Class BaseBlock

  • All Implemented Interfaces:
    Block

    public class BaseBlock
    extends Object
    implements Block
    • Method Detail

      • getBlockHeader

        public String getBlockHeader()
        Description copied from interface: Block
        The header of this Block.
        Specified by:
        getBlockHeader in interface Block
        Returns:
        String of the header
      • getCategory

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

        public Column getColumn​(String name)
        Description copied from interface: Block
        Retrieve a Column by name. This is relevant for CCDC files that identify columns by 'flat' names such as "cell_length_a"
        Specified by:
        getColumn in interface Block
        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
      • getSaveFrames

        public List<Block> getSaveFrames()
        Description copied from interface: Block
        All save frames associated to this Block.
        Specified by:
        getSaveFrames in interface Block
        Returns:
        collection of save frames
      • getAtomSite

        public AtomSite getAtomSite()
        Description copied from interface: Block
        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.
        Specified by:
        getAtomSite in interface Block
        Returns:
        AtomSite
      • getAtomSiteAnisotrop

        public AtomSiteAnisotrop getAtomSiteAnisotrop()
        Description copied from interface: Block
        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.
        Specified by:
        getAtomSiteAnisotrop in interface Block
        Returns:
        AtomSiteAnisotrop
      • getAtomSites

        public AtomSites getAtomSites()
        Description copied from interface: Block
        Data items in the ATOM_SITES category record details about the crystallographic cell and cell transformations, which are common to all atom sites.
        Specified by:
        getAtomSites in interface Block
        Returns:
        AtomSites
      • getAtomSitesAlt

        public AtomSitesAlt getAtomSitesAlt()
        Description copied from interface: Block
        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.
        Specified by:
        getAtomSitesAlt in interface Block
        Returns:
        AtomSitesAlt
      • getAtomSitesAltEns

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

        public AtomSitesAltGen getAtomSitesAltGen()
        Description copied from interface: Block
        Data items in the ATOM_SITES_ALT_GEN category record details about the interpretation of multiple conformations in the structure.
        Specified by:
        getAtomSitesAltGen in interface Block
        Returns:
        AtomSitesAltGen
      • getAtomSitesFootnote

        public AtomSitesFootnote getAtomSitesFootnote()
        Description copied from interface: Block
        Data items in the ATOM_SITES_FOOTNOTE category record detailed comments about an atom site or a group of atom sites.
        Specified by:
        getAtomSitesFootnote in interface Block
        Returns:
        AtomSitesFootnote
      • getAtomType

        public AtomType getAtomType()
        Description copied from interface: Block
        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.
        Specified by:
        getAtomType in interface Block
        Returns:
        AtomType
      • getAudit

        public Audit getAudit()
        Description copied from interface: Block
        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.
        Specified by:
        getAudit in interface Block
        Returns:
        Audit
      • getAuditAuthor

        public AuditAuthor getAuditAuthor()
        Description copied from interface: Block
        Data items in the AUDIT_AUTHOR category record details about the author(s) of the data block.
        Specified by:
        getAuditAuthor in interface Block
        Returns:
        AuditAuthor
      • getAuditConform

        public AuditConform getAuditConform()
        Description copied from interface: Block
        Data items in the AUDIT_CONFORM category describe the dictionary versions against which the data names appearing in the current data block are conformant.
        Specified by:
        getAuditConform in interface Block
        Returns:
        AuditConform
      • getAuditContactAuthor

        public AuditContactAuthor getAuditContactAuthor()
        Description copied from interface: Block
        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.
        Specified by:
        getAuditContactAuthor in interface Block
        Returns:
        AuditContactAuthor
      • getCell

        public Cell getCell()
        Description copied from interface: Block
        Data items in the CELL category record details about the crystallographic cell parameters.
        Specified by:
        getCell in interface Block
        Returns:
        Cell
      • getCellMeasurement

        public CellMeasurement getCellMeasurement()
        Description copied from interface: Block
        Data items in the CELL_MEASUREMENT category record details about the measurement of the crystallographic cell parameters.
        Specified by:
        getCellMeasurement in interface Block
        Returns:
        CellMeasurement
      • getCellMeasurementRefln

        public CellMeasurementRefln getCellMeasurementRefln()
        Description copied from interface: Block
        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.
        Specified by:
        getCellMeasurementRefln in interface Block
        Returns:
        CellMeasurementRefln
      • getChemComp

        public ChemComp getChemComp()
        Description copied from interface: Block
        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.
        Specified by:
        getChemComp in interface Block
        Returns:
        ChemComp
      • getChemCompAngle

        public ChemCompAngle getChemCompAngle()
        Description copied from interface: Block
        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.
        Specified by:
        getChemCompAngle in interface Block
        Returns:
        ChemCompAngle
      • getChemCompAtom

        public ChemCompAtom getChemCompAtom()
        Description copied from interface: Block
        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.
        Specified by:
        getChemCompAtom in interface Block
        Returns:
        ChemCompAtom
      • getChemCompBond

        public ChemCompBond getChemCompBond()
        Description copied from interface: Block
        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.
        Specified by:
        getChemCompBond in interface Block
        Returns:
        ChemCompBond
      • getChemCompChir

        public ChemCompChir getChemCompChir()
        Description copied from interface: Block
        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.
        Specified by:
        getChemCompChir in interface Block
        Returns:
        ChemCompChir
      • getChemCompChirAtom

        public ChemCompChirAtom getChemCompChirAtom()
        Description copied from interface: Block
        Data items in the CHEM_COMP_CHIR_ATOM category enumerate the atoms bonded to a chiral atom within a chemical component.
        Specified by:
        getChemCompChirAtom in interface Block
        Returns:
        ChemCompChirAtom
      • getChemCompLink

        public ChemCompLink getChemCompLink()
        Description copied from interface: Block
        Data items in the CHEM_COMP_LINK category give details about the links between chemical components.
        Specified by:
        getChemCompLink in interface Block
        Returns:
        ChemCompLink
      • getChemCompPlane

        public ChemCompPlane getChemCompPlane()
        Description copied from interface: Block
        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.
        Specified by:
        getChemCompPlane in interface Block
        Returns:
        ChemCompPlane
      • getChemCompPlaneAtom

        public ChemCompPlaneAtom getChemCompPlaneAtom()
        Description copied from interface: Block
        Data items in the CHEM_COMP_PLANE_ATOM category enumerate the atoms in a plane within a chemical component.
        Specified by:
        getChemCompPlaneAtom in interface Block
        Returns:
        ChemCompPlaneAtom
      • getChemCompTor

        public ChemCompTor getChemCompTor()
        Description copied from interface: Block
        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.
        Specified by:
        getChemCompTor in interface Block
        Returns:
        ChemCompTor
      • getChemCompTorValue

        public ChemCompTorValue getChemCompTorValue()
        Description copied from interface: Block
        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.
        Specified by:
        getChemCompTorValue in interface Block
        Returns:
        ChemCompTorValue
      • getChemLink

        public ChemLink getChemLink()
        Description copied from interface: Block
        Data items in the CHEM_LINK category give details about the links between chemical components.
        Specified by:
        getChemLink in interface Block
        Returns:
        ChemLink
      • getChemLinkAngle

        public ChemLinkAngle getChemLinkAngle()
        Description copied from interface: Block
        Data items in the CHEM_LINK_ANGLE category record details about angles in a link between chemical components.
        Specified by:
        getChemLinkAngle in interface Block
        Returns:
        ChemLinkAngle
      • getChemLinkBond

        public ChemLinkBond getChemLinkBond()
        Description copied from interface: Block
        Data items in the CHEM_LINK_BOND category record details about bonds in a link between components in the chemical structure.
        Specified by:
        getChemLinkBond in interface Block
        Returns:
        ChemLinkBond
      • getChemLinkChir

        public ChemLinkChir getChemLinkChir()
        Description copied from interface: Block
        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.
        Specified by:
        getChemLinkChir in interface Block
        Returns:
        ChemLinkChir
      • getChemLinkChirAtom

        public ChemLinkChirAtom getChemLinkChirAtom()
        Description copied from interface: Block
        Data items in the CHEM_LINK_CHIR_ATOM category enumerate the atoms bonded to a chiral atom in a link between two chemical components.
        Specified by:
        getChemLinkChirAtom in interface Block
        Returns:
        ChemLinkChirAtom
      • getChemLinkPlane

        public ChemLinkPlane getChemLinkPlane()
        Description copied from interface: Block
        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.
        Specified by:
        getChemLinkPlane in interface Block
        Returns:
        ChemLinkPlane
      • getChemLinkPlaneAtom

        public ChemLinkPlaneAtom getChemLinkPlaneAtom()
        Description copied from interface: Block
        Data items in the CHEM_LINK_PLANE_ATOM category enumerate the atoms in a plane in a link between two chemical components.
        Specified by:
        getChemLinkPlaneAtom in interface Block
        Returns:
        ChemLinkPlaneAtom
      • getChemLinkTor

        public ChemLinkTor getChemLinkTor()
        Description copied from interface: Block
        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.
        Specified by:
        getChemLinkTor in interface Block
        Returns:
        ChemLinkTor
      • getChemLinkTorValue

        public ChemLinkTorValue getChemLinkTorValue()
        Description copied from interface: Block
        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.
        Specified by:
        getChemLinkTorValue in interface Block
        Returns:
        ChemLinkTorValue
      • getChemical

        public Chemical getChemical()
        Description copied from interface: Block
        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.
        Specified by:
        getChemical in interface Block
        Returns:
        Chemical
      • getChemicalConnAtom

        public ChemicalConnAtom getChemicalConnAtom()
        Description copied from interface: Block
        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.
        Specified by:
        getChemicalConnAtom in interface Block
        Returns:
        ChemicalConnAtom
      • getChemicalConnBond

        public ChemicalConnBond getChemicalConnBond()
        Description copied from interface: Block
        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.
        Specified by:
        getChemicalConnBond in interface Block
        Returns:
        ChemicalConnBond
      • getChemicalFormula

        public ChemicalFormula getChemicalFormula()
        Description copied from interface: Block
        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.
        Specified by:
        getChemicalFormula in interface Block
        Returns:
        ChemicalFormula
      • getCitation

        public Citation getCitation()
        Description copied from interface: Block
        Data items in the CITATION category record details about the literature cited as being relevant to the contents of the data block.
        Specified by:
        getCitation in interface Block
        Returns:
        Citation
      • getCitationAuthor

        public CitationAuthor getCitationAuthor()
        Description copied from interface: Block
        Data items in the CITATION_AUTHOR category record details about the authors associated with the citations in the CITATION list.
        Specified by:
        getCitationAuthor in interface Block
        Returns:
        CitationAuthor
      • getCitationEditor

        public CitationEditor getCitationEditor()
        Description copied from interface: Block
        Data items in the CITATION_EDITOR category record details about the editors associated with the books or book chapters cited in the CITATION list.
        Specified by:
        getCitationEditor in interface Block
        Returns:
        CitationEditor
      • getComputing

        public Computing getComputing()
        Description copied from interface: Block
        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.
        Specified by:
        getComputing in interface Block
        Returns:
        Computing
      • getDatabase

        public Database getDatabase()
        Description copied from interface: Block
        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.
        Specified by:
        getDatabase in interface Block
        Returns:
        Database
      • getDatabase2

        public Database2 getDatabase2()
        Description copied from interface: Block
        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.
        Specified by:
        getDatabase2 in interface Block
        Returns:
        Database2
      • getDatabasePDBCaveat

        public DatabasePDBCaveat getDatabasePDBCaveat()
        Description copied from interface: Block
        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.
        Specified by:
        getDatabasePDBCaveat in interface Block
        Returns:
        DatabasePDBCaveat
      • getDatabasePDBMatrix

        public DatabasePDBMatrix getDatabasePDBMatrix()
        Description copied from interface: Block
        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.
        Specified by:
        getDatabasePDBMatrix in interface Block
        Returns:
        DatabasePDBMatrix
      • getDatabasePDBRemark

        public DatabasePDBRemark getDatabasePDBRemark()
        Description copied from interface: Block
        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.
        Specified by:
        getDatabasePDBRemark in interface Block
        Returns:
        DatabasePDBRemark
      • getDatabasePDBRev

        public DatabasePDBRev getDatabasePDBRev()
        Description copied from interface: Block
        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.
        Specified by:
        getDatabasePDBRev in interface Block
        Returns:
        DatabasePDBRev
      • getDatabasePDBRevRecord

        public DatabasePDBRevRecord getDatabasePDBRevRecord()
        Description copied from interface: Block
        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.
        Specified by:
        getDatabasePDBRevRecord in interface Block
        Returns:
        DatabasePDBRevRecord
      • getDatabasePDBTvect

        public DatabasePDBTvect getDatabasePDBTvect()
        Description copied from interface: Block
        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.
        Specified by:
        getDatabasePDBTvect in interface Block
        Returns:
        DatabasePDBTvect
      • getDiffrn

        public Diffrn getDiffrn()
        Description copied from interface: Block
        Data items in the DIFFRN category record details about the diffraction data and their measurement.
        Specified by:
        getDiffrn in interface Block
        Returns:
        Diffrn
      • getDiffrnAttenuator

        public DiffrnAttenuator getDiffrnAttenuator()
        Description copied from interface: Block
        Data items in the DIFFRN_ATTENUATOR category record details about the diffraction attenuator scales employed.
        Specified by:
        getDiffrnAttenuator in interface Block
        Returns:
        DiffrnAttenuator
      • getDiffrnDetector

        public DiffrnDetector getDiffrnDetector()
        Description copied from interface: Block
        Data items in the DIFFRN_DETECTOR category describe the detector used to measure the scattered radiation, including any analyser and post-sample collimation.
        Specified by:
        getDiffrnDetector in interface Block
        Returns:
        DiffrnDetector
      • getDiffrnMeasurement

        public DiffrnMeasurement getDiffrnMeasurement()
        Description copied from interface: Block
        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.
        Specified by:
        getDiffrnMeasurement in interface Block
        Returns:
        DiffrnMeasurement
      • getDiffrnOrientMatrix

        public DiffrnOrientMatrix getDiffrnOrientMatrix()
        Description copied from interface: Block
        Data items in the DIFFRN_ORIENT_MATRIX category record details about the orientation matrix used in the measurement of the diffraction data.
        Specified by:
        getDiffrnOrientMatrix in interface Block
        Returns:
        DiffrnOrientMatrix
      • getDiffrnOrientRefln

        public DiffrnOrientRefln getDiffrnOrientRefln()
        Description copied from interface: Block
        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.
        Specified by:
        getDiffrnOrientRefln in interface Block
        Returns:
        DiffrnOrientRefln
      • getDiffrnRadiation

        public DiffrnRadiation getDiffrnRadiation()
        Description copied from interface: Block
        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.
        Specified by:
        getDiffrnRadiation in interface Block
        Returns:
        DiffrnRadiation
      • getDiffrnRadiationWavelength

        public DiffrnRadiationWavelength getDiffrnRadiationWavelength()
        Description copied from interface: Block
        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.
        Specified by:
        getDiffrnRadiationWavelength in interface Block
        Returns:
        DiffrnRadiationWavelength
      • getDiffrnRefln

        public DiffrnRefln getDiffrnRefln()
        Description copied from interface: Block
        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.
        Specified by:
        getDiffrnRefln in interface Block
        Returns:
        DiffrnRefln
      • getDiffrnReflns

        public DiffrnReflns getDiffrnReflns()
        Description copied from interface: Block
        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.
        Specified by:
        getDiffrnReflns in interface Block
        Returns:
        DiffrnReflns
      • getDiffrnScaleGroup

        public DiffrnScaleGroup getDiffrnScaleGroup()
        Description copied from interface: Block
        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.
        Specified by:
        getDiffrnScaleGroup in interface Block
        Returns:
        DiffrnScaleGroup
      • getDiffrnSource

        public DiffrnSource getDiffrnSource()
        Description copied from interface: Block
        Data items in the DIFFRN_SOURCE category record details of the source of radiation used in the diffraction experiment.
        Specified by:
        getDiffrnSource in interface Block
        Returns:
        DiffrnSource
      • getDiffrnStandardRefln

        public DiffrnStandardRefln getDiffrnStandardRefln()
        Description copied from interface: Block
        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.
        Specified by:
        getDiffrnStandardRefln in interface Block
        Returns:
        DiffrnStandardRefln
      • getDiffrnStandards

        public DiffrnStandards getDiffrnStandards()
        Description copied from interface: Block
        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.
        Specified by:
        getDiffrnStandards in interface Block
        Returns:
        DiffrnStandards
      • getEntity

        public Entity getEntity()
        Description copied from interface: Block
        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.
        Specified by:
        getEntity in interface Block
        Returns:
        Entity
      • getEntityKeywords

        public EntityKeywords getEntityKeywords()
        Description copied from interface: Block
        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.
        Specified by:
        getEntityKeywords in interface Block
        Returns:
        EntityKeywords
      • getEntityLink

        public EntityLink getEntityLink()
        Description copied from interface: Block
        Data items in the ENTITY_LINK category give details about the links between entities.
        Specified by:
        getEntityLink in interface Block
        Returns:
        EntityLink
      • getEntityNameCom

        public EntityNameCom getEntityNameCom()
        Description copied from interface: Block
        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.
        Specified by:
        getEntityNameCom in interface Block
        Returns:
        EntityNameCom
      • getEntityNameSys

        public EntityNameSys getEntityNameSys()
        Description copied from interface: Block
        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.
        Specified by:
        getEntityNameSys in interface Block
        Returns:
        EntityNameSys
      • getEntityPoly

        public EntityPoly getEntityPoly()
        Description copied from interface: Block
        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.
        Specified by:
        getEntityPoly in interface Block
        Returns:
        EntityPoly
      • getEntityPolySeq

        public EntityPolySeq getEntityPolySeq()
        Description copied from interface: Block
        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.
        Specified by:
        getEntityPolySeq in interface Block
        Returns:
        EntityPolySeq
      • getEntry

        public Entry getEntry()
        Description copied from interface: Block
        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.
        Specified by:
        getEntry in interface Block
        Returns:
        Entry
      • getEntryLink

        public EntryLink getEntryLink()
        Description copied from interface: Block
        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.
        Specified by:
        getEntryLink in interface Block
        Returns:
        EntryLink
      • getExptl

        public Exptl getExptl()
        Description copied from interface: Block
        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.
        Specified by:
        getExptl in interface Block
        Returns:
        Exptl
      • getExptlCrystal

        public ExptlCrystal getExptlCrystal()
        Description copied from interface: Block
        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.
        Specified by:
        getExptlCrystal in interface Block
        Returns:
        ExptlCrystal
      • getExptlCrystalFace

        public ExptlCrystalFace getExptlCrystalFace()
        Description copied from interface: Block
        Data items in the EXPTL_CRYSTAL_FACE category record details of the crystal faces.
        Specified by:
        getExptlCrystalFace in interface Block
        Returns:
        ExptlCrystalFace
      • getExptlCrystalGrow

        public ExptlCrystalGrow getExptlCrystalGrow()
        Description copied from interface: Block
        Data items in the EXPTL_CRYSTAL_GROW category record details about the conditions and methods used to grow the crystal.
        Specified by:
        getExptlCrystalGrow in interface Block
        Returns:
        ExptlCrystalGrow
      • getExptlCrystalGrowComp

        public ExptlCrystalGrowComp getExptlCrystalGrowComp()
        Description copied from interface: Block
        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.
        Specified by:
        getExptlCrystalGrowComp in interface Block
        Returns:
        ExptlCrystalGrowComp
      • getGeom

        public Geom getGeom()
        Description copied from interface: Block
        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.
        Specified by:
        getGeom in interface Block
        Returns:
        Geom
      • getGeomAngle

        public GeomAngle getGeomAngle()
        Description copied from interface: Block
        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.
        Specified by:
        getGeomAngle in interface Block
        Returns:
        GeomAngle
      • getGeomBond

        public GeomBond getGeomBond()
        Description copied from interface: Block
        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.
        Specified by:
        getGeomBond in interface Block
        Returns:
        GeomBond
      • getGeomContact

