns:
        PdbxEntitySrcGenCloneLigation
      • getPdbxEntitySrcGenCloneRecombination

        PdbxEntitySrcGenCloneRecombination getPdbxEntitySrcGenCloneRecombination()
        This 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.
        Returns:
        PdbxEntitySrcGenCloneRecombination
      • getPdbxEntitySrcGenExpress

        PdbxEntitySrcGenExpress getPdbxEntitySrcGenExpress()
        This 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.
        Returns:
        PdbxEntitySrcGenExpress
      • getPdbxEntitySrcGenExpressTimepoint

        PdbxEntitySrcGenExpressTimepoint getPdbxEntitySrcGenExpressTimepoint()
        This category contains details for OD time series used to monitor a given EXPRESSION step used in the overall protein production process.
        Returns:
        PdbxEntitySrcGenExpressTimepoint
      • getPdbxEntitySrcGenLysis

        PdbxEntitySrcGenLysis getPdbxEntitySrcGenLysis()
        This category contains details for the cell lysis steps used in the overall protein production process.
        Returns:
        PdbxEntitySrcGenLysis
      • getPdbxEntitySrcGenRefold

        PdbxEntitySrcGenRefold getPdbxEntitySrcGenRefold()
        This category contains details for the refolding steps used in the overall protein production process.
        Returns:
        PdbxEntitySrcGenRefold
      • getPdbxEntitySrcGenProteolysis

        PdbxEntitySrcGenProteolysis getPdbxEntitySrcGenProteolysis()
        This category contains details for the protein purification tag removal steps used in the overall protein production process
        Returns:
        PdbxEntitySrcGenProteolysis
      • getPdbxEntitySrcGenChrom

        PdbxEntitySrcGenChrom getPdbxEntitySrcGenChrom()
        This category contains details for the chromatographic steps used in the purification of the protein.
        Returns:
        PdbxEntitySrcGenChrom
      • getPdbxEntitySrcGenFract

        PdbxEntitySrcGenFract getPdbxEntitySrcGenFract()
        This 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.
        Returns:
        PdbxEntitySrcGenFract
      • getPdbxEntitySrcGenPure

        PdbxEntitySrcGenPure getPdbxEntitySrcGenPure()
        This 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.
        Returns:
        PdbxEntitySrcGenPure
      • getPdbxEntitySrcGenCharacter

        PdbxEntitySrcGenCharacter getPdbxEntitySrcGenCharacter()
        This category contains details of protein characterisation. It refers to the characteristion of the product of a specific step.
        Returns:
        PdbxEntitySrcGenCharacter
      • getPdbxConstruct

        PdbxConstruct getPdbxConstruct()
        Data 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).
        Returns:
        PdbxConstruct
      • getPdbxConstructFeature

        PdbxConstructFeature getPdbxConstructFeature()
        Data items in the PDBX_CONSTRUCT_FEATURE category may be used to specify various properties of a nucleic acid sequence used during protein production.
        Returns:
        PdbxConstructFeature
      • getPdbxRobotSystem

        PdbxRobotSystem getPdbxRobotSystem()
        The details about each robotic system used to collect data for this project.
        Returns:
        PdbxRobotSystem
      • getPdbxBuffer

        PdbxBuffer getPdbxBuffer()
        Data items in the PDBX_BUFFER category record details of the sample buffer.
        Returns:
        PdbxBuffer
      • getPdbxBufferComponents

        PdbxBufferComponents getPdbxBufferComponents()
        Constituents of buffer in sample
        Returns:
        PdbxBufferComponents
      • getPdbxDomain

        PdbxDomain getPdbxDomain()
        Data 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.
        Returns:
        PdbxDomain
      • getPdbxDomainRange

        PdbxDomainRange getPdbxDomainRange()
        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.
        Returns:
        PdbxDomainRange
      • getPdbxSequenceRange

        PdbxSequenceRange getPdbxSequenceRange()
        Data items in the PDBX_SEQUENCE_RANGE category identify the beginning and ending points of polypeptide sequence segments.
        Returns:
        PdbxSequenceRange
      • getPdbxFeatureEntry

        PdbxFeatureEntry getPdbxFeatureEntry()
        Data items in the PDBX_FEATURE_ENTRY category records information about properties pertaining to this structure entry.
        Returns:
        PdbxFeatureEntry
      • getPdbxFeatureDomain

        PdbxFeatureDomain getPdbxFeatureDomain()
        Data items in the PDBX_FEATURE_DOMAIN category records information about properties pertaining to this structure domain.
        Returns:
        PdbxFeatureDomain
      • getPdbxFeatureSequenceRange

        PdbxFeatureSequenceRange getPdbxFeatureSequenceRange()
        Data items in the PDBX_FEATURE_SEQUENCE_RANGE category records information about properties pertaining to this structure sequence_range.
        Returns:
        PdbxFeatureSequenceRange
      • getPdbxFeatureAssembly

        PdbxFeatureAssembly getPdbxFeatureAssembly()
        Data items in the PDBX_FEATURE_ASSEMBLY category records information about properties pertaining to this structural assembly.
        Returns:
        PdbxFeatureAssembly
      • getPdbxFeatureMonomer

        PdbxFeatureMonomer getPdbxFeatureMonomer()
        Data items in the PDBX_FEATURE_MONOMER category records information about properties pertaining to particular monomers in this structure.
        Returns:
        PdbxFeatureMonomer
      • getPdbxExptlPd

        PdbxExptlPd getPdbxExptlPd()
        Data items in the pdbx_exptl_pd record information about powder sample preparations.
        Returns:
        PdbxExptlPd
      • getPdbxReflnsTwin

        PdbxReflnsTwin getPdbxReflnsTwin()
        Details decribing crystallographic twinning.
        Returns:
        PdbxReflnsTwin
      • getPdbxStructInfo

        PdbxStructInfo getPdbxStructInfo()
        Special features of this structural entry.
        Returns:
        PdbxStructInfo
      • getPdbxReRefinement

        PdbxReRefinement getPdbxReRefinement()
        Describes the origin of the experimental data used in this entry.
        Returns:
        PdbxReRefinement
      • getPdbxStructAssemblyProp

        PdbxStructAssemblyProp getPdbxStructAssemblyProp()
        Properties and features of structural assemblies.
        Returns:
        PdbxStructAssemblyProp
      • getPdbxStructRefSeqFeature

        PdbxStructRefSeqFeature getPdbxStructRefSeqFeature()
        Data items in the PDBX_STRUCT_REF_SEQ_FEATURE category provide a mechanism for identifying and annotating sequence features.
        Returns:
        PdbxStructRefSeqFeature
      • getPdbxStructRefSeqFeatureProp

        PdbxStructRefSeqFeatureProp getPdbxStructRefSeqFeatureProp()
        Data items in the PDBX_STRUCT_REF_SEQ_FEATURE_PROP category provide a mechanism for identifying and annotating properties of sequence features.
        Returns:
        PdbxStructRefSeqFeatureProp
      • getPdbxStructChemCompDiagnostics

        PdbxStructChemCompDiagnostics getPdbxStructChemCompDiagnostics()
        Data items in the PDBX_STRUCT_CHEM_COMP_DIAGNOSTICS category provides structural diagnostics in chemical components instances.
        Returns:
        PdbxStructChemCompDiagnostics
      • getPdbxChemCompFeature

        PdbxChemCompFeature getPdbxChemCompFeature()
        Additional features associated with the chemical component.
        Returns:
        PdbxChemCompFeature
      • getPdbxCoordinateModel

        PdbxCoordinateModel getPdbxCoordinateModel()
        The details of the composition of the coordinate model.
        Returns:
        PdbxCoordinateModel
      • getPdbxStructChemCompFeature

        PdbxStructChemCompFeature getPdbxStructChemCompFeature()
        Data items in the PDBX_STRUCT_CHEM_COMP_FEATURE category provides structural annotations in chemical components instances.
        Returns:
        PdbxStructChemCompFeature
      • getPdbxDiffrnReflnsShell

        PdbxDiffrnReflnsShell getPdbxDiffrnReflnsShell()
        Data items in the DIFFRN_REFLNS_SHELL category record details about the reflection data set within shells of resolution.
        Returns:
        PdbxDiffrnReflnsShell
      • getPdbxBondDistanceLimits

        PdbxBondDistanceLimits getPdbxBondDistanceLimits()
        This 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.
        Returns:
        PdbxBondDistanceLimits
      • getPdbxSolnScatter

        PdbxSolnScatter getPdbxSolnScatter()
        Data items in the PDBX_SOLN_SCATTER category record details about a solution scattering experiment
        Returns:
        PdbxSolnScatter
      • getPdbxSolnScatterModel

        PdbxSolnScatterModel getPdbxSolnScatterModel()
        Data items in the PDBX_SOLN_SCATTER_MODEL category record details about the homology model fitting to the solution scatter data.
        Returns:
        PdbxSolnScatterModel
      • getPdbxChemCompDescriptor

        PdbxChemCompDescriptor getPdbxChemCompDescriptor()
        Data items in the CHEM_COMP_DESCRIPTOR category provide string descriptors of component chemical structure.
        Returns:
        PdbxChemCompDescriptor
      • getPdbxChemCompIdentifier

        PdbxChemCompIdentifier getPdbxChemCompIdentifier()
        Data items in the CHEM_COMP_IDENTIFIER category provide identifiers for chemical components.
        Returns:
        PdbxChemCompIdentifier
      • getPdbxChemCompImport

        PdbxChemCompImport getPdbxChemCompImport()
        Data 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.
        Returns:
        PdbxChemCompImport
      • getPdbxChemCompAtomEdit

        PdbxChemCompAtomEdit getPdbxChemCompAtomEdit()
        Data items in the PDBX_CHEM_COMP_ATOM_EDIT category provide atom level editing instructions to be applied to imported chemical components.
        Returns:
        PdbxChemCompAtomEdit
      • getPdbxChemCompBondEdit

        PdbxChemCompBondEdit getPdbxChemCompBondEdit()
        Data items in the PDBX_CHEM_COMP_BOND_EDIT category provide bond level editing instructions to be applied to imported chemical components.
        Returns:
        PdbxChemCompBondEdit
      • getPdbxChemCompAudit

        PdbxChemCompAudit getPdbxChemCompAudit()
        Data items in the PDBX_CHEM_COMP_AUDIT category records the status and tracking information for this component.
        Returns:
        PdbxChemCompAudit
      • getPdbxValidateCloseContact

        PdbxValidateCloseContact getPdbxValidateCloseContact()
        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. 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.
        Returns:
        PdbxValidateCloseContact
      • getPdbxValidateSymmContact

        PdbxValidateSymmContact getPdbxValidateSymmContact()
        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. 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.
        Returns:
        PdbxValidateSymmContact
      • getPdbxValidateRmsdBond

        PdbxValidateRmsdBond getPdbxValidateRmsdBond()
        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.
        Returns:
        PdbxValidateRmsdBond
      • getPdbxValidateRmsdAngle

        PdbxValidateRmsdAngle getPdbxValidateRmsdAngle()
        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 value
        Returns:
        PdbxValidateRmsdAngle
      • getPdbxValidateTorsion

        PdbxValidateTorsion getPdbxValidateTorsion()
        Data items in the PDBX_VALIDATE_TORSION category list the residues with torsion angles outside the expected ramachandran regions
        Returns:
        PdbxValidateTorsion
      • getPdbxValidatePeptideOmega