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

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

        public GeomTorsion getGeomTorsion()
        Description copied from interface: Block
        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.
        Specified by:
        getGeomTorsion in interface Block
        Returns:
        GeomTorsion
      • getJournal

        public Journal getJournal()
        Description copied from interface: Block
        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.
        Specified by:
        getJournal in interface Block
        Returns:
        Journal
      • getJournalIndex

        public JournalIndex getJournalIndex()
        Description copied from interface: Block
        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.
        Specified by:
        getJournalIndex in interface Block
        Returns:
        JournalIndex
      • getPhasing

        public Phasing getPhasing()
        Description copied from interface: Block
        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.
        Specified by:
        getPhasing in interface Block
        Returns:
        Phasing
      • getPhasingAveraging

        public PhasingAveraging getPhasingAveraging()
        Description copied from interface: Block
        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.
        Specified by:
        getPhasingAveraging in interface Block
        Returns:
        PhasingAveraging
      • getPhasingIsomorphous

        public PhasingIsomorphous getPhasingIsomorphous()
        Description copied from interface: Block
        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.
        Specified by:
        getPhasingIsomorphous in interface Block
        Returns:
        PhasingIsomorphous
      • getPhasingMAD

        public PhasingMAD getPhasingMAD()
        Description copied from interface: Block
        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.
        Specified by:
        getPhasingMAD in interface Block
        Returns:
        PhasingMAD
      • getPhasingMADClust

        public PhasingMADClust getPhasingMADClust()
        Description copied from interface: Block
        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.
        Specified by:
        getPhasingMADClust in interface Block
        Returns:
        PhasingMADClust
      • getPhasingMADExpt

        public PhasingMADExpt getPhasingMADExpt()
        Description copied from interface: Block
        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.
        Specified by:
        getPhasingMADExpt in interface Block
        Returns:
        PhasingMADExpt
      • getPhasingMADRatio

        public PhasingMADRatio getPhasingMADRatio()
        Description copied from interface: Block
        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.
        Specified by:
        getPhasingMADRatio in interface Block
        Returns:
        PhasingMADRatio
      • getPhasingMADSet

        public PhasingMADSet getPhasingMADSet()
        Description copied from interface: Block
        Data items in the PHASING_MAD_SET category record details about the individual data sets used in a MAD phasing experiment.
        Specified by:
        getPhasingMADSet in interface Block
        Returns:
        PhasingMADSet
      • getPhasingMIR

        public PhasingMIR getPhasingMIR()
        Description copied from interface: Block
        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).
        Specified by:
        getPhasingMIR in interface Block
        Returns:
        PhasingMIR
      • getPhasingMIRDer

        public PhasingMIRDer getPhasingMIRDer()
        Description copied from interface: Block
        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.
        Specified by:
        getPhasingMIRDer in interface Block
        Returns:
        PhasingMIRDer
      • getPhasingMIRDerRefln

        public PhasingMIRDerRefln getPhasingMIRDerRefln()
        Description copied from interface: Block
        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.
        Specified by:
        getPhasingMIRDerRefln in interface Block
        Returns:
        PhasingMIRDerRefln
      • getPhasingMIRDerShell

        public PhasingMIRDerShell getPhasingMIRDerShell()
        Description copied from interface: Block
        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.)
        Specified by:
        getPhasingMIRDerShell in interface Block
        Returns:
        PhasingMIRDerShell
      • getPhasingMIRDerSite

        public PhasingMIRDerSite getPhasingMIRDerSite()
        Description copied from interface: Block
        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.)
        Specified by:
        getPhasingMIRDerSite in interface Block
        Returns:
        PhasingMIRDerSite
      • getPhasingMIRShell

        public PhasingMIRShell getPhasingMIRShell()
        Description copied from interface: Block
        Data items in the PHASING_MIR_SHELL category record statistics for an isomorphous replacement phasing experiment.broken down into shells of resolution.
        Specified by:
        getPhasingMIRShell in interface Block
        Returns:
        PhasingMIRShell
      • getPhasingSet

        public PhasingSet getPhasingSet()
        Description copied from interface: Block
        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.
        Specified by:
        getPhasingSet in interface Block
        Returns:
        PhasingSet
      • getPhasingSetRefln

        public PhasingSetRefln getPhasingSetRefln()
        Description copied from interface: Block
        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.
        Specified by:
        getPhasingSetRefln in interface Block
        Returns:
        PhasingSetRefln
      • getPubl

        public Publ getPubl()
        Description copied from interface: Block
        Data items in the PUBL category are used when submitting a manuscript for publication.
        Specified by:
        getPubl in interface Block
        Returns:
        Publ
      • getPublAuthor

        public PublAuthor getPublAuthor()
        Description copied from interface: Block
        Data items in the PUBL_AUTHOR category record details of the authors of a manuscript submitted for publication.
        Specified by:
        getPublAuthor in interface Block
        Returns:
        PublAuthor
      • getPublBody

        public PublBody getPublBody()
        Description copied from interface: Block
        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.
        Specified by:
        getPublBody in interface Block
        Returns:
        PublBody
      • getPublManuscriptIncl

        public PublManuscriptIncl getPublManuscriptIncl()
        Description copied from interface: Block
        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.
        Specified by:
        getPublManuscriptIncl in interface Block
        Returns:
        PublManuscriptIncl
      • getRefine

        public Refine getRefine()
        Description copied from interface: Block
        Data items in the REFINE category record details about the structure-refinement parameters.
        Specified by:
        getRefine in interface Block
        Returns:
        Refine
      • getRefineAnalyze

        public RefineAnalyze getRefineAnalyze()
        Description copied from interface: Block
        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.
        Specified by:
        getRefineAnalyze in interface Block
        Returns:
        RefineAnalyze
      • getRefineBIso

        public RefineBIso getRefineBIso()
        Description copied from interface: Block
        Data items in the REFINE_B_ISO category record details about the treatment of isotropic B factors (displacement parameters) during refinement.
        Specified by:
        getRefineBIso in interface Block
        Returns:
        RefineBIso
      • getRefineFunctMinimized

        public RefineFunctMinimized getRefineFunctMinimized()
        Description copied from interface: Block
        Data items in the REFINE_FUNCT_MINIMIZED category record details about the individual terms of the function minimized during refinement.
        Specified by:
        getRefineFunctMinimized in interface Block
        Returns:
        RefineFunctMinimized
      • getRefineHist

        public RefineHist getRefineHist()
        Description copied from interface: Block
        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.
        Specified by:
        getRefineHist in interface Block
        Returns:
        RefineHist
      • getRefineLsRestr

        public RefineLsRestr getRefineLsRestr()
        Description copied from interface: Block
        Data items in the REFINE_LS_RESTR category record details about the restraints applied to various classes of parameters during the least-squares refinement.
        Specified by:
        getRefineLsRestr in interface Block
        Returns:
        RefineLsRestr
      • getRefineLsRestrNcs

        public RefineLsRestrNcs getRefineLsRestrNcs()
        Description copied from interface: Block
        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.
        Specified by:
        getRefineLsRestrNcs in interface Block
        Returns:
        RefineLsRestrNcs
      • getRefineLsRestrType

        public RefineLsRestrType getRefineLsRestrType()
        Description copied from interface: Block
        Data items in the REFINE_LS_RESTR_TYPE category record details about the restraint types used in the least-squares refinement.
        Specified by:
        getRefineLsRestrType in interface Block
        Returns:
        RefineLsRestrType
      • getRefineLsShell

        public RefineLsShell getRefineLsShell()
        Description copied from interface: Block
        Data items in the REFINE_LS_SHELL category record details about the results of the least-squares refinement broken down into shells of resolution.
        Specified by:
        getRefineLsShell in interface Block
        Returns:
        RefineLsShell
      • getRefineOccupancy

        public RefineOccupancy getRefineOccupancy()
        Description copied from interface: Block
        Data items in the REFINE_OCCUPANCY category record details about the treatment of atom occupancies during refinement.
        Specified by:
        getRefineOccupancy in interface Block
        Returns:
        RefineOccupancy
      • getRefln

        public Refln getRefln()
        Description copied from interface: Block
        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.
        Specified by:
        getRefln in interface Block
        Returns:
        Refln
      • getReflnSysAbs

        public ReflnSysAbs getReflnSysAbs()
        Description copied from interface: Block
        Data items in the REFLN_SYS_ABS category record details about the reflection data that should be systematically absent, given the designated space group.
        Specified by:
        getReflnSysAbs in interface Block
        Returns:
        ReflnSysAbs
      • getReflns

        public Reflns getReflns()
        Description copied from interface: Block
        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.
        Specified by:
        getReflns in interface Block
        Returns:
        Reflns
      • getReflnsScale

        public ReflnsScale getReflnsScale()
        Description copied from interface: Block
        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.
        Specified by:
        getReflnsScale in interface Block
        Returns:
        ReflnsScale
      • getReflnsShell

        public ReflnsShell getReflnsShell()
        Description copied from interface: Block
        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.
        Specified by:
        getReflnsShell in interface Block
        Returns:
        ReflnsShell
      • getSoftware

        public Software getSoftware()
        Description copied from interface: Block
        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.
        Specified by:
        getSoftware in interface Block
        Returns:
        Software
      • getStruct

        public Struct getStruct()
        Description copied from interface: Block
        Data items in the STRUCT category record details about the description of the crystallographic structure.
        Specified by:
        getStruct in interface Block
        Returns:
        Struct
      • getStructAsym

        public StructAsym getStructAsym()
        Description copied from interface: Block
        Data items in the STRUCT_ASYM category record details about the structural elements in the asymmetric unit.
        Specified by:
        getStructAsym in interface Block
        Returns:
        StructAsym
      • getStructBiol

        public StructBiol getStructBiol()
        Description copied from interface: Block
        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.
        Specified by:
        getStructBiol in interface Block
        Returns:
        StructBiol
      • getStructBiolGen

        public StructBiolGen getStructBiolGen()
        Description copied from interface: Block
        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.
        Specified by:
        getStructBiolGen in interface Block
        Returns:
        StructBiolGen
      • getStructBiolKeywords

        public StructBiolKeywords getStructBiolKeywords()
        Description copied from interface: Block
        Data items in the STRUCT_BIOL_KEYWORDS category record keywords that describe each biological unit.
        Specified by:
        getStructBiolKeywords in interface Block
        Returns:
        StructBiolKeywords
      • getStructBiolView

        public StructBiolView getStructBiolView()
        Description copied from interface: Block
        Data items in the STRUCT_BIOL_VIEW category record details about how to draw and annotate an informative view of the biological structure.
        Specified by:
        getStructBiolView in interface Block
        Returns:
        StructBiolView
      • getStructConf

        public StructConf getStructConf()
        Description copied from interface: Block
        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.
        Specified by:
        getStructConf in interface Block
        Returns:
        StructConf
      • getStructConfType

        public StructConfType getStructConfType()
        Description copied from interface: Block
        Data items in the STRUCT_CONF_TYPE category record details about the criteria used to identify backbone conformations of a segment of polymer.
        Specified by:
        getStructConfType in interface Block
        Returns:
        StructConfType
      • getStructConn

        public StructConn getStructConn()
        Description copied from interface: Block
        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.
        Specified by:
        getStructConn in interface Block
        Returns:
        StructConn
      • getStructConnType

        public StructConnType getStructConnType()
        Description copied from interface: Block
        Data items in the STRUCT_CONN_TYPE category record details about the criteria used to identify interactions between portions of the structure.
        Specified by:
        getStructConnType in interface Block
        Returns:
        StructConnType
      • getStructKeywords

        public StructKeywords getStructKeywords()
        Description copied from interface: Block
        Data items in the STRUCT_KEYWORDS category specify keywords that describe the chemical structure in this entry.
        Specified by:
        getStructKeywords in interface Block
        Returns:
        StructKeywords
      • getStructMonDetails

        public StructMonDetails getStructMonDetails()
        Description copied from interface: Block
        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.
        Specified by:
        getStructMonDetails in interface Block
        Returns:
        StructMonDetails
      • getStructMonNucl

        public StructMonNucl getStructMonNucl()
        Description copied from interface: Block
        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.
        Specified by:
        getStructMonNucl in interface Block
        Returns:
        StructMonNucl
      • getStructMonProt

        public StructMonProt getStructMonProt()
        Description copied from interface: Block
        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.
        Specified by:
        getStructMonProt in interface Block
        Returns:
        StructMonProt
      • getStructMonProtCis

        public StructMonProtCis getStructMonProtCis()
        Description copied from interface: Block
        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.
        Specified by:
        getStructMonProtCis in interface Block
        Returns:
        StructMonProtCis
      • getStructNcsDom

        public StructNcsDom getStructNcsDom()
        Description copied from interface: Block
        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.
        Specified by:
        getStructNcsDom in interface Block
        Returns:
        StructNcsDom
      • getStructNcsDomLim

        public StructNcsDomLim getStructNcsDomLim()
        Description copied from interface: Block
        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.
        Specified by:
        getStructNcsDomLim in interface Block
        Returns:
        StructNcsDomLim
      • getStructNcsEns

        public StructNcsEns getStructNcsEns()
        Description copied from interface: Block
        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.
        Specified by:
        getStructNcsEns in interface Block
        Returns:
        StructNcsEns
      • getStructNcsEnsGen

        public StructNcsEnsGen getStructNcsEnsGen()
        Description copied from interface: Block
        Data items in the STRUCT_NCS_ENS_GEN category list domains related by a noncrystallographic symmetry operation and identify the operator.
        Specified by:
        getStructNcsEnsGen in interface Block
        Returns:
        StructNcsEnsGen
      • getStructNcsOper

        public StructNcsOper getStructNcsOper()
        Description copied from interface: Block
        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.
        Specified by:
        getStructNcsOper in interface Block
        Returns:
        StructNcsOper
      • getStructRef

        public StructRef getStructRef()
        Description copied from interface: Block
        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.
        Specified by:
        getStructRef in interface Block
        Returns:
        StructRef
      • getStructRefSeq

        public StructRefSeq getStructRefSeq()
        Description copied from interface: Block
        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.
        Specified by:
        getStructRefSeq in interface Block
        Returns:
        StructRefSeq
      • getStructRefSeqDif

        public StructRefSeqDif getStructRefSeqDif()
        Description copied from interface: Block
        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.
        Specified by:
        getStructRefSeqDif in interface Block
        Returns:
        StructRefSeqDif
      • getStructSheet

        public StructSheet getStructSheet()
        Description copied from interface: Block
        Data items in the STRUCT_SHEET category record details about the beta-sheets.
        Specified by:
        getStructSheet in interface Block
        Returns:
        StructSheet
      • getStructSheetHbond

        public StructSheetHbond getStructSheetHbond()
        Description copied from interface: Block
        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.
        Specified by:
        getStructSheetHbond in interface Block
        Returns:
        StructSheetHbond
      • getStructSheetOrder

        public StructSheetOrder getStructSheetOrder()
        Description copied from interface: Block
        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.
        Specified by:
        getStructSheetOrder in interface Block
        Returns:
        StructSheetOrder
      • getStructSheetRange

        public StructSheetRange getStructSheetRange()
        Description copied from interface: Block
        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.
        Specified by:
        getStructSheetRange in interface Block
        Returns:
        StructSheetRange
      • getStructSheetTopology

        public StructSheetTopology getStructSheetTopology()
        Description copied from interface: Block
        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.
        Specified by:
        getStructSheetTopology in interface Block
        Returns:
        StructSheetTopology
      • getStructSite

        public StructSite getStructSite()
        Description copied from interface: Block
        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).
        Specified by:
        getStructSite in interface Block
        Returns:
        StructSite
      • getStructSiteGen

        public StructSiteGen getStructSiteGen()
        Description copied from interface: Block
        Data items in the STRUCT_SITE_GEN category record details about the generation of portions of the structure that contribute to structurally relevant sites.
        Specified by:
        getStructSiteGen in interface Block
        Returns:
        StructSiteGen
      • getStructSiteKeywords

        public StructSiteKeywords getStructSiteKeywords()
        Description copied from interface: Block
        Data items in the STRUCT_SITE_KEYWORDS category record keywords describing the site.
        Specified by:
        getStructSiteKeywords in interface Block
        Returns:
        StructSiteKeywords
      • getStructSiteView

        public StructSiteView getStructSiteView()
        Description copied from interface: Block
        Data items in the STRUCT_SITE_VIEW category record details about how to draw and annotate an informative view of the site.
        Specified by:
        getStructSiteView in interface Block
        Returns:
        StructSiteView
      • getSymmetry

        public Symmetry getSymmetry()
        Description copied from interface: Block
        Data items in the SYMMETRY category record details about the space-group symmetry.
        Specified by:
        getSymmetry in interface Block
        Returns:
        Symmetry
      • getSymmetryEquiv

        public SymmetryEquiv getSymmetryEquiv()
        Description copied from interface: Block
        Data items in the SYMMETRY_EQUIV category list the symmetry-equivalent positions for the space group.
        Specified by:
        getSymmetryEquiv in interface Block
        Returns:
        SymmetryEquiv
      • getAuditLink

        public AuditLink getAuditLink()
        Description copied from interface: Block
        Data items in the AUDIT_LINK category record details about the relationships between data blocks in the current CIF.
        Specified by:
        getAuditLink in interface Block
        Returns:
        AuditLink
      • getDiffrnReflnsClass

        public DiffrnReflnsClass getDiffrnReflnsClass()
        Description copied from interface: Block
        Data items in the DIFFRN_REFLNS_CLASS category record details about the classes of reflections measured in the diffraction experiment.
        Specified by:
        getDiffrnReflnsClass in interface Block
        Returns:
        DiffrnReflnsClass
      • getRefineLsClass

        public RefineLsClass getRefineLsClass()
        Description copied from interface: Block
        Data items in the REFINE_LS_CLASS category record details about the reflections used for the structure refinement for each reflection class separately.
        Specified by:
        getRefineLsClass in interface Block
        Returns:
        RefineLsClass
      • getReflnsClass

        public ReflnsClass getReflnsClass()
        Description copied from interface: Block
        Data items in the REFLNS_CLASS category record details of the reflections used to determine the structural parameters for each reflection class.
        Specified by:
        getReflnsClass in interface Block
        Returns:
        ReflnsClass
      • getSpaceGroup

        public SpaceGroup getSpaceGroup()
        Description copied from interface: Block
        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.
        Specified by:
        getSpaceGroup in interface Block
        Returns:
        SpaceGroup
      • getSpaceGroupSymop

        public SpaceGroupSymop getSpaceGroupSymop()
        Description copied from interface: Block
        Contains information about the symmetry operations of the space group.
        Specified by:
        getSpaceGroupSymop in interface Block
        Returns:
        SpaceGroupSymop
      • getValenceParam

        public ValenceParam getValenceParam()
        Description copied from interface: Block
        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.
        Specified by:
        getValenceParam in interface Block
        Returns:
        ValenceParam
      • getValenceRef

        public ValenceRef getValenceRef()
        Description copied from interface: Block
        Data items in the VALENCE_REF category list the references from which the bond-valence parameters have been taken.
        Specified by:
        getValenceRef in interface Block
        Returns:
        ValenceRef
      • getPdbxAudit

        public PdbxAudit getPdbxAudit()
        Description copied from interface: Block
        The PDBX_AUDIT holds current version information.
        Specified by:
        getPdbxAudit in interface Block
        Returns:
        PdbxAudit
      • getPdbxVersion

        public PdbxVersion getPdbxVersion()
        Description copied from interface: Block
        Data items in the PDBX_VERSION category record details about the version of this entry.
        Specified by:
        getPdbxVersion in interface Block
        Returns:
        PdbxVersion
      • getPdbxAuditAuthor

        public PdbxAuditAuthor getPdbxAuditAuthor()
        Description copied from interface: Block
        Data items in the PDBX_AUDIT_AUTHOR category record details about the author(s) of the data block.
        Specified by:
        getPdbxAuditAuthor in interface Block
        Returns:
        PdbxAuditAuthor
      • getPdbxDatabaseMessage

        public PdbxDatabaseMessage getPdbxDatabaseMessage()
        Description copied from interface: Block
        The PDBX_DATABASE_MESSAGE category provides information about correspondance related to a structure deposition.
        Specified by:
        getPdbxDatabaseMessage in interface Block
        Returns:
        PdbxDatabaseMessage
      • getPdbxDatabasePDBObsSpr

        public PdbxDatabasePDBObsSpr getPdbxDatabasePDBObsSpr()
        Description copied from interface: Block
        The PDBX_DATABASE_PDB_OBS_SPR category provides placeholders for information on obsolete/superseded PDB entries
        Specified by:
        getPdbxDatabasePDBObsSpr in interface Block
        Returns:
        PdbxDatabasePDBObsSpr
      • getPdbxDatabaseProc

        public PdbxDatabaseProc getPdbxDatabaseProc()
        Description copied from interface: Block
        Internal records to track the data processing cycle.
        Specified by:
        getPdbxDatabaseProc in interface Block
        Returns:
        PdbxDatabaseProc
      • getPdbxDatabaseRemark

        public PdbxDatabaseRemark getPdbxDatabaseRemark()
        Description copied from interface: Block
        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).
        Specified by:
        getPdbxDatabaseRemark in interface Block
        Returns:
        PdbxDatabaseRemark
      • getPdbxDatabaseStatus

        public PdbxDatabaseStatus getPdbxDatabaseStatus()
        Description copied from interface: Block
        These are internal RCSB records to keep track of data processing and status of the entry.
        Specified by:
        getPdbxDatabaseStatus in interface Block
        Returns:
        PdbxDatabaseStatus
      • getPdbxEntityName

        public PdbxEntityName getPdbxEntityName()
        Description copied from interface: Block
        The PDBX_ENTITY_NAME records additional name information for each entity.
        Specified by:
        getPdbxEntityName in interface Block
        Returns:
        PdbxEntityName
      • getPdbxPrereleaseSeq

        public PdbxPrereleaseSeq getPdbxPrereleaseSeq()
        Description copied from interface: Block
        This category provides a placeholder for pre-release sequence information. After release this category should be discarded.
        Specified by:
        getPdbxPrereleaseSeq in interface Block
        Returns:
        PdbxPrereleaseSeq
      • getPdbxPolySeqScheme

        public PdbxPolySeqScheme getPdbxPolySeqScheme()
        Description copied from interface: Block
        The PDBX_POLY_SEQ_SCHEME category provides residue level nomenclature mapping for polymer entities.
        Specified by:
        getPdbxPolySeqScheme in interface Block
        Returns:
        PdbxPolySeqScheme
      • getPdbxNonpolyScheme

        public PdbxNonpolyScheme getPdbxNonpolyScheme()
        Description copied from interface: Block
        The PDBX_NONPOLY_SCHEME category provides residue level nomenclature mapping for non-polymer entities.
        Specified by:
        getPdbxNonpolyScheme in interface Block
        Returns:
        PdbxNonpolyScheme
      • getPdbxRefine

        public PdbxRefine getPdbxRefine()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxRefine in interface Block
        Returns:
        PdbxRefine
      • getPdbxStructSheetHbond

        public PdbxStructSheetHbond getPdbxStructSheetHbond()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxStructSheetHbond in interface Block
        Returns:
        PdbxStructSheetHbond
      • getPdbxXplorFile

        public PdbxXplorFile getPdbxXplorFile()
        Description copied from interface: Block
        Parameter and topology files used in X-PLOR/CNS refinement.
        Specified by:
        getPdbxXplorFile in interface Block
        Returns:
        PdbxXplorFile
      • getPdbxRefineAuxFile

        public PdbxRefineAuxFile getPdbxRefineAuxFile()
        Description copied from interface: Block
        Auxilary parameter and topology files used in refinement.
        Specified by:
        getPdbxRefineAuxFile in interface Block
        Returns:
        PdbxRefineAuxFile
      • getPdbxDatabaseRelated

        public PdbxDatabaseRelated getPdbxDatabaseRelated()
        Description copied from interface: Block
        Data items in PDBX_DATABASE_RELATED contain references to entries that are related to the this entry.
        Specified by:
        getPdbxDatabaseRelated in interface Block
        Returns:
        PdbxDatabaseRelated
      • getPdbxEntityAssembly

        public PdbxEntityAssembly getPdbxEntityAssembly()
        Description copied from interface: Block
        The PDBX_ENTITY_ASSEMBLY category provides a chemical description of the biological assembly studied in terms of its constituent entities.
        Specified by:
        getPdbxEntityAssembly in interface Block
        Returns:
        PdbxEntityAssembly
      • getPdbxExptlCrystalGrowComp

        public PdbxExptlCrystalGrowComp getPdbxExptlCrystalGrowComp()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxExptlCrystalGrowComp in interface Block
        Returns:
        PdbxExptlCrystalGrowComp
      • getPdbxExptlCrystalGrowSol

        public PdbxExptlCrystalGrowSol getPdbxExptlCrystalGrowSol()
        Description copied from interface: Block
        Data items in the PDBX_EXPTL_CRYSTAL_GROW_SOL category record details about the solutions that were 'mixed' to produce the crystal.
        Specified by:
        getPdbxExptlCrystalGrowSol in interface Block
        Returns:
        PdbxExptlCrystalGrowSol
      • getPdbxExptlCrystalCryoTreatment

        public PdbxExptlCrystalCryoTreatment getPdbxExptlCrystalCryoTreatment()
        Description copied from interface: Block
        Data items in the PDBX_EXPTL_CRYSTAL_CRYO_TREATMENT category record details cryogenic treatments applied to this crystal.
        Specified by:
        getPdbxExptlCrystalCryoTreatment in interface Block
        Returns:
        PdbxExptlCrystalCryoTreatment
      • getPdbxRefineTls

        public PdbxRefineTls getPdbxRefineTls()
        Description copied from interface: Block
        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
        Specified by:
        getPdbxRefineTls in interface Block
        Returns:
        PdbxRefineTls
      • getPdbxRefineTlsGroup

        public PdbxRefineTlsGroup getPdbxRefineTlsGroup()
        Description copied from interface: Block
        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
        Specified by:
        getPdbxRefineTlsGroup in interface Block
        Returns:
        PdbxRefineTlsGroup
      • getPdbxContactAuthor

        public PdbxContactAuthor getPdbxContactAuthor()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxContactAuthor in interface Block
        Returns:
        PdbxContactAuthor
      • getPdbxSGProject

        public PdbxSGProject getPdbxSGProject()
        Description copied from interface: Block
        Data items in the PDBX_CONTACT_AUTHOR category record details about the Structural Genomics Project and name and initials for each Center.
        Specified by:
        getPdbxSGProject in interface Block
        Returns:
        PdbxSGProject
      • getPdbxAtomSiteAnisoTls

        public PdbxAtomSiteAnisoTls getPdbxAtomSiteAnisoTls()
        Description copied from interface: Block
        Data items in the PDBX_ATOM_SITE_ANISO_TLS category record details about the TLS contribution to anisotropic displacement parameters.
        Specified by:
        getPdbxAtomSiteAnisoTls in interface Block
        Returns:
        PdbxAtomSiteAnisoTls
      • getPdbxNmrDetails

        public PdbxNmrDetails getPdbxNmrDetails()
        Description copied from interface: Block
        Experimental details of the NMR study that have not been described elsewhere in this deposition.
        Specified by:
        getPdbxNmrDetails in interface Block
        Returns:
        PdbxNmrDetails
      • getPdbxNmrSampleDetails

        public PdbxNmrSampleDetails getPdbxNmrSampleDetails()
        Description copied from interface: Block
        Complete description of each NMR sample, including the solvent system used.
        Specified by:
        getPdbxNmrSampleDetails in interface Block
        Returns:
        PdbxNmrSampleDetails
      • getPdbxNmrExptlSample

        public PdbxNmrExptlSample getPdbxNmrExptlSample()
        Description copied from interface: Block
        The chemical constituents of each NMR sample. Each sample is identified by a number and each component in the sample is identified by name.
        Specified by:
        getPdbxNmrExptlSample in interface Block
        Returns:
        PdbxNmrExptlSample
      • getPdbxNmrExptlSampleConditions

        public PdbxNmrExptlSampleConditions getPdbxNmrExptlSampleConditions()
        Description copied from interface: Block
        The experimental conditions used to for each sample. Each set of conditions is identified by a numerical code.
        Specified by:
        getPdbxNmrExptlSampleConditions in interface Block
        Returns:
        PdbxNmrExptlSampleConditions
      • getPdbxNmrSpectrometer

        public PdbxNmrSpectrometer getPdbxNmrSpectrometer()
        Description copied from interface: Block
        The details about each spectrometer used to collect data for this deposition.
        Specified by:
        getPdbxNmrSpectrometer in interface Block
        Returns:
        PdbxNmrSpectrometer
      • getPdbxNmrExptl

        public PdbxNmrExptl getPdbxNmrExptl()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxNmrExptl in interface Block
        Returns:
        PdbxNmrExptl
      • getPdbxNmrSoftware

        public PdbxNmrSoftware getPdbxNmrSoftware()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxNmrSoftware in interface Block
        Returns:
        PdbxNmrSoftware
      • getPdbxNmrConstraints

        public PdbxNmrConstraints getPdbxNmrConstraints()
        Description copied from interface: Block
        This section provides a tabulation of constraint data.
        Specified by:
        getPdbxNmrConstraints in interface Block
        Returns:
        PdbxNmrConstraints
      • getPdbxNmrEnsemble

        public PdbxNmrEnsemble getPdbxNmrEnsemble()
        Description copied from interface: Block
        This category contains the information that describes the ensemble of deposited structures. If only an average structure has been deposited skip this section.
        Specified by:
        getPdbxNmrEnsemble in interface Block
        Returns:
        PdbxNmrEnsemble
      • getPdbxNmrEnsembleRms

        public PdbxNmrEnsembleRms getPdbxNmrEnsembleRms()
        Description copied from interface: Block
        Structural statistics are derived from molecular dynamics and simulated annealing programs.
        Specified by:
        getPdbxNmrEnsembleRms in interface Block
        Returns:
        PdbxNmrEnsembleRms
      • getPdbxNmrRepresentative

        public PdbxNmrRepresentative getPdbxNmrRepresentative()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxNmrRepresentative in interface Block
        Returns:
        PdbxNmrRepresentative
      • getPdbxNmrRefine

        public PdbxNmrRefine getPdbxNmrRefine()
        Description copied from interface: Block
        Describe the method and details of the refinement of the deposited structure.
        Specified by:
        getPdbxNmrRefine in interface Block
        Returns:
        PdbxNmrRefine
      • getPdbxNmrForceConstants

        public PdbxNmrForceConstants getPdbxNmrForceConstants()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxNmrForceConstants in interface Block
        Returns:
        PdbxNmrForceConstants
      • getNdbStructConfNa

        public NdbStructConfNa getNdbStructConfNa()
        Description copied from interface: Block
        Data items in the NDB_STRUCT_CONF_NA category describes secondary structure features in this entry.
        Specified by:
        getNdbStructConfNa in interface Block
        Returns:
        NdbStructConfNa
      • getNdbStructFeatureNa

        public NdbStructFeatureNa getNdbStructFeatureNa()
        Description copied from interface: Block
        Data items in the NDB_STRUCT_FEATURE_NA category describes tertiary and other special structural features in this entry.
        Specified by:
        getNdbStructFeatureNa in interface Block
        Returns:
        NdbStructFeatureNa
      • getNdbStructNaBasePair

        public NdbStructNaBasePair getNdbStructNaBasePair()
        Description copied from interface: Block
        Data items in the NDB_STRUCT_NA_BASE_PAIR category record details of base pairing interactions.
        Specified by:
        getNdbStructNaBasePair in interface Block
        Returns:
        NdbStructNaBasePair
      • getNdbStructNaBasePairStep

        public NdbStructNaBasePairStep getNdbStructNaBasePairStep()
        Description copied from interface: Block
        Data items in the NDB_STRUCT_NA_BASE_PAIR_STEP category record details of base pair step interactions.
        Specified by:
        getNdbStructNaBasePairStep in interface Block
        Returns:
        NdbStructNaBasePairStep
      • getPdbxPhasingDm

        public PdbxPhasingDm getPdbxPhasingDm()
        Description copied from interface: Block
        Data items in the PDBX_PHASING_DM category record details about density modification
        Specified by:
        getPdbxPhasingDm in interface Block
        Returns:
        PdbxPhasingDm
      • getPdbxPhasingDmShell

        public PdbxPhasingDmShell getPdbxPhasingDmShell()
        Description copied from interface: Block
        Data items in the PDBX_PHASING_DM_SHELL category record details about density modification in resolution shell.
        Specified by:
        getPdbxPhasingDmShell in interface Block
        Returns:
        PdbxPhasingDmShell
      • getPdbxPhasingMADShell

        public PdbxPhasingMADShell getPdbxPhasingMADShell()
        Description copied from interface: Block
        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)
        Specified by:
        getPdbxPhasingMADShell in interface Block
        Returns:
        PdbxPhasingMADShell
      • getPdbxPhasingMADSet

        public PdbxPhasingMADSet getPdbxPhasingMADSet()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxPhasingMADSet in interface Block
        Returns:
        PdbxPhasingMADSet
      • getPdbxPhasingMADSetShell

        public PdbxPhasingMADSetShell getPdbxPhasingMADSetShell()
        Description copied from interface: Block
        The same as category pdbx_phasing_MAD_set, but broken into shells.
        Specified by:
        getPdbxPhasingMADSetShell in interface Block
        Returns:
        PdbxPhasingMADSetShell
      • getPdbxPhasingMADSetSite

        public PdbxPhasingMADSetSite getPdbxPhasingMADSetSite()
        Description copied from interface: Block
        record the details (coordinates etc.) of anomalous scatters.
        Specified by:
        getPdbxPhasingMADSetSite in interface Block
        Returns:
        PdbxPhasingMADSetSite
      • getPdbxPhasingMR

        public PdbxPhasingMR getPdbxPhasingMR()
        Description copied from interface: Block
        Data items in the PDBX_PHASING_MR category record details about molecular replacement.
        Specified by:
        getPdbxPhasingMR in interface Block
        Returns:
        PdbxPhasingMR
      • getPdbxRefineComponent

        public PdbxRefineComponent getPdbxRefineComponent()
        Description copied from interface: Block
        Data items in the PDBX_REFINE_COMPONENT category record statistics of the final model relative to the density map.
        Specified by:
        getPdbxRefineComponent in interface Block
        Returns:
        PdbxRefineComponent
      • getPdbxEntityProdProtocol

        public PdbxEntityProdProtocol getPdbxEntityProdProtocol()
        Description copied from interface: Block
        This category contains descriptive protocols for the production of this entity.
        Specified by:
        getPdbxEntityProdProtocol in interface Block
        Returns:
        PdbxEntityProdProtocol
      • getPdbxEntitySrcGenProdOther

        public PdbxEntitySrcGenProdOther getPdbxEntitySrcGenProdOther()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxEntitySrcGenProdOther in interface Block
        Returns:
        PdbxEntitySrcGenProdOther
      • getPdbxEntitySrcGenProdPcr

        public PdbxEntitySrcGenProdPcr getPdbxEntitySrcGenProdPcr()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxEntitySrcGenProdPcr in interface Block
        Returns:
        PdbxEntitySrcGenProdPcr
      • getPdbxEntitySrcGenProdDigest

        public PdbxEntitySrcGenProdDigest getPdbxEntitySrcGenProdDigest()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxEntitySrcGenProdDigest in interface Block
        Returns:
        PdbxEntitySrcGenProdDigest
      • getPdbxEntitySrcGenClone

        public PdbxEntitySrcGenClone getPdbxEntitySrcGenClone()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxEntitySrcGenClone in interface Block
        Returns:
        PdbxEntitySrcGenClone
      • getPdbxEntitySrcGenCloneLigation

        public PdbxEntitySrcGenCloneLigation getPdbxEntitySrcGenCloneLigation()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxEntitySrcGenCloneLigation in interface Block
        Returns:
        PdbxEntitySrcGenCloneLigation
      • getPdbxEntitySrcGenCloneRecombination

        public PdbxEntitySrcGenCloneRecombination getPdbxEntitySrcGenCloneRecombination()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxEntitySrcGenCloneRecombination in interface Block
        Returns:
        PdbxEntitySrcGenCloneRecombination
      • getPdbxEntitySrcGenExpress

        public PdbxEntitySrcGenExpress getPdbxEntitySrcGenExpress()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxEntitySrcGenExpress in interface Block
        Returns:
        PdbxEntitySrcGenExpress
      • getPdbxEntitySrcGenExpressTimepoint

        public PdbxEntitySrcGenExpressTimepoint getPdbxEntitySrcGenExpressTimepoint()
        Description copied from interface: Block
        This category contains details for OD time series used to monitor a given EXPRESSION step used in the overall protein production process.
        Specified by:
        getPdbxEntitySrcGenExpressTimepoint in interface Block
        Returns:
        PdbxEntitySrcGenExpressTimepoint
      • getPdbxEntitySrcGenLysis