        PdbxValidatePeptideOmega getPdbxValidatePeptideOmega()
        Data 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.
        Returns:
        PdbxValidatePeptideOmega
      • getPdbxValidateChiral

        PdbxValidateChiral getPdbxValidateChiral()
        Data 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
        Returns:
        PdbxValidateChiral
      • getPdbxValidatePlanes

        PdbxValidatePlanes getPdbxValidatePlanes()
        Data items in the PDBX_VALIDATE_PLANES category list the residues that contain unexpected deviations from planes centers.
        Returns:
        PdbxValidatePlanes
      • getPdbxValidatePlanesAtom

        PdbxValidatePlanesAtom getPdbxValidatePlanesAtom()
        Data items in the PDBX_VALIDATE_PLANES_ATOM category list the residues that contain unexpected deviations from planes centers.
        Returns:
        PdbxValidatePlanesAtom
      • getPdbxValidateMainChainPlane

        PdbxValidateMainChainPlane getPdbxValidateMainChainPlane()
        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 torsion
        Returns:
        PdbxValidateMainChainPlane
      • getPdbxStructConnAngle

        PdbxStructConnAngle getPdbxStructConnAngle()
        Data items in the PDBX_STRUCT_CONN_ANGLE category record the angles in connections between portions of the structure.
        Returns:
        PdbxStructConnAngle
      • getPdbxUnobsOrZeroOccResidues

        PdbxUnobsOrZeroOccResidues getPdbxUnobsOrZeroOccResidues()
        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.
        Returns:
        PdbxUnobsOrZeroOccResidues
      • getPdbxUnobsOrZeroOccAtoms

        PdbxUnobsOrZeroOccAtoms getPdbxUnobsOrZeroOccAtoms()
        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/
        Returns:
        PdbxUnobsOrZeroOccAtoms
      • getPdbxEntryDetails

        PdbxEntryDetails getPdbxEntryDetails()
        Data items in the PDBX_ENTRY_DETAILS category provide additional details about this entry.
        Returns:
        PdbxEntryDetails
      • getPdbxStructModResidue

        PdbxStructModResidue getPdbxStructModResidue()
        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.
        Returns:
        PdbxStructModResidue
      • getPdbxStructRefSeqInsertion

        PdbxStructRefSeqInsertion getPdbxStructRefSeqInsertion()
        Data items in the PDBX_STRUCT_REF_SEQ_INSERTION category annotate insertions in the sequence of the entity described in the referenced database entry.
        Returns:
        PdbxStructRefSeqInsertion
      • getPdbxStructRefSeqDeletion

        PdbxStructRefSeqDeletion getPdbxStructRefSeqDeletion()
        Data items in the PDBX_STRUCT_REF_SEQ_INSERTION category annotate deletions in the sequence of the entity described in the referenced database entry.
        Returns:
        PdbxStructRefSeqDeletion
      • getPdbxRemediationAtomSiteMapping

        PdbxRemediationAtomSiteMapping getPdbxRemediationAtomSiteMapping()
        Data 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.
        Returns:
        PdbxRemediationAtomSiteMapping
      • getPdbxValidatePolymerLinkage

        PdbxValidatePolymerLinkage getPdbxValidatePolymerLinkage()
        Data items in the PDBX_VALIDATE_POLYMER_LINKAGE category list the polymer linkages within the entry that are outside of typlical covalent distances.
        Returns:
        PdbxValidatePolymerLinkage
      • getPdbxHelicalSymmetry

        PdbxHelicalSymmetry getPdbxHelicalSymmetry()
        Data items in the PDBX_HELICAL_SYMMETRY category record details about the helical symmetry group associated with this entry.
        Returns:
        PdbxHelicalSymmetry
      • getPdbxPointSymmetry

        PdbxPointSymmetry getPdbxPointSymmetry()
        Data items in the PDBX_POINT_SYMMETRY category record details about the point symmetry group associated with this entry.
        Returns:
        PdbxPointSymmetry
      • getPdbxStructEntityInst

        PdbxStructEntityInst getPdbxStructEntityInst()
        Data 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.
        Returns:
        PdbxStructEntityInst
      • getPdbxStructOperList

        PdbxStructOperList getPdbxStructOperList()
        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.
        Returns:
        PdbxStructOperList
      • getPdbxStructAssembly

        PdbxStructAssembly getPdbxStructAssembly()
        Data items in the PDBX_STRUCT_ASSEMBLY category record details about the structural elements that form macromolecular assemblies.
        Returns:
        PdbxStructAssembly
      • getPdbxStructAssemblyGen

        PdbxStructAssemblyGen getPdbxStructAssemblyGen()
        Data 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.
        Returns:
        PdbxStructAssemblyGen
      • getPdbxStructAsymGen

        PdbxStructAsymGen getPdbxStructAsymGen()
        Data 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.
        Returns:
        PdbxStructAsymGen
      • getPdbxStructMsymGen

        PdbxStructMsymGen getPdbxStructMsymGen()
        Data 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.
        Returns:
        PdbxStructMsymGen
      • getPdbxStructLegacyOperList

        PdbxStructLegacyOperList getPdbxStructLegacyOperList()
        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. This category provides a container for matrices used to construct icosahedral assemblies in legacy entries.
        Returns:
        PdbxStructLegacyOperList
      • getPdbxChemCompAtomFeature

        PdbxChemCompAtomFeature getPdbxChemCompAtomFeature()
        Data items in the PDBX_CHEM_COMP_ATOM_FEATURE category provide a selected list of atom level features for the chemical component.
        Returns:
        PdbxChemCompAtomFeature
      • getPdbxReferenceMoleculeFamily

        PdbxReferenceMoleculeFamily getPdbxReferenceMoleculeFamily()
        Data items in the PDBX_REFERENCE_MOLECULE_FAMILY category identify entity families.
        Returns:
        PdbxReferenceMoleculeFamily
      • getPdbxReferenceMoleculeList

        PdbxReferenceMoleculeList getPdbxReferenceMoleculeList()
        Data items in the PDBX_REFERENCE_MOLECULE_LIST category record reference information about small polymer molecules.
        Returns:
        PdbxReferenceMoleculeList
      • getPdbxReferenceMolecule

        PdbxReferenceMolecule getPdbxReferenceMolecule()
        Data items in the PDBX_REFERENCE_MOLECULE category record reference information about small polymer molecules.
        Returns:
        PdbxReferenceMolecule
      • getPdbxReferenceEntityList

        PdbxReferenceEntityList getPdbxReferenceEntityList()
        Data items in the PDBX_REFERENCE_ENTITY_LIST category record the list of entities within each reference molecule.
        Returns:
        PdbxReferenceEntityList
      • getPdbxReferenceEntityNonpoly

        PdbxReferenceEntityNonpoly getPdbxReferenceEntityNonpoly()
        Data items in the PDBX_REFERENCE_ENTITY_NONPOLY category record the list of entities within each reference molecule.
        Returns:
        PdbxReferenceEntityNonpoly
      • getPdbxReferenceEntityLink

        PdbxReferenceEntityLink getPdbxReferenceEntityLink()
        Data items in the PDBX_REFERENCE_ENTITY_LINK category give details about the linkages between entities within reference molecules.
        Returns:
        PdbxReferenceEntityLink
      • getPdbxReferenceEntityPolyLink

        PdbxReferenceEntityPolyLink getPdbxReferenceEntityPolyLink()
        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.
        Returns:
        PdbxReferenceEntityPolyLink
      • getPdbxReferenceEntityPoly

        PdbxReferenceEntityPoly getPdbxReferenceEntityPoly()
        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.
        Returns:
        PdbxReferenceEntityPoly
      • getPdbxReferenceEntityPolySeq

        PdbxReferenceEntityPolySeq getPdbxReferenceEntityPolySeq()
        Data items in the PDBX_REFERENCE_ENTITY_POLY_SEQ category specify the sequence of monomers in a polymer.
        Returns:
        PdbxReferenceEntityPolySeq
      • getPdbxReferenceEntitySequence

        PdbxReferenceEntitySequence getPdbxReferenceEntitySequence()
        Additional features associated with the reference entity.
        Returns:
        PdbxReferenceEntitySequence
      • getPdbxReferenceEntitySrcNat

        PdbxReferenceEntitySrcNat getPdbxReferenceEntitySrcNat()
        Data items in the PDBX_REFERENCE_ENTITY_SRC_NAT category record details of the source from which the entity was obtained.
        Returns:
        PdbxReferenceEntitySrcNat
      • getPdbxReferenceMoleculeDetails

        PdbxReferenceMoleculeDetails getPdbxReferenceMoleculeDetails()
        Data items in the PDBX_REFERENCE_MOLECULE_DETAILS category records textual details about small polymer molecules.
        Returns:
        PdbxReferenceMoleculeDetails
      • getPdbxReferenceMoleculeSynonyms

        PdbxReferenceMoleculeSynonyms getPdbxReferenceMoleculeSynonyms()
        Data items in the PDBX_REFERENCE_MOLECULE_SYNONYMS category records synonym names for reference entities.
        Returns:
        PdbxReferenceMoleculeSynonyms
      • getPdbxReferenceEntitySubcomponents

        PdbxReferenceEntitySubcomponents getPdbxReferenceEntitySubcomponents()
        Data items in the PDBX_REFERENCE_ENTITY_SUBCOMPONENTS category records subcomponent sequence from which this entity could be built.
        Returns:
        PdbxReferenceEntitySubcomponents
      • getPdbxReferenceMoleculeAnnotation

        PdbxReferenceMoleculeAnnotation getPdbxReferenceMoleculeAnnotation()
        Data items in the PDBX_REFERENCE_MOLECULE_ANNOTATION category specify additional annotation relevant to the molecular entities.
        Returns:
        PdbxReferenceMoleculeAnnotation
      • getPdbxReferenceMoleculeFeatures

        PdbxReferenceMoleculeFeatures getPdbxReferenceMoleculeFeatures()
        Additional features associated with the reference entity.
        Returns:
        PdbxReferenceMoleculeFeatures
      • getPdbxReferenceMoleculeRelatedStructures

        PdbxReferenceMoleculeRelatedStructures getPdbxReferenceMoleculeRelatedStructures()
        Data items in the PDBX_REFERENCE_MOLECULE_RELATED_STRUCTURES category record details of the structural examples in related databases for this entity.
        Returns:
        PdbxReferenceMoleculeRelatedStructures
      • getPdbxStructGroupList

        PdbxStructGroupList getPdbxStructGroupList()
        Data items in the PDBX_STRUCT_GROUP_LIST define groups of related components or atoms.
        Returns:
        PdbxStructGroupList
      • getPdbxStructGroupComponents

        PdbxStructGroupComponents getPdbxStructGroupComponents()
        Data 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.
        Returns:
        PdbxStructGroupComponents
      • getPdbxStructGroupComponentRange

        PdbxStructGroupComponentRange getPdbxStructGroupComponentRange()
        Data items in the PDBX_STRUCT_GROUP_COMPONENT_RANGE category define a structural group as a continuous span chemical components.
        Returns:
        PdbxStructGroupComponentRange
      • getPdbxPrdAudit

        PdbxPrdAudit getPdbxPrdAudit()
        Data items in the PDBX_PRD_AUDIT category records the status and tracking information for this molecule.
        Returns:
        PdbxPrdAudit
      • getPdbxFamilyPrdAudit

        PdbxFamilyPrdAudit getPdbxFamilyPrdAudit()
        Data items in the PDBX_FAMILY_PRD_AUDIT category records the status and tracking information for this family.
        Returns:
        PdbxFamilyPrdAudit
      • getPdbxMolecule

        PdbxMolecule getPdbxMolecule()
        Data items in the PDBX_MOLECULE category identify reference molecules within a PDB entry.
        Returns:
        PdbxMolecule
      • getPdbxMoleculeFeatures

        PdbxMoleculeFeatures getPdbxMoleculeFeatures()
        Data items in the PDBX_MOLECULE_FEATURES category record features of molecules within a PDB entry.
        Returns:
        PdbxMoleculeFeatures
      • getPdbxFamilyGroupIndex

        PdbxFamilyGroupIndex getPdbxFamilyGroupIndex()
        Data items in the PDBX_FAMILY_GROUP_INDEX category record the family membership in family groups.
        Returns:
        PdbxFamilyGroupIndex
      • getPdbxDistantSolventAtoms

        PdbxDistantSolventAtoms getPdbxDistantSolventAtoms()
        Data items in the PDBX_DISTANT_SOLVENT_ATOMS category list the solvent atoms remote from any macromolecule.
        Returns:
        PdbxDistantSolventAtoms
      • getPdbxStructSpecialSymmetry

        PdbxStructSpecialSymmetry getPdbxStructSpecialSymmetry()
        Data items in the PDBX_STRUCT_SPECIAL_SYMMETRY category list the molecular components that lie on special symmetry positions.
        Returns:
        PdbxStructSpecialSymmetry
      • getPdbxReferencePublicationList

        PdbxReferencePublicationList getPdbxReferencePublicationList()
        Data items in the PDBX_REFERENCE_PUBLICATION_LIST hold reference information related to PDB citation data.
        Returns:
        PdbxReferencePublicationList
      • getPdbxNmrAssignedChemShiftList

        PdbxNmrAssignedChemShiftList getPdbxNmrAssignedChemShiftList()
        Items in the assigned_chem_shift_list category provide information about a list of reported assigned chemical shift values.
        Returns:
        PdbxNmrAssignedChemShiftList
      • getPdbxNmrChemShiftExperiment

        PdbxNmrChemShiftExperiment getPdbxNmrChemShiftExperiment()
        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.
        Returns:
        PdbxNmrChemShiftExperiment
      • getPdbxNmrChemShiftRef

        PdbxNmrChemShiftRef getPdbxNmrChemShiftRef()
        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.
        Returns:
        PdbxNmrChemShiftRef
      • getPdbxNmrChemShiftReference

        PdbxNmrChemShiftReference getPdbxNmrChemShiftReference()
        Items in the chem_shift_reference category define a set of chemical shift referencing parameters.
        Returns:
        PdbxNmrChemShiftReference
      • getPdbxNmrChemShiftSoftware

        PdbxNmrChemShiftSoftware getPdbxNmrChemShiftSoftware()
        Items in the chem_shift_software category provide pointers to the software category and methods category.
        Returns:
        PdbxNmrChemShiftSoftware
      • getPdbxNmrConstraintFile

        PdbxNmrConstraintFile getPdbxNmrConstraintFile()
        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.
        Returns:
        PdbxNmrConstraintFile
      • getPdbxNmrSoftwareTask

        PdbxNmrSoftwareTask getPdbxNmrSoftwareTask()
        Items in the pdbx_nmr_software_task category provide information about software workflow in the NMR experiment.
        Returns:
        PdbxNmrSoftwareTask
      • getPdbxNmrSpectralDim

        PdbxNmrSpectralDim getPdbxNmrSpectralDim()
        Items in the spectral_dim category describe the parameters of each dimension in the NMR experiment used to generate the spectral peak list.
        Returns:
        PdbxNmrSpectralDim
      • getPdbxNmrSpectralPeakList

        PdbxNmrSpectralPeakList getPdbxNmrSpectralPeakList()
        Items in the pdbx_nmr_spectral_peak_list category provide information about a list of reported spectral peak characteristic values.
        Returns:
        PdbxNmrSpectralPeakList
      • getPdbxNmrSpectralPeakSoftware

        PdbxNmrSpectralPeakSoftware getPdbxNmrSpectralPeakSoftware()
        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.
        Returns:
        PdbxNmrSpectralPeakSoftware
      • getPdbxNmrSystematicChemShiftOffset

        PdbxNmrSystematicChemShiftOffset getPdbxNmrSystematicChemShiftOffset()
        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.
        Returns:
        PdbxNmrSystematicChemShiftOffset
      • getPdbxNmrUpload

        PdbxNmrUpload getPdbxNmrUpload()
        Items in the pdbx_nmr_upload category provide information about the data files uploaded by a depositor using the deposition system.
        Returns:
        PdbxNmrUpload
      • getPdbxAuditSupport

        PdbxAuditSupport getPdbxAuditSupport()
        Data items in the PDBX_AUDIT_SUPPORT category record details about funding support for the entry.
        Returns:
        PdbxAuditSupport
      • getPdbxChemCompSubcomponentStructConn

        PdbxChemCompSubcomponentStructConn getPdbxChemCompSubcomponentStructConn()
        Data items in the pdbx_chem_comp_subcomponent_struct_conn list the chemical interactions among the subcomponents in the chemical component.
        Returns:
        PdbxChemCompSubcomponentStructConn
      • getPdbxChemCompSubcomponentEntityList

        PdbxChemCompSubcomponentEntityList getPdbxChemCompSubcomponentEntityList()
        Data items in the pdbx_chem_comp_subcomponent_entity_list category list the constituent chemical entities and entity features in this chemical component.
        Returns:
        PdbxChemCompSubcomponentEntityList
      • getEntitySrcNat

        EntitySrcNat getEntitySrcNat()
        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.
        Returns:
        EntitySrcNat
      • getEntitySrcGen

        EntitySrcGen getEntitySrcGen()
        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. 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).
        Returns:
        EntitySrcGen
      • getPdbxEntitySrcSyn

        PdbxEntitySrcSyn getPdbxEntitySrcSyn()
        The data items in category PDBX_ENTITY_SRC_SYN record the source details about chemically synthesized molecules.
        Returns:
        PdbxEntitySrcSyn
      • getPdbxEntityPolyCompLinkList

        PdbxEntityPolyCompLinkList getPdbxEntityPolyCompLinkList()
        Data items in the PDBX_ENTITY_POLY_COMP_LINK_LIST category enumerate the the linkages between components within the polymer entity.
        Returns:
        PdbxEntityPolyCompLinkList
      • getPdbxLinkedEntity

        PdbxLinkedEntity getPdbxLinkedEntity()
        Data items in the PDBX_LINKED_ENTITY category record information about molecules composed of linked entities.
        Returns:
        PdbxLinkedEntity
      • getPdbxLinkedEntityInstanceList

        PdbxLinkedEntityInstanceList getPdbxLinkedEntityInstanceList()
        Data items in the PDBX_LINKED_ENTITY_INSTANCE_LIST category identify instance molecules represented as linked entities within an entry.
        Returns:
        PdbxLinkedEntityInstanceList
      • getPdbxLinkedEntityList

        PdbxLinkedEntityList getPdbxLinkedEntityList()
        Data items in the PDBX_LINKED_ENTITY_LIST category record the list of entity constituents for this molecule.
        Returns:
        PdbxLinkedEntityList
      • getPdbxLinkedEntityLinkList

        PdbxLinkedEntityLinkList getPdbxLinkedEntityLinkList()
        Data items in the PDBX_LINKED_ENTITY_LINK_LIST category give details about the linkages with molecules represented as linked entities.
        Returns:
        PdbxLinkedEntityLinkList
      • getPdbxEntityDescriptor

        PdbxEntityDescriptor getPdbxEntityDescriptor()
        Data items in the PDBX_ENTITY_DESCRIPTOR category provide string descriptors of entity chemical structure.
        Returns:
        PdbxEntityDescriptor
      • getPdbxReferenceLinkedEntity

        PdbxReferenceLinkedEntity getPdbxReferenceLinkedEntity()
        Data items in the pdbx_reference_linked_entity category describe common observed interaction patterns within linked entities.
        Returns:
        PdbxReferenceLinkedEntity
      • getPdbxReferenceLinkedEntityCompList

        PdbxReferenceLinkedEntityCompList getPdbxReferenceLinkedEntityCompList()
        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.
        Returns:
        PdbxReferenceLinkedEntityCompList
      • getPdbxReferenceLinkedEntityCompLink

        PdbxReferenceLinkedEntityCompLink getPdbxReferenceLinkedEntityCompLink()
        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.
        Returns:
        PdbxReferenceLinkedEntityCompLink
      • getPdbxReferenceLinkedEntityLink

        PdbxReferenceLinkedEntityLink getPdbxReferenceLinkedEntityLink()
        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.
        Returns:
        PdbxReferenceLinkedEntityLink
      • getPdbxRelatedExpDataSet

        PdbxRelatedExpDataSet getPdbxRelatedExpDataSet()
        Data items in the PDBX_RELATED_DATA_SET category record references to experimental data sets related to the entry.
        Returns:
        PdbxRelatedExpDataSet
      • getPdbxDatabaseStatusHistory

        PdbxDatabaseStatusHistory getPdbxDatabaseStatusHistory()
        The pdbx_database_status_history category records the time evolution of entry processing status.
        Returns:
        PdbxDatabaseStatusHistory
      • getEmAssembly

        EmAssembly getEmAssembly()
        Data items in the EM_ASSEMBLY category record details about the imaged EM sample.
        Returns:
        EmAssembly
      • getEmEntityAssembly

        EmEntityAssembly getEmEntityAssembly()
        Data items in the EM_ENTITY_ASSEMBLY category record details about each component of the complex.
        Returns:
        EmEntityAssembly
      • getEmVirusEntity

        EmVirusEntity getEmVirusEntity()
        Data items in the EM_VIRUS_ENTITY category record details of the icosahedral virus.
        Returns:
        EmVirusEntity
      • getEmSamplePreparation

        EmSamplePreparation getEmSamplePreparation()
        Data items in the EM_SAMPLE_PREPARATION category record details of sample conditions prior to and upon loading onto grid support.
        Returns:
        EmSamplePreparation
      • getEmSampleSupport

        EmSampleSupport getEmSampleSupport()
        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 applied
        Returns:
        EmSampleSupport
      • getEmBuffer

        EmBuffer getEmBuffer()
        Data items in the BUFFER category record details of the sample buffer.
        Returns:
        EmBuffer
      • getEmVitrification

        EmVitrification getEmVitrification()
        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 microscope
        Returns:
        EmVitrification
      • getEmImaging

        EmImaging getEmImaging()
        Data items in the EM_IMAGING category record details about the parameters used in imaging the sample in the electron microscope.
        Returns:
        EmImaging
      • getEmDetector

        EmDetector getEmDetector()
        Data items in the EM_DETECTOR category record details of the image detector type.
        Returns:
        EmDetector
      • getEmImageScans

        EmImageScans getEmImageScans()
        Data items in the EM_IMAGE_SCANS category record details of the image scanning device (microdensitometer) and parameters for digitization of the image.
        Returns:
        EmImageScans
      • getEm2dProjectionSelection

        Em2dProjectionSelection getEm2dProjectionSelection()
        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.
        Returns:
        Em2dProjectionSelection
      • getEm3dReconstruction