        public PdbxEntitySrcGenLysis getPdbxEntitySrcGenLysis()
        Description copied from interface: Block
        This category contains details for the cell lysis steps used in the overall protein production process.
        Specified by:
        getPdbxEntitySrcGenLysis in interface Block
        Returns:
        PdbxEntitySrcGenLysis
      • getPdbxEntitySrcGenRefold

        public PdbxEntitySrcGenRefold getPdbxEntitySrcGenRefold()
        Description copied from interface: Block
        This category contains details for the refolding steps used in the overall protein production process.
        Specified by:
        getPdbxEntitySrcGenRefold in interface Block
        Returns:
        PdbxEntitySrcGenRefold
      • getPdbxEntitySrcGenProteolysis

        public PdbxEntitySrcGenProteolysis getPdbxEntitySrcGenProteolysis()
        Description copied from interface: Block
        This category contains details for the protein purification tag removal steps used in the overall protein production process
        Specified by:
        getPdbxEntitySrcGenProteolysis in interface Block
        Returns:
        PdbxEntitySrcGenProteolysis
      • getPdbxEntitySrcGenChrom

        public PdbxEntitySrcGenChrom getPdbxEntitySrcGenChrom()
        Description copied from interface: Block
        This category contains details for the chromatographic steps used in the purification of the protein.
        Specified by:
        getPdbxEntitySrcGenChrom in interface Block
        Returns:
        PdbxEntitySrcGenChrom
      • getPdbxEntitySrcGenFract

        public PdbxEntitySrcGenFract getPdbxEntitySrcGenFract()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxEntitySrcGenFract in interface Block
        Returns:
        PdbxEntitySrcGenFract
      • getPdbxEntitySrcGenPure

        public PdbxEntitySrcGenPure getPdbxEntitySrcGenPure()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxEntitySrcGenPure in interface Block
        Returns:
        PdbxEntitySrcGenPure
      • getPdbxEntitySrcGenCharacter

        public PdbxEntitySrcGenCharacter getPdbxEntitySrcGenCharacter()
        Description copied from interface: Block
        This category contains details of protein characterisation. It refers to the characteristion of the product of a specific step.
        Specified by:
        getPdbxEntitySrcGenCharacter in interface Block
        Returns:
        PdbxEntitySrcGenCharacter
      • getPdbxConstruct

        public PdbxConstruct getPdbxConstruct()
        Description copied from interface: Block
        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).
        Specified by:
        getPdbxConstruct in interface Block
        Returns:
        PdbxConstruct
      • getPdbxConstructFeature

        public PdbxConstructFeature getPdbxConstructFeature()
        Description copied from interface: Block
        Data items in the PDBX_CONSTRUCT_FEATURE category may be used to specify various properties of a nucleic acid sequence used during protein production.
        Specified by:
        getPdbxConstructFeature in interface Block
        Returns:
        PdbxConstructFeature
      • getPdbxRobotSystem

        public PdbxRobotSystem getPdbxRobotSystem()
        Description copied from interface: Block
        The details about each robotic system used to collect data for this project.
        Specified by:
        getPdbxRobotSystem in interface Block
        Returns:
        PdbxRobotSystem
      • getPdbxBuffer

        public PdbxBuffer getPdbxBuffer()
        Description copied from interface: Block
        Data items in the PDBX_BUFFER category record details of the sample buffer.
        Specified by:
        getPdbxBuffer in interface Block
        Returns:
        PdbxBuffer
      • getPdbxDomain

        public PdbxDomain getPdbxDomain()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxDomain in interface Block
        Returns:
        PdbxDomain
      • getPdbxDomainRange

        public PdbxDomainRange getPdbxDomainRange()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxDomainRange in interface Block
        Returns:
        PdbxDomainRange
      • getPdbxSequenceRange

        public PdbxSequenceRange getPdbxSequenceRange()
        Description copied from interface: Block
        Data items in the PDBX_SEQUENCE_RANGE category identify the beginning and ending points of polypeptide sequence segments.
        Specified by:
        getPdbxSequenceRange in interface Block
        Returns:
        PdbxSequenceRange
      • getPdbxFeatureEntry

        public PdbxFeatureEntry getPdbxFeatureEntry()
        Description copied from interface: Block
        Data items in the PDBX_FEATURE_ENTRY category records information about properties pertaining to this structure entry.
        Specified by:
        getPdbxFeatureEntry in interface Block
        Returns:
        PdbxFeatureEntry
      • getPdbxFeatureDomain

        public PdbxFeatureDomain getPdbxFeatureDomain()
        Description copied from interface: Block
        Data items in the PDBX_FEATURE_DOMAIN category records information about properties pertaining to this structure domain.
        Specified by:
        getPdbxFeatureDomain in interface Block
        Returns:
        PdbxFeatureDomain
      • getPdbxFeatureSequenceRange

        public PdbxFeatureSequenceRange getPdbxFeatureSequenceRange()
        Description copied from interface: Block
        Data items in the PDBX_FEATURE_SEQUENCE_RANGE category records information about properties pertaining to this structure sequence_range.
        Specified by:
        getPdbxFeatureSequenceRange in interface Block
        Returns:
        PdbxFeatureSequenceRange
      • getPdbxFeatureAssembly

        public PdbxFeatureAssembly getPdbxFeatureAssembly()
        Description copied from interface: Block
        Data items in the PDBX_FEATURE_ASSEMBLY category records information about properties pertaining to this structural assembly.
        Specified by:
        getPdbxFeatureAssembly in interface Block
        Returns:
        PdbxFeatureAssembly
      • getPdbxFeatureMonomer

        public PdbxFeatureMonomer getPdbxFeatureMonomer()
        Description copied from interface: Block
        Data items in the PDBX_FEATURE_MONOMER category records information about properties pertaining to particular monomers in this structure.
        Specified by:
        getPdbxFeatureMonomer in interface Block
        Returns:
        PdbxFeatureMonomer
      • getPdbxExptlPd

        public PdbxExptlPd getPdbxExptlPd()
        Description copied from interface: Block
        Data items in the pdbx_exptl_pd record information about powder sample preparations.
        Specified by:
        getPdbxExptlPd in interface Block
        Returns:
        PdbxExptlPd
      • getPdbxReflnsTwin

        public PdbxReflnsTwin getPdbxReflnsTwin()
        Description copied from interface: Block
        Details decribing crystallographic twinning.
        Specified by:
        getPdbxReflnsTwin in interface Block
        Returns:
        PdbxReflnsTwin
      • getPdbxStructInfo

        public PdbxStructInfo getPdbxStructInfo()
        Description copied from interface: Block
        Special features of this structural entry.
        Specified by:
        getPdbxStructInfo in interface Block
        Returns:
        PdbxStructInfo
      • getPdbxReRefinement

        public PdbxReRefinement getPdbxReRefinement()
        Description copied from interface: Block
        Describes the origin of the experimental data used in this entry.
        Specified by:
        getPdbxReRefinement in interface Block
        Returns:
        PdbxReRefinement
      • getPdbxStructRefSeqFeature

        public PdbxStructRefSeqFeature getPdbxStructRefSeqFeature()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_REF_SEQ_FEATURE category provide a mechanism for identifying and annotating sequence features.
        Specified by:
        getPdbxStructRefSeqFeature in interface Block
        Returns:
        PdbxStructRefSeqFeature
      • getPdbxStructRefSeqFeatureProp

        public PdbxStructRefSeqFeatureProp getPdbxStructRefSeqFeatureProp()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_REF_SEQ_FEATURE_PROP category provide a mechanism for identifying and annotating properties of sequence features.
        Specified by:
        getPdbxStructRefSeqFeatureProp in interface Block
        Returns:
        PdbxStructRefSeqFeatureProp
      • getPdbxStructChemCompDiagnostics

        public PdbxStructChemCompDiagnostics getPdbxStructChemCompDiagnostics()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_CHEM_COMP_DIAGNOSTICS category provides structural diagnostics in chemical components instances.
        Specified by:
        getPdbxStructChemCompDiagnostics in interface Block
        Returns:
        PdbxStructChemCompDiagnostics
      • getPdbxChemCompFeature

        public PdbxChemCompFeature getPdbxChemCompFeature()
        Description copied from interface: Block
        Additional features associated with the chemical component.
        Specified by:
        getPdbxChemCompFeature in interface Block
        Returns:
        PdbxChemCompFeature
      • getPdbxCoordinateModel

        public PdbxCoordinateModel getPdbxCoordinateModel()
        Description copied from interface: Block
        The details of the composition of the coordinate model.
        Specified by:
        getPdbxCoordinateModel in interface Block
        Returns:
        PdbxCoordinateModel
      • getPdbxStructChemCompFeature

        public PdbxStructChemCompFeature getPdbxStructChemCompFeature()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_CHEM_COMP_FEATURE category provides structural annotations in chemical components instances.
        Specified by:
        getPdbxStructChemCompFeature in interface Block
        Returns:
        PdbxStructChemCompFeature
      • getPdbxDiffrnReflnsShell

        public PdbxDiffrnReflnsShell getPdbxDiffrnReflnsShell()
        Description copied from interface: Block
        Data items in the DIFFRN_REFLNS_SHELL category record details about the reflection data set within shells of resolution.
        Specified by:
        getPdbxDiffrnReflnsShell in interface Block
        Returns:
        PdbxDiffrnReflnsShell
      • getPdbxBondDistanceLimits

        public PdbxBondDistanceLimits getPdbxBondDistanceLimits()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxBondDistanceLimits in interface Block
        Returns:
        PdbxBondDistanceLimits
      • getPdbxSolnScatter

        public PdbxSolnScatter getPdbxSolnScatter()
        Description copied from interface: Block
        Data items in the PDBX_SOLN_SCATTER category record details about a solution scattering experiment
        Specified by:
        getPdbxSolnScatter in interface Block
        Returns:
        PdbxSolnScatter
      • getPdbxSolnScatterModel

        public PdbxSolnScatterModel getPdbxSolnScatterModel()
        Description copied from interface: Block
        Data items in the PDBX_SOLN_SCATTER_MODEL category record details about the homology model fitting to the solution scatter data.
        Specified by:
        getPdbxSolnScatterModel in interface Block
        Returns:
        PdbxSolnScatterModel
      • getPdbxChemCompDescriptor

        public PdbxChemCompDescriptor getPdbxChemCompDescriptor()
        Description copied from interface: Block
        Data items in the CHEM_COMP_DESCRIPTOR category provide string descriptors of component chemical structure.
        Specified by:
        getPdbxChemCompDescriptor in interface Block
        Returns:
        PdbxChemCompDescriptor
      • getPdbxChemCompIdentifier

        public PdbxChemCompIdentifier getPdbxChemCompIdentifier()
        Description copied from interface: Block
        Data items in the CHEM_COMP_IDENTIFIER category provide identifiers for chemical components.
        Specified by:
        getPdbxChemCompIdentifier in interface Block
        Returns:
        PdbxChemCompIdentifier
      • getPdbxChemCompImport

        public PdbxChemCompImport getPdbxChemCompImport()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxChemCompImport in interface Block
        Returns:
        PdbxChemCompImport
      • getPdbxChemCompAtomEdit

        public PdbxChemCompAtomEdit getPdbxChemCompAtomEdit()
        Description copied from interface: Block
        Data items in the PDBX_CHEM_COMP_ATOM_EDIT category provide atom level editing instructions to be applied to imported chemical components.
        Specified by:
        getPdbxChemCompAtomEdit in interface Block
        Returns:
        PdbxChemCompAtomEdit
      • getPdbxChemCompBondEdit

        public PdbxChemCompBondEdit getPdbxChemCompBondEdit()
        Description copied from interface: Block
        Data items in the PDBX_CHEM_COMP_BOND_EDIT category provide bond level editing instructions to be applied to imported chemical components.
        Specified by:
        getPdbxChemCompBondEdit in interface Block
        Returns:
        PdbxChemCompBondEdit
      • getPdbxChemCompAudit

        public PdbxChemCompAudit getPdbxChemCompAudit()
        Description copied from interface: Block
        Data items in the PDBX_CHEM_COMP_AUDIT category records the status and tracking information for this component.
        Specified by:
        getPdbxChemCompAudit in interface Block
        Returns:
        PdbxChemCompAudit
      • getPdbxValidateCloseContact

        public PdbxValidateCloseContact getPdbxValidateCloseContact()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxValidateCloseContact in interface Block
        Returns:
        PdbxValidateCloseContact
      • getPdbxValidateSymmContact

        public PdbxValidateSymmContact getPdbxValidateSymmContact()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxValidateSymmContact in interface Block
        Returns:
        PdbxValidateSymmContact
      • getPdbxValidateRmsdBond

        public PdbxValidateRmsdBond getPdbxValidateRmsdBond()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxValidateRmsdBond in interface Block
        Returns:
        PdbxValidateRmsdBond
      • getPdbxValidateRmsdAngle

        public PdbxValidateRmsdAngle getPdbxValidateRmsdAngle()
        Description copied from interface: Block
        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
        Specified by:
        getPdbxValidateRmsdAngle in interface Block
        Returns:
        PdbxValidateRmsdAngle
      • getPdbxValidateTorsion

        public PdbxValidateTorsion getPdbxValidateTorsion()
        Description copied from interface: Block
        Data items in the PDBX_VALIDATE_TORSION category list the residues with torsion angles outside the expected ramachandran regions
        Specified by:
        getPdbxValidateTorsion in interface Block
        Returns:
        PdbxValidateTorsion
      • getPdbxValidatePeptideOmega

        public PdbxValidatePeptideOmega getPdbxValidatePeptideOmega()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxValidatePeptideOmega in interface Block
        Returns:
        PdbxValidatePeptideOmega
      • getPdbxValidateChiral

        public PdbxValidateChiral getPdbxValidateChiral()
        Description copied from interface: Block
        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
        Specified by:
        getPdbxValidateChiral in interface Block
        Returns:
        PdbxValidateChiral
      • getPdbxValidatePlanes

        public PdbxValidatePlanes getPdbxValidatePlanes()
        Description copied from interface: Block
        Data items in the PDBX_VALIDATE_PLANES category list the residues that contain unexpected deviations from planes centers.
        Specified by:
        getPdbxValidatePlanes in interface Block
        Returns:
        PdbxValidatePlanes
      • getPdbxValidatePlanesAtom

        public PdbxValidatePlanesAtom getPdbxValidatePlanesAtom()
        Description copied from interface: Block
        Data items in the PDBX_VALIDATE_PLANES_ATOM category list the residues that contain unexpected deviations from planes centers.
        Specified by:
        getPdbxValidatePlanesAtom in interface Block
        Returns:
        PdbxValidatePlanesAtom
      • getPdbxValidateMainChainPlane

        public PdbxValidateMainChainPlane getPdbxValidateMainChainPlane()
        Description copied from interface: Block
        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
        Specified by:
        getPdbxValidateMainChainPlane in interface Block
        Returns:
        PdbxValidateMainChainPlane
      • getPdbxStructConnAngle

        public PdbxStructConnAngle getPdbxStructConnAngle()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_CONN_ANGLE category record the angles in connections between portions of the structure.
        Specified by:
        getPdbxStructConnAngle in interface Block
        Returns:
        PdbxStructConnAngle
      • getPdbxUnobsOrZeroOccResidues

        public PdbxUnobsOrZeroOccResidues getPdbxUnobsOrZeroOccResidues()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxUnobsOrZeroOccResidues in interface Block
        Returns:
        PdbxUnobsOrZeroOccResidues
      • getPdbxUnobsOrZeroOccAtoms

        public PdbxUnobsOrZeroOccAtoms getPdbxUnobsOrZeroOccAtoms()
        Description copied from interface: Block
        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/
        Specified by:
        getPdbxUnobsOrZeroOccAtoms in interface Block
        Returns:
        PdbxUnobsOrZeroOccAtoms
      • getPdbxEntryDetails

        public PdbxEntryDetails getPdbxEntryDetails()
        Description copied from interface: Block
        Data items in the PDBX_ENTRY_DETAILS category provide additional details about this entry.
        Specified by:
        getPdbxEntryDetails in interface Block
        Returns:
        PdbxEntryDetails
      • getPdbxStructModResidue

        public PdbxStructModResidue getPdbxStructModResidue()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxStructModResidue in interface Block
        Returns:
        PdbxStructModResidue
      • getPdbxStructRefSeqInsertion

        public PdbxStructRefSeqInsertion getPdbxStructRefSeqInsertion()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_REF_SEQ_INSERTION category annotate insertions in the sequence of the entity described in the referenced database entry.
        Specified by:
        getPdbxStructRefSeqInsertion in interface Block
        Returns:
        PdbxStructRefSeqInsertion
      • getPdbxStructRefSeqDeletion

        public PdbxStructRefSeqDeletion getPdbxStructRefSeqDeletion()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_REF_SEQ_INSERTION category annotate deletions in the sequence of the entity described in the referenced database entry.
        Specified by:
        getPdbxStructRefSeqDeletion in interface Block
        Returns:
        PdbxStructRefSeqDeletion
      • getPdbxRemediationAtomSiteMapping

        public PdbxRemediationAtomSiteMapping getPdbxRemediationAtomSiteMapping()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxRemediationAtomSiteMapping in interface Block
        Returns:
        PdbxRemediationAtomSiteMapping
      • getPdbxValidatePolymerLinkage

        public PdbxValidatePolymerLinkage getPdbxValidatePolymerLinkage()
        Description copied from interface: Block
        Data items in the PDBX_VALIDATE_POLYMER_LINKAGE category list the polymer linkages within the entry that are outside of typlical covalent distances.
        Specified by:
        getPdbxValidatePolymerLinkage in interface Block
        Returns:
        PdbxValidatePolymerLinkage
      • getPdbxHelicalSymmetry

        public PdbxHelicalSymmetry getPdbxHelicalSymmetry()
        Description copied from interface: Block
        Data items in the PDBX_HELICAL_SYMMETRY category record details about the helical symmetry group associated with this entry.
        Specified by:
        getPdbxHelicalSymmetry in interface Block
        Returns:
        PdbxHelicalSymmetry
      • getPdbxPointSymmetry

        public PdbxPointSymmetry getPdbxPointSymmetry()
        Description copied from interface: Block
        Data items in the PDBX_POINT_SYMMETRY category record details about the point symmetry group associated with this entry.
        Specified by:
        getPdbxPointSymmetry in interface Block
        Returns:
        PdbxPointSymmetry
      • getPdbxStructEntityInst

        public PdbxStructEntityInst getPdbxStructEntityInst()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxStructEntityInst in interface Block
        Returns:
        PdbxStructEntityInst
      • getPdbxStructOperList

        public PdbxStructOperList getPdbxStructOperList()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxStructOperList in interface Block
        Returns:
        PdbxStructOperList
      • getPdbxStructAssembly

        public PdbxStructAssembly getPdbxStructAssembly()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_ASSEMBLY category record details about the structural elements that form macromolecular assemblies.
        Specified by:
        getPdbxStructAssembly in interface Block
        Returns:
        PdbxStructAssembly
      • getPdbxStructAssemblyGen