        Em3dReconstruction getEm3dReconstruction()
        Data items in the EM_3D_RECONSTRUCTION category record details of the 3D reconstruction procedure from 2D projections.
        Returns:
        Em3dReconstruction
      • getEm3dFitting

        Em3dFitting getEm3dFitting()
        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 file
        Returns:
        Em3dFitting
      • getEm3dFittingList

        Em3dFittingList getEm3dFittingList()
        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 file
        Returns:
        Em3dFittingList
      • getEmHelicalEntity

        EmHelicalEntity getEmHelicalEntity()
        Data items in the EM_HELICAL_ENTITY category record details for a helical or filament type of assembly component.
        Returns:
        EmHelicalEntity
      • getEmExperiment

        EmExperiment getEmExperiment()
        Data items in the EM_EXPERIMENT category provide high-level classification of the EM experiment.
        Returns:
        EmExperiment
      • getEmSingleParticleEntity

        EmSingleParticleEntity getEmSingleParticleEntity()
        Data items in the EM_SINGLE_PARTICLE_ENTITY category provide the details of the symmetry for a single particle entity type.
        Returns:
        EmSingleParticleEntity
      • getEmAdmin

        EmAdmin getEmAdmin()
        Administration-related data items
        Returns:
        EmAdmin
      • getEmAuthorList

        EmAuthorList getEmAuthorList()
        Category to collect the authors of this entry
        Returns:
        EmAuthorList
      • getEmDbReference

        EmDbReference getEmDbReference()
        Category holds links to raw data sources for the entry, e.g., held by a remote server.
        Returns:
        EmDbReference
      • getEmDbReferenceAuxiliary

        EmDbReferenceAuxiliary getEmDbReferenceAuxiliary()
        Category holds links to raw data sources for the entry, e.g., held by a remote server.
        Returns:
        EmDbReferenceAuxiliary
      • getEmDepui

        EmDepui getEmDepui()
        Some internal items to power the deposition interface
        Returns:
        EmDepui
      • getEmObsolete

        EmObsolete getEmObsolete()
        List of EMD entries made obsolete by this entry.
        Returns:
        EmObsolete
      • getEmSupersede

        EmSupersede getEmSupersede()
        List of newer entries that replace this entry.
        Returns:
        EmSupersede
      • getEmEntityAssemblyMolwt

        EmEntityAssemblyMolwt getEmEntityAssemblyMolwt()
        Data items in this category record details about the molecular weight of an assembly component of the sample.
        Returns:
        EmEntityAssemblyMolwt
      • getEmEntityAssemblyNaturalsource

        EmEntityAssemblyNaturalsource getEmEntityAssemblyNaturalsource()
        Data items in this category record taxonomic details about the natural source for EM assemblies and assembly components.
        Returns:
        EmEntityAssemblyNaturalsource
      • getEmEntityAssemblyRecombinant

        EmEntityAssemblyRecombinant getEmEntityAssemblyRecombinant()
        Data items in this category record details about recombinant expression of the assembly or assembly component.
        Returns:
        EmEntityAssemblyRecombinant
      • getEmVirusNaturalHost

        EmVirusNaturalHost getEmVirusNaturalHost()
        Data items in this category record details of a virus entity.
        Returns:
        EmVirusNaturalHost
      • getEmVirusShell

        EmVirusShell getEmVirusShell()
        Data items in the EMD_VIRUS_SHELL category record details of the viral shell number, shell diameter, and icosahedral triangulation number.
        Returns:
        EmVirusShell
      • getEmSpecimen

        EmSpecimen getEmSpecimen()
        Data items in the EMD_SPECIMEN category record details about specimens prepared for imaging by electron microscopy.
        Returns:
        EmSpecimen
      • getEmEmbedding

        EmEmbedding getEmEmbedding()
        Sugar embedding category
        Returns:
        EmEmbedding
      • getEmFiducialMarkers

        EmFiducialMarkers getEmFiducialMarkers()
        Description of fiducial markers.
        Returns:
        EmFiducialMarkers
      • getEmFocusedIonBeam

        EmFocusedIonBeam getEmFocusedIonBeam()
        Description of sectioning by focused_ion_beam
        Returns:
        EmFocusedIonBeam
      • getEmGridPretreatment

        EmGridPretreatment getEmGridPretreatment()
        Data items describing glow discharge pretreatment for an EM grid
        Returns:
        EmGridPretreatment
      • getEmUltramicrotomy

        EmUltramicrotomy getEmUltramicrotomy()
        Description of sectioning by ultramicrotomy
        Returns:
        EmUltramicrotomy
      • getEmHighPressureFreezing

        EmHighPressureFreezing getEmHighPressureFreezing()
        Description of high pressure freezing
        Returns:
        EmHighPressureFreezing
      • getEmShadowing

        EmShadowing getEmShadowing()
        Data items related to shadowing of an EM specimen
        Returns:
        EmShadowing
      • getEmTomographySpecimen

        EmTomographySpecimen getEmTomographySpecimen()
        Description specimen preparation for imaging using tomography.
        Returns:
        EmTomographySpecimen
      • getEmCrystalFormation

        EmCrystalFormation getEmCrystalFormation()
        Description of growth of a 2D, 3D, or helical crystal array.
        Returns:
        EmCrystalFormation
      • getEmStaining

        EmStaining getEmStaining()
        Staining category
        Returns:
        EmStaining
      • getEmSupportFilm

        EmSupportFilm getEmSupportFilm()
        Data items to describe films supporting the specimen
        Returns:
        EmSupportFilm
      • getEmBufferComponent

        EmBufferComponent getEmBufferComponent()
        Buffer category
        Returns:
        EmBufferComponent
      • getEmDiffraction

        EmDiffraction getEmDiffraction()
        Microscopy parameters relevant only for crystallography
        Returns:
        EmDiffraction
      • getEmDiffractionShell

        EmDiffractionShell getEmDiffractionShell()
        Statistical parameters for electron diffraction measurements within a resolution shell
        Returns:
        EmDiffractionShell
      • getEmDiffractionStats

        EmDiffractionStats getEmDiffractionStats()
        Statistical parameters for electron diffraction measurements
        Returns:
        EmDiffractionStats
      • getEmTomography

        EmTomography getEmTomography()
        Microscopy parameters only relevant for tomography
        Returns:
        EmTomography
      • getEmImageRecording

        EmImageRecording getEmImageRecording()
        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.
        Returns:
        EmImageRecording
      • getEmImagingOptics

        EmImagingOptics getEmImagingOptics()
        Description of a few specialist optics apparatus
        Returns:
        EmImagingOptics
      • getEmFinalClassification

        EmFinalClassification getEmFinalClassification()
        Information about the final image classification
        Returns:
        EmFinalClassification
      • getEmStartModel

        EmStartModel getEmStartModel()
        The startup model employed to begin refinement of the parameters for a 3DEM reconstruction
        Returns:
        EmStartModel
      • getEmSoftware

        EmSoftware getEmSoftware()
        Description 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.
        Returns:
        EmSoftware
      • getEmEulerAngleAssignment

        EmEulerAngleAssignment getEmEulerAngleAssignment()
        Category to describe the euler angle assignement
        Returns:
        EmEulerAngleAssignment
      • getEmCtfCorrection

        EmCtfCorrection getEmCtfCorrection()
        Description of the Contrast Transfer Function (CTF) correction
        Returns:
        EmCtfCorrection
      • getEmVolumeSelection

        EmVolumeSelection getEmVolumeSelection()
        Volume selection in image processing
        Returns:
        EmVolumeSelection
      • getEm3dCrystalEntity

        Em3dCrystalEntity getEm3dCrystalEntity()
        Data items in the EM_SYMMETRY_3DX category record 3D crystal symmetry parameters utilized in 3DEM reconstruction averaging.
        Returns:
        Em3dCrystalEntity
      • getEm2dCrystalEntity

        Em2dCrystalEntity getEm2dCrystalEntity()
        Data items in the EM_SYMMETRY_2DX category record 2D crystal symmetry parameters utilized in a 3DEM reconstruction.
        Returns:
        Em2dCrystalEntity
      • getEmImageProcessing

        EmImageProcessing getEmImageProcessing()
        Data items in the EM_IMAGE_PROCESSING category record details of the EM image processing procedure.
        Returns:
        EmImageProcessing
      • getEmParticleSelection

        EmParticleSelection getEmParticleSelection()
        Data items in this category record details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs.
        Returns:
        EmParticleSelection
      • getEmMap

        EmMap getEmMap()
        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. 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.
        Returns:
        EmMap
      • getEmFscCurve

        EmFscCurve getEmFscCurve()
        Data items in the EMD_VALIDATION_FSC_CURVE category record details of the Fourier Shell Correlation (FSC) curve file.
        Returns:
        EmFscCurve
      • getEmInterpretFigure

        EmInterpretFigure getEmInterpretFigure()
        Listing of all layer line files associated with the EM entry
        Returns:
        EmInterpretFigure
      • getEmLayerLines

        EmLayerLines getEmLayerLines()
        Listing of all layer line files associated with the EM entry
        Returns:
        EmLayerLines
      • getEmStructureFactors

        EmStructureFactors getEmStructureFactors()
        Listing of all structure factor files associated with the EM entry
        Returns:
        EmStructureFactors
      • getEmDepositorInfo

        EmDepositorInfo getEmDepositorInfo()
        Data items in the EM_DEPOSITOR INFO category record parameters for EM depositions that are provided by the depositor
        Returns:
        EmDepositorInfo
      • getEmMapDepositorInfo

        EmMapDepositorInfo getEmMapDepositorInfo()
        Data items in the EM_MAP_DEPOSITOR INFO category record map parameters that are provided by the depositor
        Returns:
        EmMapDepositorInfo
      • getEmMaskDepositorInfo

        EmMaskDepositorInfo getEmMaskDepositorInfo()
        Data items in the EM_MASK_DEPOSITOR_INFO category record mask parameters that are provided by the depositor
        Returns:
        EmMaskDepositorInfo
      • getEmFigureDepositorInfo

        EmFigureDepositorInfo getEmFigureDepositorInfo()
        Listing of image files (figures) associated with an EMDB entry
        Returns:
        EmFigureDepositorInfo
      • getEmLayerLinesDepositorInfo

        EmLayerLinesDepositorInfo getEmLayerLinesDepositorInfo()
        Listing of layer line files associated with the EM entry
        Returns:
        EmLayerLinesDepositorInfo
      • getEmStructureFactorsDepositorInfo

        EmStructureFactorsDepositorInfo getEmStructureFactorsDepositorInfo()
        Structure factor files associated with the EM entry
        Returns:
        EmStructureFactorsDepositorInfo
      • getPdbxSeqMapDepositorInfo

        PdbxSeqMapDepositorInfo getPdbxSeqMapDepositorInfo()
        Data items in the PDBX_SEQ_MAP_DEPOSITOR_INFO record the details about the mapping sample and coordinate sequences.
        Returns:
        PdbxSeqMapDepositorInfo
      • getPdbxChemCompDepositorInfo

        PdbxChemCompDepositorInfo getPdbxChemCompDepositorInfo()
        Data items in the PDBX_CHEM_COMP_DEPOSITOR_INFO category record additional details provided by depositors about deposited chemical components.
        Returns:
        PdbxChemCompDepositorInfo
      • getPdbxStructRefSeqDepositorInfo

        PdbxStructRefSeqDepositorInfo getPdbxStructRefSeqDepositorInfo()
        Data items in the PDBX_STRUCT_REF_SEQ_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory STRUCT_REF_SEQ.
        Returns:
        PdbxStructRefSeqDepositorInfo
      • getPdbxStructRefSeqDifDepositorInfo

        PdbxStructRefSeqDifDepositorInfo getPdbxStructRefSeqDifDepositorInfo()
        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.
        Returns:
        PdbxStructRefSeqDifDepositorInfo
      • getPdbxStructAssemblyPropDepositorInfo

        PdbxStructAssemblyPropDepositorInfo getPdbxStructAssemblyPropDepositorInfo()
        Data items in the PDBX_STRUCT_ASSEMBLY_PROP_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_ASSEMBLY_PROP.
        Returns:
        PdbxStructAssemblyPropDepositorInfo
      • getPdbxStructAssemblyDepositorInfo

        PdbxStructAssemblyDepositorInfo getPdbxStructAssemblyDepositorInfo()
        Data items in the PDBX_STRUCT_ASSEMBLY_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_ASSEMBLY.
        Returns:
        PdbxStructAssemblyDepositorInfo
      • getPdbxStructAssemblyGenDepositorInfo

        PdbxStructAssemblyGenDepositorInfo getPdbxStructAssemblyGenDepositorInfo()
        Data items in the PDBX_STRUCT_ASSEMBLY_GEN_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_ASSEMBLY_GEN.
        Returns:
        PdbxStructAssemblyGenDepositorInfo
      • getPdbxStructOperListDepositorInfo

        PdbxStructOperListDepositorInfo getPdbxStructOperListDepositorInfo()
        Data items in the PDBX_STRUCT_OPER_LIST_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_OPER_LIST.
        Returns:
        PdbxStructOperListDepositorInfo
      • getPdbxPointSymmetryDepositorInfo

        PdbxPointSymmetryDepositorInfo getPdbxPointSymmetryDepositorInfo()
        Data items in the PDBX_POINT_SYMMETRY_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_POINT_SYMMETRY.
        Returns:
        PdbxPointSymmetryDepositorInfo
      • getPdbxHelicalSymmetryDepositorInfo

        PdbxHelicalSymmetryDepositorInfo getPdbxHelicalSymmetryDepositorInfo()
        Data items in the PDBX_HELICAL_SYMMETRY_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_HELICAL_SYMMETRY.
        Returns:
        PdbxHelicalSymmetryDepositorInfo
      • getPdbxStructAssemblyAuthEvidenceDepositorInfo

        PdbxStructAssemblyAuthEvidenceDepositorInfo getPdbxStructAssemblyAuthEvidenceDepositorInfo()
        Provides author supplied evidentiary support for assemblies in pdbx_struct_assembly.
        Returns:
        PdbxStructAssemblyAuthEvidenceDepositorInfo
      • getPdbxSolventAtomSiteMapping

        PdbxSolventAtomSiteMapping getPdbxSolventAtomSiteMapping()
        Data items in the PDBX_SOLVENT_ATOM_SITE_MAPPING category records mapping information between solvent atoms before and after symmetry repositioning.
        Returns:
        PdbxSolventAtomSiteMapping
      • getPdbxMoleculeFeaturesDepositorInfo

        PdbxMoleculeFeaturesDepositorInfo getPdbxMoleculeFeaturesDepositorInfo()
        Data items in the PDBX_MOLECULE_FEATURES_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_MOLECULE_FEATURES.
        Returns:
        PdbxMoleculeFeaturesDepositorInfo
      • getPdbxChemCompInstanceDepositorInfo

        PdbxChemCompInstanceDepositorInfo getPdbxChemCompInstanceDepositorInfo()
        Data items in the PDBX_CHEM_COMP_INSTANCE_DEPOSITOR_INFO category records depositor provided information about the chemical context of component instances.
        Returns:
        PdbxChemCompInstanceDepositorInfo
      • getPdbxDepuiStatusFlags

        PdbxDepuiStatusFlags getPdbxDepuiStatusFlags()
        Data items in the PDBX_DEPUI_STATUS_FLAGS category record status details used to maintain state within the wwPDB deposition system.
        Returns:
        PdbxDepuiStatusFlags
      • getPdbxDepuiUpload

        PdbxDepuiUpload getPdbxDepuiUpload()
        Data items in the PDBX_DEPUI_UPLOAD category record the details of uploaded data files.
        Returns:
        PdbxDepuiUpload
      • getPdbxDepuiValidationStatusFlags

        PdbxDepuiValidationStatusFlags getPdbxDepuiValidationStatusFlags()
        Data items in the PDBX_DEPUI_VALIDATION_STATUS_FLAGS category record status details that assess the status of selected validation diagnostics.
        Returns:
        PdbxDepuiValidationStatusFlags
      • getPdbxChemCompUploadDepositorInfo

        PdbxChemCompUploadDepositorInfo getPdbxChemCompUploadDepositorInfo()
        Data items in the PDBX_CHEM_COMP_UPLOAD_DEPOSITOR_INFO category record details of the uploaded files related to depositor provided chemical assignments.
        Returns:
        PdbxChemCompUploadDepositorInfo
      • getPdbxDepuiEntityStatusFlags

        PdbxDepuiEntityStatusFlags getPdbxDepuiEntityStatusFlags()
        Data items in the PDBX_DEPUI_ENTITY_STATUS_FLAGS category record status details related to individual entities.
        Returns:
        PdbxDepuiEntityStatusFlags
      • getPdbxDepuiEntityFeatures

        PdbxDepuiEntityFeatures getPdbxDepuiEntityFeatures()
        Data items in the PDBX_DEPUI_ENTITY_FEATURES category record status details related to the features of individual entities.
        Returns:
        PdbxDepuiEntityFeatures
      • getPdbxDepositionMessageInfo

        PdbxDepositionMessageInfo getPdbxDepositionMessageInfo()
        Data items in the PDBX_DEPOSITION_MESSAGE_INFO category record internal messages within the depositon and annotation system.
        Returns:
        PdbxDepositionMessageInfo
      • getPdbxDepositionMessageFileReference

        PdbxDepositionMessageFileReference getPdbxDepositionMessageFileReference()
        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.
        Returns:
        PdbxDepositionMessageFileReference
      • getPdbxDepuiEntryDetails

        PdbxDepuiEntryDetails getPdbxDepuiEntryDetails()
        Data items in the PDBX_DEPUI_ENTRY_DETAILS category record information required to identify the depositor and route deposition to an appropriate processing site.
        Returns:
        PdbxDepuiEntryDetails
      • getPdbxDataProcessingStatus

        PdbxDataProcessingStatus getPdbxDataProcessingStatus()
        Data items in the PDBX_DATA_PROCESSING_STATUS category record data processing instructions for workflow processing tasks.
        Returns:
        PdbxDataProcessingStatus
      • getPdbxEntityInstanceFeature

        PdbxEntityInstanceFeature getPdbxEntityInstanceFeature()
        Data items in the pdbx_entity_instance_feature category records special features of selected entity instances.
        Returns:
        PdbxEntityInstanceFeature
      • getPdbxEntitySrcGenDepositorInfo

        PdbxEntitySrcGenDepositorInfo getPdbxEntitySrcGenDepositorInfo()
        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. 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).
        Returns:
        PdbxEntitySrcGenDepositorInfo
      • getPdbxChemCompModel

        PdbxChemCompModel getPdbxChemCompModel()
        Data items in the PDBX_CHEM_COMP_MODEL category give details about each of the chemical component model instances.
        Returns:
        PdbxChemCompModel
      • getPdbxChemCompModelAtom

        PdbxChemCompModelAtom getPdbxChemCompModelAtom()
        Data items in the PDBX_CHEM_COMP_MODEL_ATOM category record coordinates for the chemical component model instance.
        Returns:
        PdbxChemCompModelAtom
      • getPdbxChemCompModelBond

        PdbxChemCompModelBond getPdbxChemCompModelBond()
        Data items in the PDBX_CHEM_COMP_MODEL_BOND category record details about the bonds between atoms in a chemical component model instance.
        Returns:
        PdbxChemCompModelBond
      • getPdbxChemCompModelFeature

        PdbxChemCompModelFeature getPdbxChemCompModelFeature()
        Additional features associated with the chemical component.
        Returns:
        PdbxChemCompModelFeature
      • getPdbxChemCompModelDescriptor

        PdbxChemCompModelDescriptor getPdbxChemCompModelDescriptor()
        Data items in the CHEM_COMP_MODEL_DESCRIPTOR category provide string descriptors for component model structures.
        Returns:
        PdbxChemCompModelDescriptor
      • getPdbxChemCompModelAudit

        PdbxChemCompModelAudit getPdbxChemCompModelAudit()
        Data items in the PDBX_CHEM_COMP_MODEL_AUDIT category records the status and tracking information for this component model instance.
        Returns:
        PdbxChemCompModelAudit
      • getPdbxChemCompModelReference

        PdbxChemCompModelReference getPdbxChemCompModelReference()
        Additional features associated with the chemical component.
        Returns:
        PdbxChemCompModelReference
      • getPdbxViewCategoryGroup

        PdbxViewCategoryGroup getPdbxViewCategoryGroup()
        Data 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.
        Returns:
        PdbxViewCategoryGroup
      • getPdbxViewCategory

        PdbxViewCategory getPdbxViewCategory()
        Data 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.
        Returns:
        PdbxViewCategory
      • getPdbxViewItem

        PdbxViewItem getPdbxViewItem()
        Data 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.
        Returns:
        PdbxViewItem
      • getPdbxCoord

        PdbxCoord getPdbxCoord()
        Gives information about what kind of coordinates are available.
        Returns:
        PdbxCoord
      • getPdbxConnect

        PdbxConnect getPdbxConnect()
        Local data items describing ligand and monomer chemical features.
        Returns:
        PdbxConnect
      • getPdbxConnectType

        PdbxConnectType getPdbxConnectType()
        Local data items describing ligand and monomer type information.
        Returns:
        PdbxConnectType
      • getPdbxConnectModification

        PdbxConnectModification getPdbxConnectModification()
        Local data items describing ligand and monomer modifications.
        Returns:
        PdbxConnectModification
      • getPdbxConnectAtom

        PdbxConnectAtom getPdbxConnectAtom()
        Local data items describing ligand and monomer atom names and connectivity.
        Returns:
        PdbxConnectAtom
      • getPdbxDatabasePDBMaster

        PdbxDatabasePDBMaster getPdbxDatabasePDBMaster()
        The PDBX_DATABASE_PDB_MASTER category provides placeholders for the count of various PDB record types.
        Returns:
        PdbxDatabasePDBMaster
      • getPdbxDatabasePdbOmit

        PdbxDatabasePdbOmit getPdbxDatabasePdbOmit()
        Data items in the PDBX_DATABASE_PDB_OMIT category record list PDB record names that should be omitted in the PDB format file.
        Returns:
        PdbxDatabasePdbOmit
      • getPdbxDbref

        PdbxDbref getPdbxDbref()
        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.
        Returns:
        PdbxDbref
      • getPdbxDrugInfo

        PdbxDrugInfo getPdbxDrugInfo()
        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.
        Returns:
        PdbxDrugInfo
      • getPdbxInhibitorInfo

        PdbxInhibitorInfo getPdbxInhibitorInfo()
        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.
        Returns:
        PdbxInhibitorInfo
      • getPdbxIonInfo

        PdbxIonInfo getPdbxIonInfo()
        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.
        Returns:
        PdbxIonInfo
      • getPdbxHybrid