        public PdbxStructAssemblyGen getPdbxStructAssemblyGen()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxStructAssemblyGen in interface Block
        Returns:
        PdbxStructAssemblyGen
      • getPdbxStructAsymGen

        public PdbxStructAsymGen getPdbxStructAsymGen()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxStructAsymGen in interface Block
        Returns:
        PdbxStructAsymGen
      • getPdbxStructMsymGen

        public PdbxStructMsymGen getPdbxStructMsymGen()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxStructMsymGen in interface Block
        Returns:
        PdbxStructMsymGen
      • getPdbxStructLegacyOperList

        public PdbxStructLegacyOperList getPdbxStructLegacyOperList()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxStructLegacyOperList in interface Block
        Returns:
        PdbxStructLegacyOperList
      • getPdbxChemCompAtomFeature

        public PdbxChemCompAtomFeature getPdbxChemCompAtomFeature()
        Description copied from interface: Block
        Data items in the PDBX_CHEM_COMP_ATOM_FEATURE category provide a selected list of atom level features for the chemical component.
        Specified by:
        getPdbxChemCompAtomFeature in interface Block
        Returns:
        PdbxChemCompAtomFeature
      • getPdbxReferenceMoleculeList

        public PdbxReferenceMoleculeList getPdbxReferenceMoleculeList()
        Description copied from interface: Block
        Data items in the PDBX_REFERENCE_MOLECULE_LIST category record reference information about small polymer molecules.
        Specified by:
        getPdbxReferenceMoleculeList in interface Block
        Returns:
        PdbxReferenceMoleculeList
      • getPdbxReferenceMolecule

        public PdbxReferenceMolecule getPdbxReferenceMolecule()
        Description copied from interface: Block
        Data items in the PDBX_REFERENCE_MOLECULE category record reference information about small polymer molecules.
        Specified by:
        getPdbxReferenceMolecule in interface Block
        Returns:
        PdbxReferenceMolecule
      • getPdbxReferenceEntityList

        public PdbxReferenceEntityList getPdbxReferenceEntityList()
        Description copied from interface: Block
        Data items in the PDBX_REFERENCE_ENTITY_LIST category record the list of entities within each reference molecule.
        Specified by:
        getPdbxReferenceEntityList in interface Block
        Returns:
        PdbxReferenceEntityList
      • getPdbxReferenceEntityNonpoly

        public PdbxReferenceEntityNonpoly getPdbxReferenceEntityNonpoly()
        Description copied from interface: Block
        Data items in the PDBX_REFERENCE_ENTITY_NONPOLY category record the list of entities within each reference molecule.
        Specified by:
        getPdbxReferenceEntityNonpoly in interface Block
        Returns:
        PdbxReferenceEntityNonpoly
      • getPdbxReferenceEntityLink

        public PdbxReferenceEntityLink getPdbxReferenceEntityLink()
        Description copied from interface: Block
        Data items in the PDBX_REFERENCE_ENTITY_LINK category give details about the linkages between entities within reference molecules.
        Specified by:
        getPdbxReferenceEntityLink in interface Block
        Returns:
        PdbxReferenceEntityLink
      • getPdbxReferenceEntityPolyLink

        public PdbxReferenceEntityPolyLink getPdbxReferenceEntityPolyLink()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxReferenceEntityPolyLink in interface Block
        Returns:
        PdbxReferenceEntityPolyLink
      • getPdbxReferenceEntityPoly

        public PdbxReferenceEntityPoly getPdbxReferenceEntityPoly()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxReferenceEntityPoly in interface Block
        Returns:
        PdbxReferenceEntityPoly
      • getPdbxReferenceEntityPolySeq

        public PdbxReferenceEntityPolySeq getPdbxReferenceEntityPolySeq()
        Description copied from interface: Block
        Data items in the PDBX_REFERENCE_ENTITY_POLY_SEQ category specify the sequence of monomers in a polymer.
        Specified by:
        getPdbxReferenceEntityPolySeq in interface Block
        Returns:
        PdbxReferenceEntityPolySeq
      • getPdbxReferenceEntitySrcNat

        public PdbxReferenceEntitySrcNat getPdbxReferenceEntitySrcNat()
        Description copied from interface: Block
        Data items in the PDBX_REFERENCE_ENTITY_SRC_NAT category record details of the source from which the entity was obtained.
        Specified by:
        getPdbxReferenceEntitySrcNat in interface Block
        Returns:
        PdbxReferenceEntitySrcNat
      • getPdbxReferenceMoleculeDetails

        public PdbxReferenceMoleculeDetails getPdbxReferenceMoleculeDetails()
        Description copied from interface: Block
        Data items in the PDBX_REFERENCE_MOLECULE_DETAILS category records textual details about small polymer molecules.
        Specified by:
        getPdbxReferenceMoleculeDetails in interface Block
        Returns:
        PdbxReferenceMoleculeDetails
      • getPdbxReferenceMoleculeSynonyms

        public PdbxReferenceMoleculeSynonyms getPdbxReferenceMoleculeSynonyms()
        Description copied from interface: Block
        Data items in the PDBX_REFERENCE_MOLECULE_SYNONYMS category records synonym names for reference entities.
        Specified by:
        getPdbxReferenceMoleculeSynonyms in interface Block
        Returns:
        PdbxReferenceMoleculeSynonyms
      • getPdbxReferenceEntitySubcomponents

        public PdbxReferenceEntitySubcomponents getPdbxReferenceEntitySubcomponents()
        Description copied from interface: Block
        Data items in the PDBX_REFERENCE_ENTITY_SUBCOMPONENTS category records subcomponent sequence from which this entity could be built.
        Specified by:
        getPdbxReferenceEntitySubcomponents in interface Block
        Returns:
        PdbxReferenceEntitySubcomponents
      • getPdbxReferenceMoleculeAnnotation

        public PdbxReferenceMoleculeAnnotation getPdbxReferenceMoleculeAnnotation()
        Description copied from interface: Block
        Data items in the PDBX_REFERENCE_MOLECULE_ANNOTATION category specify additional annotation relevant to the molecular entities.
        Specified by:
        getPdbxReferenceMoleculeAnnotation in interface Block
        Returns:
        PdbxReferenceMoleculeAnnotation
      • getPdbxReferenceMoleculeRelatedStructures

        public PdbxReferenceMoleculeRelatedStructures getPdbxReferenceMoleculeRelatedStructures()
        Description copied from interface: Block
        Data items in the PDBX_REFERENCE_MOLECULE_RELATED_STRUCTURES category record details of the structural examples in related databases for this entity.
        Specified by:
        getPdbxReferenceMoleculeRelatedStructures in interface Block
        Returns:
        PdbxReferenceMoleculeRelatedStructures
      • getPdbxStructGroupList

        public PdbxStructGroupList getPdbxStructGroupList()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_GROUP_LIST define groups of related components or atoms.
        Specified by:
        getPdbxStructGroupList in interface Block
        Returns:
        PdbxStructGroupList
      • getPdbxStructGroupComponents

        public PdbxStructGroupComponents getPdbxStructGroupComponents()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxStructGroupComponents in interface Block
        Returns:
        PdbxStructGroupComponents
      • getPdbxStructGroupComponentRange

        public PdbxStructGroupComponentRange getPdbxStructGroupComponentRange()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_GROUP_COMPONENT_RANGE category define a structural group as a continuous span chemical components.
        Specified by:
        getPdbxStructGroupComponentRange in interface Block
        Returns:
        PdbxStructGroupComponentRange
      • getPdbxPrdAudit

        public PdbxPrdAudit getPdbxPrdAudit()
        Description copied from interface: Block
        Data items in the PDBX_PRD_AUDIT category records the status and tracking information for this molecule.
        Specified by:
        getPdbxPrdAudit in interface Block
        Returns:
        PdbxPrdAudit
      • getPdbxFamilyPrdAudit

        public PdbxFamilyPrdAudit getPdbxFamilyPrdAudit()
        Description copied from interface: Block
        Data items in the PDBX_FAMILY_PRD_AUDIT category records the status and tracking information for this family.
        Specified by:
        getPdbxFamilyPrdAudit in interface Block
        Returns:
        PdbxFamilyPrdAudit
      • getPdbxMolecule

        public PdbxMolecule getPdbxMolecule()
        Description copied from interface: Block
        Data items in the PDBX_MOLECULE category identify reference molecules within a PDB entry.
        Specified by:
        getPdbxMolecule in interface Block
        Returns:
        PdbxMolecule
      • getPdbxMoleculeFeatures

        public PdbxMoleculeFeatures getPdbxMoleculeFeatures()
        Description copied from interface: Block
        Data items in the PDBX_MOLECULE_FEATURES category record features of molecules within a PDB entry.
        Specified by:
        getPdbxMoleculeFeatures in interface Block
        Returns:
        PdbxMoleculeFeatures
      • getPdbxFamilyGroupIndex

        public PdbxFamilyGroupIndex getPdbxFamilyGroupIndex()
        Description copied from interface: Block
        Data items in the PDBX_FAMILY_GROUP_INDEX category record the family membership in family groups.
        Specified by:
        getPdbxFamilyGroupIndex in interface Block
        Returns:
        PdbxFamilyGroupIndex
      • getPdbxDistantSolventAtoms

        public PdbxDistantSolventAtoms getPdbxDistantSolventAtoms()
        Description copied from interface: Block
        Data items in the PDBX_DISTANT_SOLVENT_ATOMS category list the solvent atoms remote from any macromolecule.
        Specified by:
        getPdbxDistantSolventAtoms in interface Block
        Returns:
        PdbxDistantSolventAtoms
      • getPdbxStructSpecialSymmetry

        public PdbxStructSpecialSymmetry getPdbxStructSpecialSymmetry()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_SPECIAL_SYMMETRY category list the molecular components that lie on special symmetry positions.
        Specified by:
        getPdbxStructSpecialSymmetry in interface Block
        Returns:
        PdbxStructSpecialSymmetry
      • getPdbxReferencePublicationList

        public PdbxReferencePublicationList getPdbxReferencePublicationList()
        Description copied from interface: Block
        Data items in the PDBX_REFERENCE_PUBLICATION_LIST hold reference information related to PDB citation data.
        Specified by:
        getPdbxReferencePublicationList in interface Block
        Returns:
        PdbxReferencePublicationList
      • getPdbxNmrAssignedChemShiftList

        public PdbxNmrAssignedChemShiftList getPdbxNmrAssignedChemShiftList()
        Description copied from interface: Block
        Items in the assigned_chem_shift_list category provide information about a list of reported assigned chemical shift values.
        Specified by:
        getPdbxNmrAssignedChemShiftList in interface Block
        Returns:
        PdbxNmrAssignedChemShiftList
      • getPdbxNmrChemShiftExperiment

        public PdbxNmrChemShiftExperiment getPdbxNmrChemShiftExperiment()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxNmrChemShiftExperiment in interface Block
        Returns:
        PdbxNmrChemShiftExperiment
      • getPdbxNmrChemShiftRef

        public PdbxNmrChemShiftRef getPdbxNmrChemShiftRef()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxNmrChemShiftRef in interface Block
        Returns:
        PdbxNmrChemShiftRef
      • getPdbxNmrChemShiftReference

        public PdbxNmrChemShiftReference getPdbxNmrChemShiftReference()
        Description copied from interface: Block
        Items in the chem_shift_reference category define a set of chemical shift referencing parameters.
        Specified by:
        getPdbxNmrChemShiftReference in interface Block
        Returns:
        PdbxNmrChemShiftReference
      • getPdbxNmrChemShiftSoftware

        public PdbxNmrChemShiftSoftware getPdbxNmrChemShiftSoftware()
        Description copied from interface: Block
        Items in the chem_shift_software category provide pointers to the software category and methods category.
        Specified by:
        getPdbxNmrChemShiftSoftware in interface Block
        Returns:
        PdbxNmrChemShiftSoftware
      • getPdbxNmrConstraintFile

        public PdbxNmrConstraintFile getPdbxNmrConstraintFile()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxNmrConstraintFile in interface Block
        Returns:
        PdbxNmrConstraintFile
      • getPdbxNmrSoftwareTask

        public PdbxNmrSoftwareTask getPdbxNmrSoftwareTask()
        Description copied from interface: Block
        Items in the pdbx_nmr_software_task category provide information about software workflow in the NMR experiment.
        Specified by:
        getPdbxNmrSoftwareTask in interface Block
        Returns:
        PdbxNmrSoftwareTask
      • getPdbxNmrSpectralDim

        public PdbxNmrSpectralDim getPdbxNmrSpectralDim()
        Description copied from interface: Block
        Items in the spectral_dim category describe the parameters of each dimension in the NMR experiment used to generate the spectral peak list.
        Specified by:
        getPdbxNmrSpectralDim in interface Block
        Returns:
        PdbxNmrSpectralDim
      • getPdbxNmrSpectralPeakList

        public PdbxNmrSpectralPeakList getPdbxNmrSpectralPeakList()
        Description copied from interface: Block
        Items in the pdbx_nmr_spectral_peak_list category provide information about a list of reported spectral peak characteristic values.
        Specified by:
        getPdbxNmrSpectralPeakList in interface Block
        Returns:
        PdbxNmrSpectralPeakList
      • getPdbxNmrSpectralPeakSoftware

        public PdbxNmrSpectralPeakSoftware getPdbxNmrSpectralPeakSoftware()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxNmrSpectralPeakSoftware in interface Block
        Returns:
        PdbxNmrSpectralPeakSoftware
      • getPdbxNmrSystematicChemShiftOffset

        public PdbxNmrSystematicChemShiftOffset getPdbxNmrSystematicChemShiftOffset()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxNmrSystematicChemShiftOffset in interface Block
        Returns:
        PdbxNmrSystematicChemShiftOffset
      • getPdbxNmrUpload

        public PdbxNmrUpload getPdbxNmrUpload()
        Description copied from interface: Block
        Items in the pdbx_nmr_upload category provide information about the data files uploaded by a depositor using the deposition system.
        Specified by:
        getPdbxNmrUpload in interface Block
        Returns:
        PdbxNmrUpload
      • getPdbxAuditSupport

        public PdbxAuditSupport getPdbxAuditSupport()
        Description copied from interface: Block
        Data items in the PDBX_AUDIT_SUPPORT category record details about funding support for the entry.
        Specified by:
        getPdbxAuditSupport in interface Block
        Returns:
        PdbxAuditSupport
      • getPdbxChemCompSubcomponentStructConn

        public PdbxChemCompSubcomponentStructConn getPdbxChemCompSubcomponentStructConn()
        Description copied from interface: Block
        Data items in the pdbx_chem_comp_subcomponent_struct_conn list the chemical interactions among the subcomponents in the chemical component.
        Specified by:
        getPdbxChemCompSubcomponentStructConn in interface Block
        Returns:
        PdbxChemCompSubcomponentStructConn
      • getPdbxChemCompSubcomponentEntityList

        public PdbxChemCompSubcomponentEntityList getPdbxChemCompSubcomponentEntityList()
        Description copied from interface: Block
        Data items in the pdbx_chem_comp_subcomponent_entity_list category list the constituent chemical entities and entity features in this chemical component.
        Specified by:
        getPdbxChemCompSubcomponentEntityList in interface Block
        Returns:
        PdbxChemCompSubcomponentEntityList
      • getEntitySrcNat

        public EntitySrcNat getEntitySrcNat()
        Description copied from interface: Block
        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.
        Specified by:
        getEntitySrcNat in interface Block
        Returns:
        EntitySrcNat
      • getEntitySrcGen

        public EntitySrcGen getEntitySrcGen()
        Description copied from interface: Block
        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).
        Specified by:
        getEntitySrcGen in interface Block
        Returns:
        EntitySrcGen
      • getPdbxEntitySrcSyn

        public PdbxEntitySrcSyn getPdbxEntitySrcSyn()
        Description copied from interface: Block
        The data items in category PDBX_ENTITY_SRC_SYN record the source details about chemically synthesized molecules.
        Specified by:
        getPdbxEntitySrcSyn in interface Block
        Returns:
        PdbxEntitySrcSyn
      • getPdbxEntityPolyCompLinkList

        public PdbxEntityPolyCompLinkList getPdbxEntityPolyCompLinkList()
        Description copied from interface: Block
        Data items in the PDBX_ENTITY_POLY_COMP_LINK_LIST category enumerate the the linkages between components within the polymer entity.
        Specified by:
        getPdbxEntityPolyCompLinkList in interface Block
        Returns:
        PdbxEntityPolyCompLinkList
      • getPdbxLinkedEntity

        public PdbxLinkedEntity getPdbxLinkedEntity()
        Description copied from interface: Block
        Data items in the PDBX_LINKED_ENTITY category record information about molecules composed of linked entities.
        Specified by:
        getPdbxLinkedEntity in interface Block
        Returns:
        PdbxLinkedEntity
      • getPdbxLinkedEntityInstanceList

        public PdbxLinkedEntityInstanceList getPdbxLinkedEntityInstanceList()
        Description copied from interface: Block
        Data items in the PDBX_LINKED_ENTITY_INSTANCE_LIST category identify instance molecules represented as linked entities within an entry.
        Specified by:
        getPdbxLinkedEntityInstanceList in interface Block
        Returns:
        PdbxLinkedEntityInstanceList
      • getPdbxLinkedEntityList

        public PdbxLinkedEntityList getPdbxLinkedEntityList()
        Description copied from interface: Block
        Data items in the PDBX_LINKED_ENTITY_LIST category record the list of entity constituents for this molecule.
        Specified by:
        getPdbxLinkedEntityList in interface Block
        Returns:
        PdbxLinkedEntityList
      • getPdbxLinkedEntityLinkList

        public PdbxLinkedEntityLinkList getPdbxLinkedEntityLinkList()
        Description copied from interface: Block
        Data items in the PDBX_LINKED_ENTITY_LINK_LIST category give details about the linkages with molecules represented as linked entities.
        Specified by:
        getPdbxLinkedEntityLinkList in interface Block
        Returns:
        PdbxLinkedEntityLinkList
      • getPdbxEntityDescriptor

        public PdbxEntityDescriptor getPdbxEntityDescriptor()
        Description copied from interface: Block
        Data items in the PDBX_ENTITY_DESCRIPTOR category provide string descriptors of entity chemical structure.
        Specified by:
        getPdbxEntityDescriptor in interface Block
        Returns:
        PdbxEntityDescriptor
      • getPdbxReferenceLinkedEntity

        public PdbxReferenceLinkedEntity getPdbxReferenceLinkedEntity()
        Description copied from interface: Block
        Data items in the pdbx_reference_linked_entity category describe common observed interaction patterns within linked entities.
        Specified by:
        getPdbxReferenceLinkedEntity in interface Block
        Returns:
        PdbxReferenceLinkedEntity
      • getPdbxReferenceLinkedEntityCompList

        public PdbxReferenceLinkedEntityCompList getPdbxReferenceLinkedEntityCompList()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxReferenceLinkedEntityCompList in interface Block
        Returns:
        PdbxReferenceLinkedEntityCompList
      • getPdbxReferenceLinkedEntityCompLink