        PdbxHybrid getPdbxHybrid()
        Data items in the PDBX_HYBRID category are used to describe the chimeric characteristics of a DNA/RNA structure.
        Returns:
        PdbxHybrid
      • getPdbxNaStrandInfo

        PdbxNaStrandInfo getPdbxNaStrandInfo()
        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.
        Returns:
        PdbxNaStrandInfo
      • getPdbxNonstandardList

        PdbxNonstandardList getPdbxNonstandardList()
        The information in this category is exclusively used to store the HET records of a PDB file. This record will be generated by the PROGRAM.
        Returns:
        PdbxNonstandardList
      • getPdbxPdbCompnd

        PdbxPdbCompnd getPdbxPdbCompnd()
        This is a place holder for the PDB COMPND.
        Returns:
        PdbxPdbCompnd
      • getPdbxPdbSource

        PdbxPdbSource getPdbxPdbSource()
        This is a place holder for the PDB SOURCE.
        Returns:
        PdbxPdbSource
      • getPdbxProteinInfo

        PdbxProteinInfo getPdbxProteinInfo()
        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.
        Returns:
        PdbxProteinInfo
      • getPdbxSolventInfo

        PdbxSolventInfo getPdbxSolventInfo()
        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.
        Returns:
        PdbxSolventInfo
      • getPdbxSource

        PdbxSource getPdbxSource()
        Data item will still be used until the ENTITY category is fully adopted by NDBQuery.
        Returns:
        PdbxSource
      • getPdbxStructBiolFunc

        PdbxStructBiolFunc getPdbxStructBiolFunc()
        Data items in the PDBX_STRUCT_BIOL_FUNC category record details about the function of a particular biological assembly.
        Returns:
        PdbxStructBiolFunc
      • getPdbxStructPackGen

        PdbxStructPackGen getPdbxStructPackGen()
        Data items in the PDBX_STRUCT_PACK_GEN category record details about the generation of the packing picture(s).
        Returns:
        PdbxStructPackGen
      • getPdbxTrnaInfo

        PdbxTrnaInfo getPdbxTrnaInfo()
        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.
        Returns:
        PdbxTrnaInfo
      • getPdbxUnpair

        PdbxUnpair getPdbxUnpair()
        These 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.
        Returns:
        PdbxUnpair
      • getPdbxRefineLsRestrNcs

        PdbxRefineLsRestrNcs getPdbxRefineLsRestrNcs()
        Holds details of NCS restraints in cases where multiple conditions are provided for each domain.
        Returns:
        PdbxRefineLsRestrNcs
      • getPdbxStructNcsVirusGen

        PdbxStructNcsVirusGen getPdbxStructNcsVirusGen()
        Data items in the PDBX_STRUCT_NCS_VIRUS_GEN category record details about the generation of virus structures from NCS matrix operators.
        Returns:
        PdbxStructNcsVirusGen
      • getPdbxSequenceAnnotation

        PdbxSequenceAnnotation getPdbxSequenceAnnotation()
        PDBX_SEQUENCE_ANNOTATION holds internal details about molecular sequences described in the context of PDB chains.
        Returns:
        PdbxSequenceAnnotation
      • getPdbxPostProcessDetails

        PdbxPostProcessDetails getPdbxPostProcessDetails()
        Data items in the PDBX_POST_PROCESS_DETAILS identify problems or errors encountered in the post-processing of this entry.
        Returns:
        PdbxPostProcessDetails
      • getPdbxPostProcessStatus

        PdbxPostProcessStatus getPdbxPostProcessStatus()
        Data items in the PDBX_POST_PROCESS_DETAILS record the status of post-processed entries.
        Returns:
        PdbxPostProcessStatus
      • getPdbxStructLink

        PdbxStructLink getPdbxStructLink()
        Data items in the PDBX_STRUCT_LINK category record details about covalent linkages in the structure.
        Returns:
        PdbxStructLink
      • getPdbxMissingResidueList

        PdbxMissingResidueList getPdbxMissingResidueList()
        Provides a place-holder for PDB REMARK 465 data.
        Returns:
        PdbxMissingResidueList
      • getPdbxDataProcessingCell

        PdbxDataProcessingCell getPdbxDataProcessingCell()
        Crystallographic cell specifications used in data processing.
        Returns:
        PdbxDataProcessingCell
      • getPdbxDataProcessingReflns

        PdbxDataProcessingReflns getPdbxDataProcessingReflns()
        Details of reflections used in data processing.
        Returns:
        PdbxDataProcessingReflns
      • getPdbxDataProcessingDetector

        PdbxDataProcessingDetector getPdbxDataProcessingDetector()
        Details of the detector used at data collection site.
        Returns:
        PdbxDataProcessingDetector
      • getPdbxChemCompNonstandard

        PdbxChemCompNonstandard getPdbxChemCompNonstandard()
        Data items in the PDBX_CHEM_COMP_NONSTANDARD category describes common nucleotide modifications and nonstandard features.
        Returns:
        PdbxChemCompNonstandard
      • getPdbxEntityPolyProteinClass

        PdbxEntityPolyProteinClass getPdbxEntityPolyProteinClass()
        Data items in the PDBX_ENTITY_POLY_PROTEIN_CLASS category provides a top-level protein classification.
        Returns:
        PdbxEntityPolyProteinClass
      • getPdbxEntityNameTaxonomyTree

        PdbxEntityNameTaxonomyTree getPdbxEntityNameTaxonomyTree()
        Data items in the PDBX_ENTITY_NAME_TAXONOMY_TREE category define the tree structure of the entity name taxonomy.
        Returns:
        PdbxEntityNameTaxonomyTree
      • getPdbxEntityNameTaxonomy

        PdbxEntityNameTaxonomy getPdbxEntityNameTaxonomy()
        Data items in the PDBX_ENTITY_NAME_TAXONOMY category define the names and synonyms of the entity name taxonomy.
        Returns:
        PdbxEntityNameTaxonomy
      • getPdbxEntityNameInstance

        PdbxEntityNameInstance getPdbxEntityNameInstance()
        Data items in the PDBX_ENTITY_NAME_INSTANCE category list names used to define entities with their associated database, entity, chain, and molecule identifiers.
        Returns:
        PdbxEntityNameInstance
      • getPdbxTableinfo

        PdbxTableinfo getPdbxTableinfo()
        Returns:
        PdbxTableinfo
      • getPdbxColumninfo

        PdbxColumninfo getPdbxColumninfo()
        Returns:
        PdbxColumninfo
      • getPdbxValAngle

        PdbxValAngle getPdbxValAngle()
        The 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.
        Returns:
        PdbxValAngle
      • getPdbxValBond

        PdbxValBond getPdbxValBond()
        The 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.
        Returns:
        PdbxValBond
      • getPdbxValContact

        PdbxValContact getPdbxValContact()
        The 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.
        Returns:
        PdbxValContact
      • getPdbxValSymContact

        PdbxValSymContact getPdbxValSymContact()
        The 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.
        Returns:
        PdbxValSymContact
      • getPdbxRmchOutlier

        PdbxRmchOutlier getPdbxRmchOutlier()
        Data 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.
        Returns:
        PdbxRmchOutlier
      • getPdbxMissingAtomPoly

        PdbxMissingAtomPoly getPdbxMissingAtomPoly()
        Data items in the PDBX_MISSING_ATOM_POLY category lists atoms missing in polymer residues. This is a completely derived category. Do not edit.
        Returns:
        PdbxMissingAtomPoly
      • getPdbxMissingAtomNonpoly

        PdbxMissingAtomNonpoly getPdbxMissingAtomNonpoly()
        Data items in the PDBX_MISSING_ATOM_NONPOLY category list the atoms missing in nonpolymer residues. This is a completely derived category. Do not edit.
        Returns:
        PdbxMissingAtomNonpoly
      • getPdbxValChiral

        PdbxValChiral getPdbxValChiral()
        Data items in the PDBX_VAL_CHIRAL category list the atoms with nonstandard chiralities. This is a completely derived category. Do not edit.
        Returns:
        PdbxValChiral
      • getPdbxAtlas

        PdbxAtlas getPdbxAtlas()
        Gives information about the organization of the NDB Structural Atlas.
        Returns:
        PdbxAtlas
      • getPdbxSummaryFlags

        PdbxSummaryFlags getPdbxSummaryFlags()
        Container category for a list of feature flags associated with each structure entry.
        Returns:
        PdbxSummaryFlags
      • getPdbxEntityFuncBindMode

        PdbxEntityFuncBindMode getPdbxEntityFuncBindMode()
        Data items in the PDBX_ENTITY_FUNC_BIND_MODE category describe characteristics of protein oligonucleotide binding.
        Returns:
        PdbxEntityFuncBindMode
      • getPdbxEntityFuncEnzyme

        PdbxEntityFuncEnzyme getPdbxEntityFuncEnzyme()
        Data items in the PDBX_ENTITY_FUNC_ENZYME category describe characteristics of protein oligonucleotide binding in which the binding mode is enzymatic.
        Returns:
        PdbxEntityFuncEnzyme
      • getPdbxEntityFuncRegulatory

        PdbxEntityFuncRegulatory getPdbxEntityFuncRegulatory()
        Data items in the PDBX_ENTITY_FUNC_REGULATORY category describe characteristics of protein oligonucleotide binding in which the binding mode is regulatory.
        Returns:
        PdbxEntityFuncRegulatory
      • getPdbxEntityFuncStructural

        PdbxEntityFuncStructural getPdbxEntityFuncStructural()
        Data items in the PDBX_ENTITY_FUNC_STRUCTURAL category describe characteristics of protein oligonucleotide binding in which the binding mode is structural.
        Returns:
        PdbxEntityFuncStructural
      • getPdbxEntityFuncOther

        PdbxEntityFuncOther getPdbxEntityFuncOther()
        Data items in the PDBX_ENTITY_FUNC_OTHER category describe characteristics of protein oligonucleotide binding in which the binding mode is not classified.
        Returns:
        PdbxEntityFuncOther
      • getPdbxEntityPolyDomain

        PdbxEntityPolyDomain getPdbxEntityPolyDomain()
        Data items in the PDBX_ENTITY_POLY_DOMAIN category specify domains of monomers within a polymer.
        Returns:
        PdbxEntityPolyDomain
      • getPdbxNaStructKeywds

        PdbxNaStructKeywds getPdbxNaStructKeywds()
        Data items in the PDBX_NA_STRUCT_KEYWDS category record give details about structural features of the NA.
        Returns:
        PdbxNaStructKeywds
      • getPdbxEntityPolyNaType

        PdbxEntityPolyNaType getPdbxEntityPolyNaType()
        Data items in the PDBX_ENTITY_POLY_NA_TYPE category describe type of nucleic acid polymer entities.
        Returns:
        PdbxEntityPolyNaType
      • getPdbxEntityPolyNaNonstandard

        PdbxEntityPolyNaNonstandard getPdbxEntityPolyNaNonstandard()
        Data items in the PDBX_ENTITY_POLY_NA_NONSTANDARD category describe the nonstandard features of the nucleic acid polymer entities.
        Returns:
        PdbxEntityPolyNaNonstandard
      • getPdbxVirtualAngle

        PdbxVirtualAngle getPdbxVirtualAngle()
        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.
        Returns:
        PdbxVirtualAngle
      • getPdbxVirtualBond

        PdbxVirtualBond getPdbxVirtualBond()
        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.
        Returns:
        PdbxVirtualBond
      • getPdbxVirtualTorsion