        public PdbxReferenceLinkedEntityCompLink getPdbxReferenceLinkedEntityCompLink()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxReferenceLinkedEntityCompLink in interface Block
        Returns:
        PdbxReferenceLinkedEntityCompLink
      • getPdbxReferenceLinkedEntityLink

        public PdbxReferenceLinkedEntityLink getPdbxReferenceLinkedEntityLink()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxReferenceLinkedEntityLink in interface Block
        Returns:
        PdbxReferenceLinkedEntityLink
      • getPdbxRelatedExpDataSet

        public PdbxRelatedExpDataSet getPdbxRelatedExpDataSet()
        Description copied from interface: Block
        Data items in the PDBX_RELATED_DATA_SET category record references to experimental data sets related to the entry.
        Specified by:
        getPdbxRelatedExpDataSet in interface Block
        Returns:
        PdbxRelatedExpDataSet
      • getPdbxDatabaseStatusHistory

        public PdbxDatabaseStatusHistory getPdbxDatabaseStatusHistory()
        Description copied from interface: Block
        The pdbx_database_status_history category records the time evolution of entry processing status.
        Specified by:
        getPdbxDatabaseStatusHistory in interface Block
        Returns:
        PdbxDatabaseStatusHistory
      • getEmAssembly

        public EmAssembly getEmAssembly()
        Description copied from interface: Block
        Data items in the EM_ASSEMBLY category record details about the imaged EM sample.
        Specified by:
        getEmAssembly in interface Block
        Returns:
        EmAssembly
      • getEmEntityAssembly

        public EmEntityAssembly getEmEntityAssembly()
        Description copied from interface: Block
        Data items in the EM_ENTITY_ASSEMBLY category record details about each component of the complex.
        Specified by:
        getEmEntityAssembly in interface Block
        Returns:
        EmEntityAssembly
      • getEmVirusEntity

        public EmVirusEntity getEmVirusEntity()
        Description copied from interface: Block
        Data items in the EM_VIRUS_ENTITY category record details of the icosahedral virus.
        Specified by:
        getEmVirusEntity in interface Block
        Returns:
        EmVirusEntity
      • getEmSamplePreparation

        public EmSamplePreparation getEmSamplePreparation()
        Description copied from interface: Block
        Data items in the EM_SAMPLE_PREPARATION category record details of sample conditions prior to and upon loading onto grid support.
        Specified by:
        getEmSamplePreparation in interface Block
        Returns:
        EmSamplePreparation
      • getEmSampleSupport

        public EmSampleSupport getEmSampleSupport()
        Description copied from interface: Block
        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
        Specified by:
        getEmSampleSupport in interface Block
        Returns:
        EmSampleSupport
      • getEmBuffer

        public EmBuffer getEmBuffer()
        Description copied from interface: Block
        Data items in the BUFFER category record details of the sample buffer.
        Specified by:
        getEmBuffer in interface Block
        Returns:
        EmBuffer
      • getEmVitrification

        public EmVitrification getEmVitrification()
        Description copied from interface: Block
        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
        Specified by:
        getEmVitrification in interface Block
        Returns:
        EmVitrification
      • getEmImaging

        public EmImaging getEmImaging()
        Description copied from interface: Block
        Data items in the EM_IMAGING category record details about the parameters used in imaging the sample in the electron microscope.
        Specified by:
        getEmImaging in interface Block
        Returns:
        EmImaging
      • getEmDetector

        public EmDetector getEmDetector()
        Description copied from interface: Block
        Data items in the EM_DETECTOR category record details of the image detector type.
        Specified by:
        getEmDetector in interface Block
        Returns:
        EmDetector
      • getEmImageScans

        public EmImageScans getEmImageScans()
        Description copied from interface: Block
        Data items in the EM_IMAGE_SCANS category record details of the image scanning device (microdensitometer) and parameters for digitization of the image.
        Specified by:
        getEmImageScans in interface Block
        Returns:
        EmImageScans
      • getEm2dProjectionSelection

        public Em2dProjectionSelection getEm2dProjectionSelection()
        Description copied from interface: Block
        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.
        Specified by:
        getEm2dProjectionSelection in interface Block
        Returns:
        Em2dProjectionSelection
      • getEm3dReconstruction

        public Em3dReconstruction getEm3dReconstruction()
        Description copied from interface: Block
        Data items in the EM_3D_RECONSTRUCTION category record details of the 3D reconstruction procedure from 2D projections.
        Specified by:
        getEm3dReconstruction in interface Block
        Returns:
        Em3dReconstruction
      • getEm3dFitting

        public Em3dFitting getEm3dFitting()
        Description copied from interface: Block
        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
        Specified by:
        getEm3dFitting in interface Block
        Returns:
        Em3dFitting
      • getEm3dFittingList

        public Em3dFittingList getEm3dFittingList()
        Description copied from interface: Block
        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
        Specified by:
        getEm3dFittingList in interface Block
        Returns:
        Em3dFittingList
      • getEmHelicalEntity

        public EmHelicalEntity getEmHelicalEntity()
        Description copied from interface: Block
        Data items in the EM_HELICAL_ENTITY category record details for a helical or filament type of assembly component.
        Specified by:
        getEmHelicalEntity in interface Block
        Returns:
        EmHelicalEntity
      • getEmExperiment

        public EmExperiment getEmExperiment()
        Description copied from interface: Block
        Data items in the EM_EXPERIMENT category provide high-level classification of the EM experiment.
        Specified by:
        getEmExperiment in interface Block
        Returns:
        EmExperiment
      • getEmSingleParticleEntity

        public EmSingleParticleEntity getEmSingleParticleEntity()
        Description copied from interface: Block
        Data items in the EM_SINGLE_PARTICLE_ENTITY category provide the details of the symmetry for a single particle entity type.
        Specified by:
        getEmSingleParticleEntity in interface Block
        Returns:
        EmSingleParticleEntity
      • getEmAdmin

        public EmAdmin getEmAdmin()
        Description copied from interface: Block
        Administration-related data items
        Specified by:
        getEmAdmin in interface Block
        Returns:
        EmAdmin
      • getEmAuthorList

        public EmAuthorList getEmAuthorList()
        Description copied from interface: Block
        Category to collect the authors of this entry
        Specified by:
        getEmAuthorList in interface Block
        Returns:
        EmAuthorList
      • getEmDbReference

        public EmDbReference getEmDbReference()
        Description copied from interface: Block
        Category holds links to raw data sources for the entry, e.g., held by a remote server.
        Specified by:
        getEmDbReference in interface Block
        Returns:
        EmDbReference
      • getEmDbReferenceAuxiliary

        public EmDbReferenceAuxiliary getEmDbReferenceAuxiliary()
        Description copied from interface: Block
        Category holds links to raw data sources for the entry, e.g., held by a remote server.
        Specified by:
        getEmDbReferenceAuxiliary in interface Block
        Returns:
        EmDbReferenceAuxiliary
      • getEmDepui

        public EmDepui getEmDepui()
        Description copied from interface: Block
        Some internal items to power the deposition interface
        Specified by:
        getEmDepui in interface Block
        Returns:
        EmDepui
      • getEmObsolete

        public EmObsolete getEmObsolete()
        Description copied from interface: Block
        List of EMD entries made obsolete by this entry.
        Specified by:
        getEmObsolete in interface Block
        Returns:
        EmObsolete
      • getEmSupersede

        public EmSupersede getEmSupersede()
        Description copied from interface: Block
        List of newer entries that replace this entry.
        Specified by:
        getEmSupersede in interface Block
        Returns:
        EmSupersede
      • getEmEntityAssemblyMolwt

        public EmEntityAssemblyMolwt getEmEntityAssemblyMolwt()
        Description copied from interface: Block
        Data items in this category record details about the molecular weight of an assembly component of the sample.
        Specified by:
        getEmEntityAssemblyMolwt in interface Block
        Returns:
        EmEntityAssemblyMolwt
      • getEmEntityAssemblyNaturalsource

        public EmEntityAssemblyNaturalsource getEmEntityAssemblyNaturalsource()
        Description copied from interface: Block
        Data items in this category record taxonomic details about the natural source for EM assemblies and assembly components.
        Specified by:
        getEmEntityAssemblyNaturalsource in interface Block
        Returns:
        EmEntityAssemblyNaturalsource
      • getEmEntityAssemblyRecombinant

        public EmEntityAssemblyRecombinant getEmEntityAssemblyRecombinant()
        Description copied from interface: Block
        Data items in this category record details about recombinant expression of the assembly or assembly component.
        Specified by:
        getEmEntityAssemblyRecombinant in interface Block
        Returns:
        EmEntityAssemblyRecombinant
      • getEmVirusNaturalHost

        public EmVirusNaturalHost getEmVirusNaturalHost()
        Description copied from interface: Block
        Data items in this category record details of a virus entity.
        Specified by:
        getEmVirusNaturalHost in interface Block
        Returns:
        EmVirusNaturalHost
      • getEmVirusShell

        public EmVirusShell getEmVirusShell()
        Description copied from interface: Block
        Data items in the EMD_VIRUS_SHELL category record details of the viral shell number, shell diameter, and icosahedral triangulation number.
        Specified by:
        getEmVirusShell in interface Block
        Returns:
        EmVirusShell
      • getEmSpecimen

        public EmSpecimen getEmSpecimen()
        Description copied from interface: Block
        Data items in the EMD_SPECIMEN category record details about specimens prepared for imaging by electron microscopy.
        Specified by:
        getEmSpecimen in interface Block
        Returns:
        EmSpecimen
      • getEmEmbedding

        public EmEmbedding getEmEmbedding()
        Description copied from interface: Block
        Sugar embedding category
        Specified by:
        getEmEmbedding in interface Block
        Returns:
        EmEmbedding
      • getEmFocusedIonBeam

        public EmFocusedIonBeam getEmFocusedIonBeam()
        Description copied from interface: Block
        Description of sectioning by focused_ion_beam
        Specified by:
        getEmFocusedIonBeam in interface Block
        Returns:
        EmFocusedIonBeam
      • getEmGridPretreatment

        public EmGridPretreatment getEmGridPretreatment()
        Description copied from interface: Block
        Data items describing glow discharge pretreatment for an EM grid
        Specified by:
        getEmGridPretreatment in interface Block
        Returns:
        EmGridPretreatment
      • getEmUltramicrotomy

        public EmUltramicrotomy getEmUltramicrotomy()
        Description copied from interface: Block
        Description of sectioning by ultramicrotomy
        Specified by:
        getEmUltramicrotomy in interface Block
        Returns:
        EmUltramicrotomy
      • getEmShadowing

        public EmShadowing getEmShadowing()
        Description copied from interface: Block
        Data items related to shadowing of an EM specimen
        Specified by:
        getEmShadowing in interface Block
        Returns:
        EmShadowing
      • getEmTomographySpecimen

        public EmTomographySpecimen getEmTomographySpecimen()
        Description copied from interface: Block
        Description specimen preparation for imaging using tomography.
        Specified by:
        getEmTomographySpecimen in interface Block
        Returns:
        EmTomographySpecimen
      • getEmCrystalFormation

        public EmCrystalFormation getEmCrystalFormation()
        Description copied from interface: Block
        Description of growth of a 2D, 3D, or helical crystal array.
        Specified by:
        getEmCrystalFormation in interface Block
        Returns:
        EmCrystalFormation
      • getEmStaining

        public EmStaining getEmStaining()
        Description copied from interface: Block
        Staining category
        Specified by:
        getEmStaining in interface Block
        Returns:
        EmStaining
      • getEmSupportFilm

        public EmSupportFilm getEmSupportFilm()
        Description copied from interface: Block
        Data items to describe films supporting the specimen
        Specified by:
        getEmSupportFilm in interface Block
        Returns:
        EmSupportFilm
      • getEmDiffraction

        public EmDiffraction getEmDiffraction()
        Description copied from interface: Block
        Microscopy parameters relevant only for crystallography
        Specified by:
        getEmDiffraction in interface Block
        Returns:
        EmDiffraction
      • getEmDiffractionShell

        public EmDiffractionShell getEmDiffractionShell()
        Description copied from interface: Block
        Statistical parameters for electron diffraction measurements within a resolution shell
        Specified by:
        getEmDiffractionShell in interface Block
        Returns:
        EmDiffractionShell
      • getEmDiffractionStats

        public EmDiffractionStats getEmDiffractionStats()
        Description copied from interface: Block
        Statistical parameters for electron diffraction measurements
        Specified by:
        getEmDiffractionStats in interface Block
        Returns:
        EmDiffractionStats
      • getEmTomography

        public EmTomography getEmTomography()
        Description copied from interface: Block
        Microscopy parameters only relevant for tomography
        Specified by:
        getEmTomography in interface Block
        Returns:
        EmTomography
      • getEmImageRecording

        public EmImageRecording getEmImageRecording()
        Description copied from interface: Block
        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.
        Specified by:
        getEmImageRecording in interface Block
        Returns:
        EmImageRecording
      • getEmImagingOptics

        public EmImagingOptics getEmImagingOptics()
        Description copied from interface: Block
        Description of a few specialist optics apparatus
        Specified by:
        getEmImagingOptics in interface Block
        Returns:
        EmImagingOptics
      • getEmStartModel

        public EmStartModel getEmStartModel()
        Description copied from interface: Block
        The startup model employed to begin refinement of the parameters for a 3DEM reconstruction
        Specified by:
        getEmStartModel in interface Block
        Returns:
        EmStartModel
      • getEmSoftware

        public EmSoftware getEmSoftware()
        Description copied from interface: Block
        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.
        Specified by:
        getEmSoftware in interface Block
        Returns:
        EmSoftware
      • getEmCtfCorrection

        public EmCtfCorrection getEmCtfCorrection()
        Description copied from interface: Block
        Description of the Contrast Transfer Function (CTF) correction
        Specified by:
        getEmCtfCorrection in interface Block
        Returns:
        EmCtfCorrection
      • getEm3dCrystalEntity

        public Em3dCrystalEntity getEm3dCrystalEntity()
        Description copied from interface: Block
        Data items in the EM_SYMMETRY_3DX category record 3D crystal symmetry parameters utilized in 3DEM reconstruction averaging.
        Specified by:
        getEm3dCrystalEntity in interface Block
        Returns:
        Em3dCrystalEntity
      • getEm2dCrystalEntity

        public Em2dCrystalEntity getEm2dCrystalEntity()
        Description copied from interface: Block
        Data items in the EM_SYMMETRY_2DX category record 2D crystal symmetry parameters utilized in a 3DEM reconstruction.
        Specified by:
        getEm2dCrystalEntity in interface Block
        Returns:
        Em2dCrystalEntity
      • getEmImageProcessing

        public EmImageProcessing getEmImageProcessing()
        Description copied from interface: Block
        Data items in the EM_IMAGE_PROCESSING category record details of the EM image processing procedure.
        Specified by:
        getEmImageProcessing in interface Block
        Returns:
        EmImageProcessing
      • getEmParticleSelection

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

        public EmMap getEmMap()
        Description copied from interface: Block
        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.
        Specified by:
        getEmMap in interface Block
        Returns:
        EmMap
      • getEmFscCurve

        public EmFscCurve getEmFscCurve()
        Description copied from interface: Block
        Data items in the EMD_VALIDATION_FSC_CURVE category record details of the Fourier Shell Correlation (FSC) curve file.
        Specified by:
        getEmFscCurve in interface Block
        Returns:
        EmFscCurve
      • getEmInterpretFigure

        public EmInterpretFigure getEmInterpretFigure()
        Description copied from interface: Block
        Listing of all layer line files associated with the EM entry
        Specified by:
        getEmInterpretFigure in interface Block
        Returns:
        EmInterpretFigure
      • getEmLayerLines

        public EmLayerLines getEmLayerLines()
        Description copied from interface: Block
        Listing of all layer line files associated with the EM entry
        Specified by:
        getEmLayerLines in interface Block
        Returns:
        EmLayerLines
      • getEmStructureFactors

        public EmStructureFactors getEmStructureFactors()
        Description copied from interface: Block
        Listing of all structure factor files associated with the EM entry
        Specified by:
        getEmStructureFactors in interface Block
        Returns:
        EmStructureFactors
      • getEmDepositorInfo

        public EmDepositorInfo getEmDepositorInfo()
        Description copied from interface: Block
        Data items in the EM_DEPOSITOR INFO category record parameters for EM depositions that are provided by the depositor
        Specified by:
        getEmDepositorInfo in interface Block
        Returns:
        EmDepositorInfo
      • getEmMapDepositorInfo

        public EmMapDepositorInfo getEmMapDepositorInfo()
        Description copied from interface: Block
        Data items in the EM_MAP_DEPOSITOR INFO category record map parameters that are provided by the depositor
        Specified by:
        getEmMapDepositorInfo in interface Block
        Returns:
        EmMapDepositorInfo
      • getEmMaskDepositorInfo

        public EmMaskDepositorInfo getEmMaskDepositorInfo()
        Description copied from interface: Block
        Data items in the EM_MASK_DEPOSITOR_INFO category record mask parameters that are provided by the depositor
        Specified by:
        getEmMaskDepositorInfo in interface Block
        Returns:
        EmMaskDepositorInfo
      • getEmFigureDepositorInfo

        public EmFigureDepositorInfo getEmFigureDepositorInfo()
        Description copied from interface: Block
        Listing of image files (figures) associated with an EMDB entry
        Specified by:
        getEmFigureDepositorInfo in interface Block
        Returns:
        EmFigureDepositorInfo
      • getPdbxSeqMapDepositorInfo

        public PdbxSeqMapDepositorInfo getPdbxSeqMapDepositorInfo()
        Description copied from interface: Block
        Data items in the PDBX_SEQ_MAP_DEPOSITOR_INFO record the details about the mapping sample and coordinate sequences.
        Specified by:
        getPdbxSeqMapDepositorInfo in interface Block
        Returns:
        PdbxSeqMapDepositorInfo
      • getPdbxChemCompDepositorInfo

        public PdbxChemCompDepositorInfo getPdbxChemCompDepositorInfo()
        Description copied from interface: Block
        Data items in the PDBX_CHEM_COMP_DEPOSITOR_INFO category record additional details provided by depositors about deposited chemical components.
        Specified by:
        getPdbxChemCompDepositorInfo in interface Block
        Returns:
        PdbxChemCompDepositorInfo
      • getPdbxStructRefSeqDepositorInfo

        public PdbxStructRefSeqDepositorInfo getPdbxStructRefSeqDepositorInfo()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_REF_SEQ_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory STRUCT_REF_SEQ.
        Specified by:
        getPdbxStructRefSeqDepositorInfo in interface Block
        Returns:
        PdbxStructRefSeqDepositorInfo
      • getPdbxStructRefSeqDifDepositorInfo

        public PdbxStructRefSeqDifDepositorInfo getPdbxStructRefSeqDifDepositorInfo()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxStructRefSeqDifDepositorInfo in interface Block
        Returns:
        PdbxStructRefSeqDifDepositorInfo
      • getPdbxStructAssemblyPropDepositorInfo