        PdbxVirtualTorsion getPdbxVirtualTorsion()
        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.
        Returns:
        PdbxVirtualTorsion
      • getPdbxSequencePattern

        PdbxSequencePattern getPdbxSequencePattern()
        Data items in the PDBX_SEQUENCE_PATTERN category record the number of occurences of common step sequence patterns (e.g. AA, CG, AT).
        Returns:
        PdbxSequencePattern
      • getPdbxStereochemistry

        PdbxStereochemistry getPdbxStereochemistry()
        Data items in the PDBX_STEREOCHEMISTRY identify chiral centers and associated chiral volumes.
        Returns:
        PdbxStereochemistry
      • getPdbxRmsDevsCovalent

        PdbxRmsDevsCovalent getPdbxRmsDevsCovalent()
        Data items in the PDBX_RMS_DEVS_COVALENT record the summary RMS deviations for nucleic acid covalent geometry relative to small molecule crystal standards.
        Returns:
        PdbxRmsDevsCovalent
      • getPdbxRmsDevsCovByMonomer

        PdbxRmsDevsCovByMonomer getPdbxRmsDevsCovByMonomer()
        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.
        Returns:
        PdbxRmsDevsCovByMonomer
      • getPdbxSugarPhosphateGeometry

        PdbxSugarPhosphateGeometry getPdbxSugarPhosphateGeometry()
        Data items in the PDBX_SUGAR_PHOSPHATE_GEOMETRY record the RMS deviations covalent geometry for each momoner relative to small molecule crystal standards.
        Returns:
        PdbxSugarPhosphateGeometry
      • getPdbxNmrComputing

        PdbxNmrComputing getPdbxNmrComputing()
        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. The description should include both the name of the software and the version used.
        Returns:
        PdbxNmrComputing
      • getPdbxAuditConformExtension

        PdbxAuditConformExtension getPdbxAuditConformExtension()
        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.
        Returns:
        PdbxAuditConformExtension
      • getPdbxDccMapman

        PdbxDccMapman getPdbxDccMapman()
        Data items in the category record details from the output of mapman used by the DCC program.
        Returns:
        PdbxDccMapman
      • getPdbxDccRsccMapman

        PdbxDccRsccMapman getPdbxDccRsccMapman()
        Data items in this category record residual map properties such as correlation, real space Rfactors and the Zscore calculated from refmac and mapman.
        Returns:
        PdbxDccRsccMapman
      • getPdbxDccRsccMapmanOverall

        PdbxDccRsccMapmanOverall getPdbxDccRsccMapmanOverall()
        Data items in the category record overall map properties such as correlation, real space Rfactors and the Zscore calculated from refmac and mapman.
        Returns:
        PdbxDccRsccMapmanOverall
      • getPdbxDccDensity

        PdbxDccDensity getPdbxDccDensity()
        Data items in the category record various overall metrics calculated by DCC and various wrapped programs (such as Xtriage, pointless, REFMAC ...).
        Returns:
        PdbxDccDensity
      • getPdbxDccGeometry

        PdbxDccGeometry getPdbxDccGeometry()
        Data 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.
        Returns:
        PdbxDccGeometry
      • getPdbxDccDensityCorr

        PdbxDccDensityCorr getPdbxDccDensityCorr()
        Data items in the category record calculated metrics from various programs (such as phenix, refmac, cns, sfcheck).
        Returns:
        PdbxDccDensityCorr
      • getPdbxDccMap

        PdbxDccMap getPdbxDccMap()
        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.
        Returns:
        PdbxDccMap
      • getPdbxDepositGroup

        PdbxDepositGroup getPdbxDepositGroup()
        Data items in the pdbx_deposit_group category provide identifiers and related information for groups of entries deposited in a collection.
        Returns:
        PdbxDepositGroup
      • getPdbxDepositGroupIndex

        PdbxDepositGroupIndex getPdbxDepositGroupIndex()
        Data items in the pdbx_deposit_group_index category provides details about the individual data files in the collection of deposited entries.
        Returns:
        PdbxDepositGroupIndex
      • getPdbxStructAssemblyAuthEvidence

        PdbxStructAssemblyAuthEvidence getPdbxStructAssemblyAuthEvidence()
        Provides author supplied evidentiary support for assemblies in pdbx_struct_assembly.
        Returns:
        PdbxStructAssemblyAuthEvidence
      • getPdbxStructAssemblyAuthClassification

        PdbxStructAssemblyAuthClassification getPdbxStructAssemblyAuthClassification()
        Provides reason a particular assembly in pdbx_struct_assembly is of interest.
        Returns:
        PdbxStructAssemblyAuthClassification
      • getPdbxCrystalAlignment

        PdbxCrystalAlignment getPdbxCrystalAlignment()
        Data in the PDBX_CRYSTAL_ALIGNMENT are produced by log files from programs during indexing
        Returns:
        PdbxCrystalAlignment
      • getPdbxAuditRevisionHistory

        PdbxAuditRevisionHistory getPdbxAuditRevisionHistory()
        Data items in the PDBX_AUDIT_REVISION_HISTORY category record the revision history for a data entry.
        Returns:
        PdbxAuditRevisionHistory
      • getPdbxAuditRevisionGroup

        PdbxAuditRevisionGroup getPdbxAuditRevisionGroup()
        Data items in the PDBX_AUDIT_revision_group category report the content groups associated with a PDBX_AUDIT_REVISION_HISTORY record.
        Returns:
        PdbxAuditRevisionGroup
      • getPdbxAuditRevisionCategory

        PdbxAuditRevisionCategory getPdbxAuditRevisionCategory()
        Data items in the PDBX_AUDIT_REVISION_CATEGORY category report the data categories associated with a PDBX_AUDIT_REVISION_HISTORY record.
        Returns:
        PdbxAuditRevisionCategory
      • getPdbxAuditRevisionDetails

        PdbxAuditRevisionDetails getPdbxAuditRevisionDetails()
        Data items in the PDBX_audit_revision_details category record descriptions of changes associated with PDBX_AUDIT_REVISION_HISTORY records.
        Returns:
        PdbxAuditRevisionDetails
      • getPdbxAuditRevisionItem

        PdbxAuditRevisionItem getPdbxAuditRevisionItem()
        Data items in the PDBX_AUDIT_REVISION_ITEM category report the data items associated with a PDBX_AUDIT_REVISION_HISTORY record.
        Returns:
        PdbxAuditRevisionItem
      • getPdbxSupportingExpDataSet

        PdbxSupportingExpDataSet getPdbxSupportingExpDataSet()
        Data items in the PDBX_SUPPORTING_EXP_DATA_SET category record to experimental data set dependencies for this entry.
        Returns:
        PdbxSupportingExpDataSet
      • getPdbxSerialCrystallographyMeasurement

        PdbxSerialCrystallographyMeasurement getPdbxSerialCrystallographyMeasurement()
        Data items in the PDBX_SERIAL_CRYSTALLOGRAPHY_MEASUREMENT category record details the beam that is impinging on the sample
        Returns:
        PdbxSerialCrystallographyMeasurement
      • getPdbxSerialCrystallographySampleDelivery

        PdbxSerialCrystallographySampleDelivery getPdbxSerialCrystallographySampleDelivery()
        Data items in the PDBX_SERIAL_CRYSTALLOGRAPHY_SAMPLE_DELIVERY category record general details about the sample delivery
        Returns:
        PdbxSerialCrystallographySampleDelivery
      • getPdbxSerialCrystallographySampleDeliveryInjection

        PdbxSerialCrystallographySampleDeliveryInjection getPdbxSerialCrystallographySampleDeliveryInjection()
        Data items in the PDBX_SERIAL_CRYSTALLOGRAPHY_SAMPLE_DELIVERY_INJECTION category record details about sample delivery by injection
        Returns:
        PdbxSerialCrystallographySampleDeliveryInjection
      • getPdbxSerialCrystallographySampleDeliveryFixedTarget

        PdbxSerialCrystallographySampleDeliveryFixedTarget getPdbxSerialCrystallographySampleDeliveryFixedTarget()
        Data items in the PDBX_SERIAL_CRYSTALLOGRAPHY_SAMPLE_DELIVERY_FIXED_TARGET category record details about sample delivery using a fixed taget.
        Returns:
        PdbxSerialCrystallographySampleDeliveryFixedTarget
      • getPdbxSerialCrystallographyDataReduction

        PdbxSerialCrystallographyDataReduction getPdbxSerialCrystallographyDataReduction()
        Data 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.
        Returns:
        PdbxSerialCrystallographyDataReduction
      • getPdbxChemCompSynonyms

        PdbxChemCompSynonyms getPdbxChemCompSynonyms()
        PDBX_CHEM_COMP_SYNONYMS holds chemical name and synonym correspondences.
        Returns:
        PdbxChemCompSynonyms
      • getPdbxChemCompRelated

        PdbxChemCompRelated getPdbxChemCompRelated()
        PDBX_CHEM_COMP_RELATED describes the relationship between two chemical components.
        Returns:
        PdbxChemCompRelated
      • getPdbxChemCompAtomRelated

        PdbxChemCompAtomRelated getPdbxChemCompAtomRelated()
        PDBX_CHEM_COMP_ATOM_RELATED provides atom level nomenclature mapping between two related chemical components.
        Returns:
        PdbxChemCompAtomRelated
      • getPdbxEntityBranchList

        PdbxEntityBranchList getPdbxEntityBranchList()
        Data 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.
        Returns:
        PdbxEntityBranchList
      • getPdbxEntityBranchLink

        PdbxEntityBranchLink getPdbxEntityBranchLink()
        Data items in the PDBX_ENTITY_BRANCH_LINK category give details about the linkages between components within a branched entity.
        Returns:
        PdbxEntityBranchLink
      • getPdbxEntityBranch

        PdbxEntityBranch getPdbxEntityBranch()
        Data items in the PDBX_ENTITY_BRANCH category specify the list of branched entities and the type.
        Returns:
        PdbxEntityBranch
      • getPdbxBranchScheme

        PdbxBranchScheme getPdbxBranchScheme()
        The PDBX_BRANCH_SCHEME category provides residue level nomenclature mapping for branch chain entities.
        Returns:
        PdbxBranchScheme
      • getIhmStartingModelDetails

        IhmStartingModelDetails getIhmStartingModelDetails()
        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.
        Returns:
        IhmStartingModelDetails
      • getIhmStartingComparativeModels

        IhmStartingComparativeModels getIhmStartingComparativeModels()
        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.
        Returns:
        IhmStartingComparativeModels
      • getIhmStartingComputationalModels

        IhmStartingComputationalModels getIhmStartingComputationalModels()
        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.
        Returns:
        IhmStartingComputationalModels
      • getIhmStartingModelSeqDif

        IhmStartingModelSeqDif getIhmStartingModelSeqDif()
        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. The point differences may be due to point mutations introduced in the starting model or the presence of modified amino acid residues.
        Returns:
        IhmStartingModelSeqDif
      • getIhmModelRepresentation

        IhmModelRepresentation getIhmModelRepresentation()
        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. This category handles the multi-scale model representation, if employed.
        Returns:
        IhmModelRepresentation
      • getIhmStructAssembly

        IhmStructAssembly getIhmStructAssembly()
        Data items in the IHM_STRUCT_ASSEMBLY category records the details of the structural assemblies and used in the IHM modeling.
        Returns:
        IhmStructAssembly
      • getIhmStructAssemblyDetails