        public PdbxStructAssemblyPropDepositorInfo getPdbxStructAssemblyPropDepositorInfo()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_ASSEMBLY_PROP_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_ASSEMBLY_PROP.
        Specified by:
        getPdbxStructAssemblyPropDepositorInfo in interface Block
        Returns:
        PdbxStructAssemblyPropDepositorInfo
      • getPdbxStructAssemblyDepositorInfo

        public PdbxStructAssemblyDepositorInfo getPdbxStructAssemblyDepositorInfo()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_ASSEMBLY_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_ASSEMBLY.
        Specified by:
        getPdbxStructAssemblyDepositorInfo in interface Block
        Returns:
        PdbxStructAssemblyDepositorInfo
      • getPdbxStructAssemblyGenDepositorInfo

        public PdbxStructAssemblyGenDepositorInfo getPdbxStructAssemblyGenDepositorInfo()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_ASSEMBLY_GEN_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_ASSEMBLY_GEN.
        Specified by:
        getPdbxStructAssemblyGenDepositorInfo in interface Block
        Returns:
        PdbxStructAssemblyGenDepositorInfo
      • getPdbxStructOperListDepositorInfo

        public PdbxStructOperListDepositorInfo getPdbxStructOperListDepositorInfo()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_OPER_LIST_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_STRUCT_OPER_LIST.
        Specified by:
        getPdbxStructOperListDepositorInfo in interface Block
        Returns:
        PdbxStructOperListDepositorInfo
      • getPdbxPointSymmetryDepositorInfo

        public PdbxPointSymmetryDepositorInfo getPdbxPointSymmetryDepositorInfo()
        Description copied from interface: Block
        Data items in the PDBX_POINT_SYMMETRY_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_POINT_SYMMETRY.
        Specified by:
        getPdbxPointSymmetryDepositorInfo in interface Block
        Returns:
        PdbxPointSymmetryDepositorInfo
      • getPdbxHelicalSymmetryDepositorInfo

        public PdbxHelicalSymmetryDepositorInfo getPdbxHelicalSymmetryDepositorInfo()
        Description copied from interface: Block
        Data items in the PDBX_HELICAL_SYMMETRY_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_HELICAL_SYMMETRY.
        Specified by:
        getPdbxHelicalSymmetryDepositorInfo in interface Block
        Returns:
        PdbxHelicalSymmetryDepositorInfo
      • getPdbxSolventAtomSiteMapping

        public PdbxSolventAtomSiteMapping getPdbxSolventAtomSiteMapping()
        Description copied from interface: Block
        Data items in the PDBX_SOLVENT_ATOM_SITE_MAPPING category records mapping information between solvent atoms before and after symmetry repositioning.
        Specified by:
        getPdbxSolventAtomSiteMapping in interface Block
        Returns:
        PdbxSolventAtomSiteMapping
      • getPdbxMoleculeFeaturesDepositorInfo

        public PdbxMoleculeFeaturesDepositorInfo getPdbxMoleculeFeaturesDepositorInfo()
        Description copied from interface: Block
        Data items in the PDBX_MOLECULE_FEATURES_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory PDBX_MOLECULE_FEATURES.
        Specified by:
        getPdbxMoleculeFeaturesDepositorInfo in interface Block
        Returns:
        PdbxMoleculeFeaturesDepositorInfo
      • getPdbxChemCompInstanceDepositorInfo

        public PdbxChemCompInstanceDepositorInfo getPdbxChemCompInstanceDepositorInfo()
        Description copied from interface: Block
        Data items in the PDBX_CHEM_COMP_INSTANCE_DEPOSITOR_INFO category records depositor provided information about the chemical context of component instances.
        Specified by:
        getPdbxChemCompInstanceDepositorInfo in interface Block
        Returns:
        PdbxChemCompInstanceDepositorInfo
      • getPdbxDepuiStatusFlags

        public PdbxDepuiStatusFlags getPdbxDepuiStatusFlags()
        Description copied from interface: Block
        Data items in the PDBX_DEPUI_STATUS_FLAGS category record status details used to maintain state within the wwPDB deposition system.
        Specified by:
        getPdbxDepuiStatusFlags in interface Block
        Returns:
        PdbxDepuiStatusFlags
      • getPdbxDepuiUpload

        public PdbxDepuiUpload getPdbxDepuiUpload()
        Description copied from interface: Block
        Data items in the PDBX_DEPUI_UPLOAD category record the details of uploaded data files.
        Specified by:
        getPdbxDepuiUpload in interface Block
        Returns:
        PdbxDepuiUpload
      • getPdbxDepuiValidationStatusFlags

        public PdbxDepuiValidationStatusFlags getPdbxDepuiValidationStatusFlags()
        Description copied from interface: Block
        Data items in the PDBX_DEPUI_VALIDATION_STATUS_FLAGS category record status details that assess the status of selected validation diagnostics.
        Specified by:
        getPdbxDepuiValidationStatusFlags in interface Block
        Returns:
        PdbxDepuiValidationStatusFlags
      • getPdbxChemCompUploadDepositorInfo

        public PdbxChemCompUploadDepositorInfo getPdbxChemCompUploadDepositorInfo()
        Description copied from interface: Block
        Data items in the PDBX_CHEM_COMP_UPLOAD_DEPOSITOR_INFO category record details of the uploaded files related to depositor provided chemical assignments.
        Specified by:
        getPdbxChemCompUploadDepositorInfo in interface Block
        Returns:
        PdbxChemCompUploadDepositorInfo
      • getPdbxDepuiEntityStatusFlags

        public PdbxDepuiEntityStatusFlags getPdbxDepuiEntityStatusFlags()
        Description copied from interface: Block
        Data items in the PDBX_DEPUI_ENTITY_STATUS_FLAGS category record status details related to individual entities.
        Specified by:
        getPdbxDepuiEntityStatusFlags in interface Block
        Returns:
        PdbxDepuiEntityStatusFlags
      • getPdbxDepuiEntityFeatures

        public PdbxDepuiEntityFeatures getPdbxDepuiEntityFeatures()
        Description copied from interface: Block
        Data items in the PDBX_DEPUI_ENTITY_FEATURES category record status details related to the features of individual entities.
        Specified by:
        getPdbxDepuiEntityFeatures in interface Block
        Returns:
        PdbxDepuiEntityFeatures
      • getPdbxDepositionMessageInfo

        public PdbxDepositionMessageInfo getPdbxDepositionMessageInfo()
        Description copied from interface: Block
        Data items in the PDBX_DEPOSITION_MESSAGE_INFO category record internal messages within the depositon and annotation system.
        Specified by:
        getPdbxDepositionMessageInfo in interface Block
        Returns:
        PdbxDepositionMessageInfo
      • getPdbxDepositionMessageFileReference

        public PdbxDepositionMessageFileReference getPdbxDepositionMessageFileReference()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxDepositionMessageFileReference in interface Block
        Returns:
        PdbxDepositionMessageFileReference
      • getPdbxDepuiEntryDetails

        public PdbxDepuiEntryDetails getPdbxDepuiEntryDetails()
        Description copied from interface: Block
        Data items in the PDBX_DEPUI_ENTRY_DETAILS category record information required to identify the depositor and route deposition to an appropriate processing site.
        Specified by:
        getPdbxDepuiEntryDetails in interface Block
        Returns:
        PdbxDepuiEntryDetails
      • getPdbxDataProcessingStatus

        public PdbxDataProcessingStatus getPdbxDataProcessingStatus()
        Description copied from interface: Block
        Data items in the PDBX_DATA_PROCESSING_STATUS category record data processing instructions for workflow processing tasks.
        Specified by:
        getPdbxDataProcessingStatus in interface Block
        Returns:
        PdbxDataProcessingStatus
      • getPdbxEntityInstanceFeature

        public PdbxEntityInstanceFeature getPdbxEntityInstanceFeature()
        Description copied from interface: Block
        Data items in the pdbx_entity_instance_feature category records special features of selected entity instances.
        Specified by:
        getPdbxEntityInstanceFeature in interface Block
        Returns:
        PdbxEntityInstanceFeature
      • getPdbxEntitySrcGenDepositorInfo

        public PdbxEntitySrcGenDepositorInfo getPdbxEntitySrcGenDepositorInfo()
        Description copied from interface: Block
        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).
        Specified by:
        getPdbxEntitySrcGenDepositorInfo in interface Block
        Returns:
        PdbxEntitySrcGenDepositorInfo
      • getPdbxChemCompModel

        public PdbxChemCompModel getPdbxChemCompModel()
        Description copied from interface: Block
        Data items in the PDBX_CHEM_COMP_MODEL category give details about each of the chemical component model instances.
        Specified by:
        getPdbxChemCompModel in interface Block
        Returns:
        PdbxChemCompModel
      • getPdbxChemCompModelAtom

        public PdbxChemCompModelAtom getPdbxChemCompModelAtom()
        Description copied from interface: Block
        Data items in the PDBX_CHEM_COMP_MODEL_ATOM category record coordinates for the chemical component model instance.
        Specified by:
        getPdbxChemCompModelAtom in interface Block
        Returns:
        PdbxChemCompModelAtom
      • getPdbxChemCompModelBond

        public PdbxChemCompModelBond getPdbxChemCompModelBond()
        Description copied from interface: Block
        Data items in the PDBX_CHEM_COMP_MODEL_BOND category record details about the bonds between atoms in a chemical component model instance.
        Specified by:
        getPdbxChemCompModelBond in interface Block
        Returns:
        PdbxChemCompModelBond
      • getPdbxChemCompModelDescriptor

        public PdbxChemCompModelDescriptor getPdbxChemCompModelDescriptor()
        Description copied from interface: Block
        Data items in the CHEM_COMP_MODEL_DESCRIPTOR category provide string descriptors for component model structures.
        Specified by:
        getPdbxChemCompModelDescriptor in interface Block
        Returns:
        PdbxChemCompModelDescriptor
      • getPdbxChemCompModelAudit

        public PdbxChemCompModelAudit getPdbxChemCompModelAudit()
        Description copied from interface: Block
        Data items in the PDBX_CHEM_COMP_MODEL_AUDIT category records the status and tracking information for this component model instance.
        Specified by:
        getPdbxChemCompModelAudit in interface Block
        Returns:
        PdbxChemCompModelAudit
      • getPdbxViewCategoryGroup

        public PdbxViewCategoryGroup getPdbxViewCategoryGroup()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxViewCategoryGroup in interface Block
        Returns:
        PdbxViewCategoryGroup
      • getPdbxViewCategory

        public PdbxViewCategory getPdbxViewCategory()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxViewCategory in interface Block
        Returns:
        PdbxViewCategory
      • getPdbxViewItem

        public PdbxViewItem getPdbxViewItem()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxViewItem in interface Block
        Returns:
        PdbxViewItem
      • getPdbxCoord

        public PdbxCoord getPdbxCoord()
        Description copied from interface: Block
        Gives information about what kind of coordinates are available.
        Specified by:
        getPdbxCoord in interface Block
        Returns:
        PdbxCoord
      • getPdbxConnect

        public PdbxConnect getPdbxConnect()
        Description copied from interface: Block
        Local data items describing ligand and monomer chemical features.
        Specified by:
        getPdbxConnect in interface Block
        Returns:
        PdbxConnect
      • getPdbxConnectType

        public PdbxConnectType getPdbxConnectType()
        Description copied from interface: Block
        Local data items describing ligand and monomer type information.
        Specified by:
        getPdbxConnectType in interface Block
        Returns:
        PdbxConnectType
      • getPdbxConnectAtom

        public PdbxConnectAtom getPdbxConnectAtom()
        Description copied from interface: Block
        Local data items describing ligand and monomer atom names and connectivity.
        Specified by:
        getPdbxConnectAtom in interface Block
        Returns:
        PdbxConnectAtom
      • getPdbxDatabasePDBMaster

        public PdbxDatabasePDBMaster getPdbxDatabasePDBMaster()
        Description copied from interface: Block
        The PDBX_DATABASE_PDB_MASTER category provides placeholders for the count of various PDB record types.
        Specified by:
        getPdbxDatabasePDBMaster in interface Block
        Returns:
        PdbxDatabasePDBMaster
      • getPdbxDatabasePdbOmit

        public PdbxDatabasePdbOmit getPdbxDatabasePdbOmit()
        Description copied from interface: Block
        Data items in the PDBX_DATABASE_PDB_OMIT category record list PDB record names that should be omitted in the PDB format file.
        Specified by:
        getPdbxDatabasePdbOmit in interface Block
        Returns:
        PdbxDatabasePdbOmit
      • getPdbxDbref

        public PdbxDbref getPdbxDbref()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxDbref in interface Block
        Returns:
        PdbxDbref
      • getPdbxDrugInfo

        public PdbxDrugInfo getPdbxDrugInfo()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxDrugInfo in interface Block
        Returns:
        PdbxDrugInfo
      • getPdbxInhibitorInfo

        public PdbxInhibitorInfo getPdbxInhibitorInfo()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxInhibitorInfo in interface Block
        Returns:
        PdbxInhibitorInfo
      • getPdbxIonInfo

        public PdbxIonInfo getPdbxIonInfo()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxIonInfo in interface Block
        Returns:
        PdbxIonInfo
      • getPdbxHybrid

        public PdbxHybrid getPdbxHybrid()
        Description copied from interface: Block
        Data items in the PDBX_HYBRID category are used to describe the chimeric characteristics of a DNA/RNA structure.
        Specified by:
        getPdbxHybrid in interface Block
        Returns:
        PdbxHybrid
      • getPdbxNaStrandInfo

        public PdbxNaStrandInfo getPdbxNaStrandInfo()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxNaStrandInfo in interface Block
        Returns:
        PdbxNaStrandInfo
      • getPdbxNonstandardList

        public PdbxNonstandardList getPdbxNonstandardList()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxNonstandardList in interface Block
        Returns:
        PdbxNonstandardList
      • getPdbxPdbCompnd

        public PdbxPdbCompnd getPdbxPdbCompnd()
        Description copied from interface: Block
        This is a place holder for the PDB COMPND.
        Specified by:
        getPdbxPdbCompnd in interface Block
        Returns:
        PdbxPdbCompnd
      • getPdbxPdbSource

        public PdbxPdbSource getPdbxPdbSource()
        Description copied from interface: Block
        This is a place holder for the PDB SOURCE.
        Specified by:
        getPdbxPdbSource in interface Block
        Returns:
        PdbxPdbSource
      • getPdbxProteinInfo

        public PdbxProteinInfo getPdbxProteinInfo()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxProteinInfo in interface Block
        Returns:
        PdbxProteinInfo
      • getPdbxSolventInfo

        public PdbxSolventInfo getPdbxSolventInfo()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxSolventInfo in interface Block
        Returns:
        PdbxSolventInfo
      • getPdbxSource

        public PdbxSource getPdbxSource()
        Description copied from interface: Block
        Data item will still be used until the ENTITY category is fully adopted by NDBQuery.
        Specified by:
        getPdbxSource in interface Block
        Returns:
        PdbxSource
      • getPdbxStructBiolFunc

        public PdbxStructBiolFunc getPdbxStructBiolFunc()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_BIOL_FUNC category record details about the function of a particular biological assembly.
        Specified by:
        getPdbxStructBiolFunc in interface Block
        Returns:
        PdbxStructBiolFunc
      • getPdbxStructPackGen

        public PdbxStructPackGen getPdbxStructPackGen()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_PACK_GEN category record details about the generation of the packing picture(s).
        Specified by:
        getPdbxStructPackGen in interface Block
        Returns:
        PdbxStructPackGen
      • getPdbxTrnaInfo

        public PdbxTrnaInfo getPdbxTrnaInfo()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxTrnaInfo in interface Block
        Returns:
        PdbxTrnaInfo
      • getPdbxUnpair

        public PdbxUnpair getPdbxUnpair()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxUnpair in interface Block
        Returns:
        PdbxUnpair
      • getPdbxRefineLsRestrNcs

        public PdbxRefineLsRestrNcs getPdbxRefineLsRestrNcs()
        Description copied from interface: Block
        Holds details of NCS restraints in cases where multiple conditions are provided for each domain.
        Specified by:
        getPdbxRefineLsRestrNcs in interface Block
        Returns:
        PdbxRefineLsRestrNcs
      • getPdbxStructNcsVirusGen

        public PdbxStructNcsVirusGen getPdbxStructNcsVirusGen()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_NCS_VIRUS_GEN category record details about the generation of virus structures from NCS matrix operators.
        Specified by:
        getPdbxStructNcsVirusGen in interface Block
        Returns:
        PdbxStructNcsVirusGen
      • getPdbxSequenceAnnotation

        public PdbxSequenceAnnotation getPdbxSequenceAnnotation()
        Description copied from interface: Block
        PDBX_SEQUENCE_ANNOTATION holds internal details about molecular sequences described in the context of PDB chains.
        Specified by:
        getPdbxSequenceAnnotation in interface Block
        Returns:
        PdbxSequenceAnnotation
      • getPdbxPostProcessDetails

        public PdbxPostProcessDetails getPdbxPostProcessDetails()
        Description copied from interface: Block
        Data items in the PDBX_POST_PROCESS_DETAILS identify problems or errors encountered in the post-processing of this entry.
        Specified by:
        getPdbxPostProcessDetails in interface Block
        Returns:
        PdbxPostProcessDetails
      • getPdbxPostProcessStatus

        public PdbxPostProcessStatus getPdbxPostProcessStatus()
        Description copied from interface: Block
        Data items in the PDBX_POST_PROCESS_DETAILS record the status of post-processed entries.
        Specified by:
        getPdbxPostProcessStatus in interface Block
        Returns:
        PdbxPostProcessStatus
      • getPdbxStructLink

        public PdbxStructLink getPdbxStructLink()
        Description copied from interface: Block
        Data items in the PDBX_STRUCT_LINK category record details about covalent linkages in the structure.
        Specified by:
        getPdbxStructLink in interface Block
        Returns:
        PdbxStructLink
      • getPdbxChemCompNonstandard

        public PdbxChemCompNonstandard getPdbxChemCompNonstandard()
        Description copied from interface: Block
        Data items in the PDBX_CHEM_COMP_NONSTANDARD category describes common nucleotide modifications and nonstandard features.
        Specified by:
        getPdbxChemCompNonstandard in interface Block
        Returns:
        PdbxChemCompNonstandard
      • getPdbxEntityPolyProteinClass

        public PdbxEntityPolyProteinClass getPdbxEntityPolyProteinClass()
        Description copied from interface: Block
        Data items in the PDBX_ENTITY_POLY_PROTEIN_CLASS category provides a top-level protein classification.
        Specified by:
        getPdbxEntityPolyProteinClass in interface Block
        Returns:
        PdbxEntityPolyProteinClass
      • getPdbxEntityNameTaxonomyTree

        public PdbxEntityNameTaxonomyTree getPdbxEntityNameTaxonomyTree()
        Description copied from interface: Block
        Data items in the PDBX_ENTITY_NAME_TAXONOMY_TREE category define the tree structure of the entity name taxonomy.
        Specified by:
        getPdbxEntityNameTaxonomyTree in interface Block
        Returns:
        PdbxEntityNameTaxonomyTree
      • getPdbxEntityNameTaxonomy