        IhmStructAssemblyDetails getIhmStructAssemblyDetails()
        Data items in the IHM_STRUCT_ASSEMBLY_DETAILS category provides additional details regarding the structure assembly.
        Returns:
        IhmStructAssemblyDetails
      • getIhmStructAssemblyClassList

        IhmStructAssemblyClassList getIhmStructAssemblyClassList()
        Data 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.
        Returns:
        IhmStructAssemblyClassList
      • getIhmStructAssemblyClass

        IhmStructAssemblyClass getIhmStructAssemblyClass()
        Data 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.
        Returns:
        IhmStructAssemblyClass
      • getIhmModelingProtocol

        IhmModelingProtocol getIhmModelingProtocol()
        Data items in the IHM_MODELING_PROTOCOL category records the step-wise details of the integrative modeling workflow.
        Returns:
        IhmModelingProtocol
      • getIhmMultiStateModeling

        IhmMultiStateModeling getIhmMultiStateModeling()
        Data items in the IHM_MULTI_STATE_MODELING category records the details of the multi-state modeling protocol, if applicable.
        Returns:
        IhmMultiStateModeling
      • getIhmOrderedEnsemble

        IhmOrderedEnsemble getIhmOrderedEnsemble()
        Data 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.
        Returns:
        IhmOrderedEnsemble
      • getIhmModelingPostProcess

        IhmModelingPostProcess getIhmModelingPostProcess()
        Data items in the IHM_MODELING_POST_PROCESS category records the details of the post processing of the models/results of the modeling protocol.
        Returns:
        IhmModelingPostProcess
      • getIhmEnsembleInfo

        IhmEnsembleInfo getIhmEnsembleInfo()
        Data items in the IHM_ENSEMBLE_INFO category records the details of the model clusters or ensembles obtained after sampling.
        Returns:
        IhmEnsembleInfo
      • getIhmModelList

        IhmModelList getIhmModelList()
        Data items in the IHM_MODEL_LIST category record the details of the models being deposited.
        Returns:
        IhmModelList
      • getIhmModelRepresentative

        IhmModelRepresentative getIhmModelRepresentative()
        Data items in the IHM_MODEL_REPRESENTATIVE category record the details of the representative model in an ensemble or cluster.
        Returns:
        IhmModelRepresentative
      • getIhmDatasetList

        IhmDatasetList getIhmDatasetList()
        Category 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.
        Returns:
        IhmDatasetList
      • getIhmDatasetGroup

        IhmDatasetGroup getIhmDatasetGroup()
        Category provides a mechanism to group datasets.
        Returns:
        IhmDatasetGroup
      • getIhmRelatedDatasets

        IhmRelatedDatasets getIhmRelatedDatasets()
        Category holds information about related datasets, where one is derived from the other.
        Returns:
        IhmRelatedDatasets
      • getIhmDatasetRelatedDbReference

        IhmDatasetRelatedDbReference getIhmDatasetRelatedDbReference()
        Category 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.
        Returns:
        IhmDatasetRelatedDbReference
      • getIhmExternalReferenceInfo

        IhmExternalReferenceInfo getIhmExternalReferenceInfo()
        Category 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).
        Returns:
        IhmExternalReferenceInfo
      • getIhmExternalFiles

        IhmExternalFiles getIhmExternalFiles()
        Category 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.
        Returns:
        IhmExternalFiles
      • getIhmDatasetExternalReference

        IhmDatasetExternalReference getIhmDatasetExternalReference()
        Category provides additional details regarding input data hosted externally at other resources.
        Returns:
        IhmDatasetExternalReference
      • getIhmLocalizationDensityFiles

        IhmLocalizationDensityFiles getIhmLocalizationDensityFiles()
        Data 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.).
        Returns:
        IhmLocalizationDensityFiles
      • getIhmPredictedContactRestraint

        IhmPredictedContactRestraint getIhmPredictedContactRestraint()
        Data 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.
        Returns:
        IhmPredictedContactRestraint
      • getIhmHydroxylRadicalFpRestraint

        IhmHydroxylRadicalFpRestraint getIhmHydroxylRadicalFpRestraint()
        Data 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.
        Returns:
        IhmHydroxylRadicalFpRestraint
      • getIhmCrossLinkList

        IhmCrossLinkList getIhmCrossLinkList()
        Data items in the IHM_CROSS_LINK_LIST category records the list of spatial restraints derived from chemical crosslinking experiment.
        Returns:
        IhmCrossLinkList
      • getIhmCrossLinkRestraint

        IhmCrossLinkRestraint getIhmCrossLinkRestraint()
        Data 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.
        Returns:
        IhmCrossLinkRestraint
      • getIhmCrossLinkResult

        IhmCrossLinkResult getIhmCrossLinkResult()
        Data items in the IHM_CROSS_LINK_RESULT category records the results of the crosslinking restraints in the IHM modeling.
        Returns:
        IhmCrossLinkResult
      • getIhmCrossLinkResultParameters

        IhmCrossLinkResultParameters getIhmCrossLinkResultParameters()
        Data items in the IHM_CROSS_LINK_RESULT_PARAMETERS category records the results of the crosslinking restraint parameters in the IHM modeling.
        Returns:
        IhmCrossLinkResultParameters
      • getIhm2demClassAverageRestraint

        Ihm2demClassAverageRestraint getIhm2demClassAverageRestraint()
        Data items in the IHM_2DEM_CLASS_AVERAGE_RESTRAINT category records the details of the 2DEM class averages used in the IHM modeling.
        Returns:
        Ihm2demClassAverageRestraint
      • getIhm2demClassAverageFitting

        Ihm2demClassAverageFitting getIhm2demClassAverageFitting()
        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. 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.
        Returns:
        Ihm2demClassAverageFitting
      • getIhm3demRestraint

        Ihm3demRestraint getIhm3demRestraint()
        Data items in the IHM_3DEM_RESTRAINT category records the details of the 3DEM maps used as restraints in the IHM modeling.
        Returns:
        Ihm3demRestraint
      • getIhmSasRestraint

        IhmSasRestraint getIhmSasRestraint()
        Data items in the IHM_SAS_RESTRAINT category records the details of the SAS data used as restraints in the IHM modeling.
        Returns:
        IhmSasRestraint
      • getIhmStartingModelCoord

        IhmStartingModelCoord getIhmStartingModelCoord()
        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.
        Returns:
        IhmStartingModelCoord
      • getIhmSphereObjSite

        IhmSphereObjSite getIhmSphereObjSite()
        Data items in the IHM_SPHERE_OBJ_SITE category records the details of the spherical objects modeled in the integrative structural model.
        Returns:
        IhmSphereObjSite
      • getIhmGaussianObjSite

        IhmGaussianObjSite getIhmGaussianObjSite()
        Data items in the IHM_GAUSSIAN_OBJ_SITE category records the details of the gaussian objects modeled in the integrative structural model.
        Returns:
        IhmGaussianObjSite
      • getIhmGaussianObjEnsemble

        IhmGaussianObjEnsemble getIhmGaussianObjEnsemble()
        Data items in the IHM_GAUSSIAN_OBJ_ENSEMBLE category records the details of the gaussian objects representing an ensemble or cluster of models.
        Returns:
        IhmGaussianObjEnsemble
      • getIhmResiduesNotModeled

        IhmResiduesNotModeled getIhmResiduesNotModeled()
        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.
        Returns:
        IhmResiduesNotModeled
      • getIhmFeatureList

        IhmFeatureList getIhmFeatureList()
        IHM_FEATURE_LIST is the high level category that provides defintions to select atoms/residues from polymeric and non-polymeric entities.
        Returns:
        IhmFeatureList
      • getIhmPseudoSiteFeature

        IhmPseudoSiteFeature getIhmPseudoSiteFeature()
        Data items in the IHM_PSEUDO_SITE_FEATURE category records the details of pseudo positions for the features listed in IHM_FEATURE_LIST.
        Returns:
        IhmPseudoSiteFeature
      • getIhmPolyAtomFeature

        IhmPolyAtomFeature getIhmPolyAtomFeature()
        Data items in the IHM_POLY_ATOM_FEATURE category provides the defintions required to select specific atoms.
        Returns:
        IhmPolyAtomFeature
      • getIhmPolyResidueFeature

        IhmPolyResidueFeature getIhmPolyResidueFeature()
        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.
        Returns:
        IhmPolyResidueFeature
      • getIhmNonPolyFeature

        IhmNonPolyFeature getIhmNonPolyFeature()
        Data items in the IHM_NON_POLY_FEATURE category provides the defintions required to select a non-polymeric (ligand) feature.
        Returns:
        IhmNonPolyFeature
      • getIhmInterfaceResidueFeature

        IhmInterfaceResidueFeature getIhmInterfaceResidueFeature()
        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. 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.
        Returns:
        IhmInterfaceResidueFeature
      • getIhmDerivedDistanceRestraint

        IhmDerivedDistanceRestraint getIhmDerivedDistanceRestraint()
        Data 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.
        Returns:
        IhmDerivedDistanceRestraint
      • getIhmGeometricObjectList

        IhmGeometricObjectList getIhmGeometricObjectList()
        Data items in the IHM_GEOMETRIC_OBJECT_LIST category records the list of geometric objects used as restraints in the integrative modeling study.
        Returns:
        IhmGeometricObjectList
      • getIhmGeometricObjectCenter

        IhmGeometricObjectCenter getIhmGeometricObjectCenter()
        Data items in the IHM_GEOMETRIC_OBJECT_CENTER category records the center of geometric objects used as restraints in the integrative modeling study.
        Returns:
        IhmGeometricObjectCenter
      • getIhmGeometricObjectTransformation

        IhmGeometricObjectTransformation getIhmGeometricObjectTransformation()
        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. If no transformation is provide, identity transformation is assumed.
        Returns:
        IhmGeometricObjectTransformation
      • getIhmGeometricObjectSphere

        IhmGeometricObjectSphere getIhmGeometricObjectSphere()
        Data items in the IHM_GEOMETRIC_OBJECT_SPHERE category records the parameters of a sphere.
        Returns:
        IhmGeometricObjectSphere
      • getIhmGeometricObjectTorus

        IhmGeometricObjectTorus getIhmGeometricObjectTorus()
        Data 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.
        Returns:
        IhmGeometricObjectTorus
      • getIhmGeometricObjectHalfTorus

        IhmGeometricObjectHalfTorus getIhmGeometricObjectHalfTorus()
        Data items in the IHM_GEOMETRIC_OBJECT_HALF_TORUS category records the parameters of half-torus that represents a membrane.
        Returns:
        IhmGeometricObjectHalfTorus
      • getIhmGeometricObjectAxis

        IhmGeometricObjectAxis getIhmGeometricObjectAxis()
        Data items in the IHM_GEOMETRIC_OBJECT_AXIS category records the details of an axis used in a spatial restraint.
        Returns:
        IhmGeometricObjectAxis
      • getIhmGeometricObjectPlane

        IhmGeometricObjectPlane getIhmGeometricObjectPlane()
        Data items in the IHM_GEOMETRIC_OBJECT_PLANE category records the details of a plane used in a spatial restraint.
        Returns:
        IhmGeometricObjectPlane
      • getIhmGeometricObjectDistanceRestraint

        IhmGeometricObjectDistanceRestraint getIhmGeometricObjectDistanceRestraint()
        Data 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.
        Returns:
        IhmGeometricObjectDistanceRestraint