        public PdbxEntityNameTaxonomy getPdbxEntityNameTaxonomy()
        Description copied from interface: Block
        Data items in the PDBX_ENTITY_NAME_TAXONOMY category define the names and synonyms of the entity name taxonomy.
        Specified by:
        getPdbxEntityNameTaxonomy in interface Block
        Returns:
        PdbxEntityNameTaxonomy
      • getPdbxEntityNameInstance

        public PdbxEntityNameInstance getPdbxEntityNameInstance()
        Description copied from interface: Block
        Data items in the PDBX_ENTITY_NAME_INSTANCE category list names used to define entities with their associated database, entity, chain, and molecule identifiers.
        Specified by:
        getPdbxEntityNameInstance in interface Block
        Returns:
        PdbxEntityNameInstance
      • getPdbxValAngle

        public PdbxValAngle getPdbxValAngle()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxValAngle in interface Block
        Returns:
        PdbxValAngle
      • getPdbxValBond

        public PdbxValBond getPdbxValBond()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxValBond in interface Block
        Returns:
        PdbxValBond
      • getPdbxValContact

        public PdbxValContact getPdbxValContact()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxValContact in interface Block
        Returns:
        PdbxValContact
      • getPdbxValSymContact

        public PdbxValSymContact getPdbxValSymContact()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxValSymContact in interface Block
        Returns:
        PdbxValSymContact
      • getPdbxRmchOutlier

        public PdbxRmchOutlier getPdbxRmchOutlier()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxRmchOutlier in interface Block
        Returns:
        PdbxRmchOutlier
      • getPdbxMissingAtomPoly

        public PdbxMissingAtomPoly getPdbxMissingAtomPoly()
        Description copied from interface: Block
        Data items in the PDBX_MISSING_ATOM_POLY category lists atoms missing in polymer residues. This is a completely derived category. Do not edit.
        Specified by:
        getPdbxMissingAtomPoly in interface Block
        Returns:
        PdbxMissingAtomPoly
      • getPdbxMissingAtomNonpoly

        public PdbxMissingAtomNonpoly getPdbxMissingAtomNonpoly()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxMissingAtomNonpoly in interface Block
        Returns:
        PdbxMissingAtomNonpoly
      • getPdbxValChiral

        public PdbxValChiral getPdbxValChiral()
        Description copied from interface: Block
        Data items in the PDBX_VAL_CHIRAL category list the atoms with nonstandard chiralities. This is a completely derived category. Do not edit.
        Specified by:
        getPdbxValChiral in interface Block
        Returns:
        PdbxValChiral
      • getPdbxAtlas

        public PdbxAtlas getPdbxAtlas()
        Description copied from interface: Block
        Gives information about the organization of the NDB Structural Atlas.
        Specified by:
        getPdbxAtlas in interface Block
        Returns:
        PdbxAtlas
      • getPdbxSummaryFlags

        public PdbxSummaryFlags getPdbxSummaryFlags()
        Description copied from interface: Block
        Container category for a list of feature flags associated with each structure entry.
        Specified by:
        getPdbxSummaryFlags in interface Block
        Returns:
        PdbxSummaryFlags
      • getPdbxEntityFuncBindMode

        public PdbxEntityFuncBindMode getPdbxEntityFuncBindMode()
        Description copied from interface: Block
        Data items in the PDBX_ENTITY_FUNC_BIND_MODE category describe characteristics of protein oligonucleotide binding.
        Specified by:
        getPdbxEntityFuncBindMode in interface Block
        Returns:
        PdbxEntityFuncBindMode
      • getPdbxEntityFuncEnzyme

        public PdbxEntityFuncEnzyme getPdbxEntityFuncEnzyme()
        Description copied from interface: Block
        Data items in the PDBX_ENTITY_FUNC_ENZYME category describe characteristics of protein oligonucleotide binding in which the binding mode is enzymatic.
        Specified by:
        getPdbxEntityFuncEnzyme in interface Block
        Returns:
        PdbxEntityFuncEnzyme
      • getPdbxEntityFuncRegulatory

        public PdbxEntityFuncRegulatory getPdbxEntityFuncRegulatory()
        Description copied from interface: Block
        Data items in the PDBX_ENTITY_FUNC_REGULATORY category describe characteristics of protein oligonucleotide binding in which the binding mode is regulatory.
        Specified by:
        getPdbxEntityFuncRegulatory in interface Block
        Returns:
        PdbxEntityFuncRegulatory
      • getPdbxEntityFuncStructural

        public PdbxEntityFuncStructural getPdbxEntityFuncStructural()
        Description copied from interface: Block
        Data items in the PDBX_ENTITY_FUNC_STRUCTURAL category describe characteristics of protein oligonucleotide binding in which the binding mode is structural.
        Specified by:
        getPdbxEntityFuncStructural in interface Block
        Returns:
        PdbxEntityFuncStructural
      • getPdbxEntityFuncOther

        public PdbxEntityFuncOther getPdbxEntityFuncOther()
        Description copied from interface: Block
        Data items in the PDBX_ENTITY_FUNC_OTHER category describe characteristics of protein oligonucleotide binding in which the binding mode is not classified.
        Specified by:
        getPdbxEntityFuncOther in interface Block
        Returns:
        PdbxEntityFuncOther
      • getPdbxEntityPolyDomain

        public PdbxEntityPolyDomain getPdbxEntityPolyDomain()
        Description copied from interface: Block
        Data items in the PDBX_ENTITY_POLY_DOMAIN category specify domains of monomers within a polymer.
        Specified by:
        getPdbxEntityPolyDomain in interface Block
        Returns:
        PdbxEntityPolyDomain
      • getPdbxNaStructKeywds

        public PdbxNaStructKeywds getPdbxNaStructKeywds()
        Description copied from interface: Block
        Data items in the PDBX_NA_STRUCT_KEYWDS category record give details about structural features of the NA.
        Specified by:
        getPdbxNaStructKeywds in interface Block
        Returns:
        PdbxNaStructKeywds
      • getPdbxEntityPolyNaType

        public PdbxEntityPolyNaType getPdbxEntityPolyNaType()
        Description copied from interface: Block
        Data items in the PDBX_ENTITY_POLY_NA_TYPE category describe type of nucleic acid polymer entities.
        Specified by:
        getPdbxEntityPolyNaType in interface Block
        Returns:
        PdbxEntityPolyNaType
      • getPdbxEntityPolyNaNonstandard

        public PdbxEntityPolyNaNonstandard getPdbxEntityPolyNaNonstandard()
        Description copied from interface: Block
        Data items in the PDBX_ENTITY_POLY_NA_NONSTANDARD category describe the nonstandard features of the nucleic acid polymer entities.
        Specified by:
        getPdbxEntityPolyNaNonstandard in interface Block
        Returns:
        PdbxEntityPolyNaNonstandard
      • getPdbxVirtualAngle

        public PdbxVirtualAngle getPdbxVirtualAngle()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxVirtualAngle in interface Block
        Returns:
        PdbxVirtualAngle
      • getPdbxVirtualBond

        public PdbxVirtualBond getPdbxVirtualBond()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxVirtualBond in interface Block
        Returns:
        PdbxVirtualBond
      • getPdbxVirtualTorsion

        public PdbxVirtualTorsion getPdbxVirtualTorsion()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxVirtualTorsion in interface Block
        Returns:
        PdbxVirtualTorsion
      • getPdbxSequencePattern

        public PdbxSequencePattern getPdbxSequencePattern()
        Description copied from interface: Block
        Data items in the PDBX_SEQUENCE_PATTERN category record the number of occurences of common step sequence patterns (e.g. AA, CG, AT).
        Specified by:
        getPdbxSequencePattern in interface Block
        Returns:
        PdbxSequencePattern
      • getPdbxStereochemistry

        public PdbxStereochemistry getPdbxStereochemistry()
        Description copied from interface: Block
        Data items in the PDBX_STEREOCHEMISTRY identify chiral centers and associated chiral volumes.
        Specified by:
        getPdbxStereochemistry in interface Block
        Returns:
        PdbxStereochemistry
      • getPdbxRmsDevsCovalent

        public PdbxRmsDevsCovalent getPdbxRmsDevsCovalent()
        Description copied from interface: Block
        Data items in the PDBX_RMS_DEVS_COVALENT record the summary RMS deviations for nucleic acid covalent geometry relative to small molecule crystal standards.
        Specified by:
        getPdbxRmsDevsCovalent in interface Block
        Returns:
        PdbxRmsDevsCovalent
      • getPdbxRmsDevsCovByMonomer

        public PdbxRmsDevsCovByMonomer getPdbxRmsDevsCovByMonomer()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxRmsDevsCovByMonomer in interface Block
        Returns:
        PdbxRmsDevsCovByMonomer
      • getPdbxSugarPhosphateGeometry

        public PdbxSugarPhosphateGeometry getPdbxSugarPhosphateGeometry()
        Description copied from interface: Block
        Data items in the PDBX_SUGAR_PHOSPHATE_GEOMETRY record the RMS deviations covalent geometry for each momoner relative to small molecule crystal standards.
        Specified by:
        getPdbxSugarPhosphateGeometry in interface Block
        Returns:
        PdbxSugarPhosphateGeometry
      • getPdbxNmrComputing

        public PdbxNmrComputing getPdbxNmrComputing()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxNmrComputing in interface Block
        Returns:
        PdbxNmrComputing
      • getPdbxAuditConformExtension

        public PdbxAuditConformExtension getPdbxAuditConformExtension()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxAuditConformExtension in interface Block
        Returns:
        PdbxAuditConformExtension
      • getPdbxDccMapman

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

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

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

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

        public PdbxDccGeometry getPdbxDccGeometry()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxDccGeometry in interface Block
        Returns:
        PdbxDccGeometry
      • getPdbxDccDensityCorr

        public PdbxDccDensityCorr getPdbxDccDensityCorr()
        Description copied from interface: Block
        Data items in the category record calculated metrics from various programs (such as phenix, refmac, cns, sfcheck).
        Specified by:
        getPdbxDccDensityCorr in interface Block
        Returns:
        PdbxDccDensityCorr
      • getPdbxDccMap

        public PdbxDccMap getPdbxDccMap()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxDccMap in interface Block
        Returns:
        PdbxDccMap
      • getPdbxDepositGroup

        public PdbxDepositGroup getPdbxDepositGroup()
        Description copied from interface: Block
        Data items in the pdbx_deposit_group category provide identifiers and related information for groups of entries deposited in a collection.
        Specified by:
        getPdbxDepositGroup in interface Block
        Returns:
        PdbxDepositGroup
      • getPdbxDepositGroupIndex

        public PdbxDepositGroupIndex getPdbxDepositGroupIndex()
        Description copied from interface: Block
        Data items in the pdbx_deposit_group_index category provides details about the individual data files in the collection of deposited entries.
        Specified by:
        getPdbxDepositGroupIndex in interface Block
        Returns:
        PdbxDepositGroupIndex
      • getPdbxCrystalAlignment

        public PdbxCrystalAlignment getPdbxCrystalAlignment()
        Description copied from interface: Block
        Data in the PDBX_CRYSTAL_ALIGNMENT are produced by log files from programs during indexing
        Specified by:
        getPdbxCrystalAlignment in interface Block
        Returns:
        PdbxCrystalAlignment
      • getPdbxAuditRevisionHistory

        public PdbxAuditRevisionHistory getPdbxAuditRevisionHistory()
        Description copied from interface: Block
        Data items in the PDBX_AUDIT_REVISION_HISTORY category record the revision history for a data entry.
        Specified by:
        getPdbxAuditRevisionHistory in interface Block
        Returns:
        PdbxAuditRevisionHistory
      • getPdbxAuditRevisionGroup

        public PdbxAuditRevisionGroup getPdbxAuditRevisionGroup()
        Description copied from interface: Block
        Data items in the PDBX_AUDIT_revision_group category report the content groups associated with a PDBX_AUDIT_REVISION_HISTORY record.
        Specified by:
        getPdbxAuditRevisionGroup in interface Block
        Returns:
        PdbxAuditRevisionGroup
      • getPdbxAuditRevisionCategory

        public PdbxAuditRevisionCategory getPdbxAuditRevisionCategory()
        Description copied from interface: Block
        Data items in the PDBX_AUDIT_REVISION_CATEGORY category report the data categories associated with a PDBX_AUDIT_REVISION_HISTORY record.
        Specified by:
        getPdbxAuditRevisionCategory in interface Block
        Returns:
        PdbxAuditRevisionCategory
      • getPdbxAuditRevisionDetails

        public PdbxAuditRevisionDetails getPdbxAuditRevisionDetails()
        Description copied from interface: Block
        Data items in the PDBX_audit_revision_details category record descriptions of changes associated with PDBX_AUDIT_REVISION_HISTORY records.
        Specified by:
        getPdbxAuditRevisionDetails in interface Block
        Returns:
        PdbxAuditRevisionDetails
      • getPdbxAuditRevisionItem

        public PdbxAuditRevisionItem getPdbxAuditRevisionItem()
        Description copied from interface: Block
        Data items in the PDBX_AUDIT_REVISION_ITEM category report the data items associated with a PDBX_AUDIT_REVISION_HISTORY record.
        Specified by:
        getPdbxAuditRevisionItem in interface Block
        Returns:
        PdbxAuditRevisionItem
      • getPdbxSupportingExpDataSet

        public PdbxSupportingExpDataSet getPdbxSupportingExpDataSet()
        Description copied from interface: Block
        Data items in the PDBX_SUPPORTING_EXP_DATA_SET category record to experimental data set dependencies for this entry.
        Specified by:
        getPdbxSupportingExpDataSet in interface Block
        Returns:
        PdbxSupportingExpDataSet
      • getPdbxSerialCrystallographyDataReduction

        public PdbxSerialCrystallographyDataReduction getPdbxSerialCrystallographyDataReduction()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxSerialCrystallographyDataReduction in interface Block
        Returns:
        PdbxSerialCrystallographyDataReduction
      • getPdbxChemCompSynonyms

        public PdbxChemCompSynonyms getPdbxChemCompSynonyms()
        Description copied from interface: Block
        PDBX_CHEM_COMP_SYNONYMS holds chemical name and synonym correspondences.
        Specified by:
        getPdbxChemCompSynonyms in interface Block
        Returns:
        PdbxChemCompSynonyms
      • getPdbxChemCompRelated

        public PdbxChemCompRelated getPdbxChemCompRelated()
        Description copied from interface: Block
        PDBX_CHEM_COMP_RELATED describes the relationship between two chemical components.
        Specified by:
        getPdbxChemCompRelated in interface Block
        Returns:
        PdbxChemCompRelated
      • getPdbxChemCompAtomRelated

        public PdbxChemCompAtomRelated getPdbxChemCompAtomRelated()
        Description copied from interface: Block
        PDBX_CHEM_COMP_ATOM_RELATED provides atom level nomenclature mapping between two related chemical components.
        Specified by:
        getPdbxChemCompAtomRelated in interface Block
        Returns:
        PdbxChemCompAtomRelated
      • getPdbxEntityBranchList

        public PdbxEntityBranchList getPdbxEntityBranchList()
        Description copied from interface: Block
        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.
        Specified by:
        getPdbxEntityBranchList in interface Block
        Returns:
        PdbxEntityBranchList
      • getPdbxEntityBranchLink

        public PdbxEntityBranchLink getPdbxEntityBranchLink()
        Description copied from interface: Block
        Data items in the PDBX_ENTITY_BRANCH_LINK category give details about the linkages between components within a branched entity.
        Specified by:
        getPdbxEntityBranchLink in interface Block
        Returns:
        PdbxEntityBranchLink
      • getPdbxEntityBranch

        public PdbxEntityBranch getPdbxEntityBranch()
        Description copied from interface: Block
        Data items in the PDBX_ENTITY_BRANCH category specify the list of branched entities and the type.
        Specified by:
        getPdbxEntityBranch in interface Block
        Returns:
        PdbxEntityBranch
      • getPdbxBranchScheme

        public PdbxBranchScheme getPdbxBranchScheme()
        Description copied from interface: Block
        The PDBX_BRANCH_SCHEME category provides residue level nomenclature mapping for branch chain entities.
        Specified by:
        getPdbxBranchScheme in interface Block
        Returns:
        PdbxBranchScheme
      • getIhmStartingModelDetails

        public IhmStartingModelDetails getIhmStartingModelDetails()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmStartingModelDetails in interface Block
        Returns:
        IhmStartingModelDetails
      • getIhmStartingComparativeModels

        public IhmStartingComparativeModels getIhmStartingComparativeModels()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmStartingComparativeModels in interface Block
        Returns:
        IhmStartingComparativeModels
      • getIhmStartingComputationalModels

        public IhmStartingComputationalModels getIhmStartingComputationalModels()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmStartingComputationalModels in interface Block
        Returns:
        IhmStartingComputationalModels
      • getIhmStartingModelSeqDif

        public IhmStartingModelSeqDif getIhmStartingModelSeqDif()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmStartingModelSeqDif in interface Block
        Returns:
        IhmStartingModelSeqDif
      • getIhmModelRepresentation

        public IhmModelRepresentation getIhmModelRepresentation()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmModelRepresentation in interface Block
        Returns:
        IhmModelRepresentation
      • getIhmStructAssembly

        public IhmStructAssembly getIhmStructAssembly()
        Description copied from interface: Block
        Data items in the IHM_STRUCT_ASSEMBLY category records the details of the structural assemblies and used in the IHM modeling.
        Specified by:
        getIhmStructAssembly in interface Block
        Returns:
        IhmStructAssembly
      • getIhmStructAssemblyDetails

        public IhmStructAssemblyDetails getIhmStructAssemblyDetails()
        Description copied from interface: Block
        Data items in the IHM_STRUCT_ASSEMBLY_DETAILS category provides additional details regarding the structure assembly.
        Specified by:
        getIhmStructAssemblyDetails in interface Block
        Returns:
        IhmStructAssemblyDetails
      • getIhmStructAssemblyClassList

        public IhmStructAssemblyClassList getIhmStructAssemblyClassList()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmStructAssemblyClassList in interface Block
        Returns:
        IhmStructAssemblyClassList
      • getIhmStructAssemblyClass

        public IhmStructAssemblyClass getIhmStructAssemblyClass()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmStructAssemblyClass in interface Block
        Returns:
        IhmStructAssemblyClass
      • getIhmModelingProtocol

        public IhmModelingProtocol getIhmModelingProtocol()
        Description copied from interface: Block
        Data items in the IHM_MODELING_PROTOCOL category records the step-wise details of the integrative modeling workflow.
        Specified by:
        getIhmModelingProtocol in interface Block
        Returns:
        IhmModelingProtocol
      • getIhmMultiStateModeling

        public IhmMultiStateModeling getIhmMultiStateModeling()
        Description copied from interface: Block
        Data items in the IHM_MULTI_STATE_MODELING category records the details of the multi-state modeling protocol, if applicable.
        Specified by:
        getIhmMultiStateModeling in interface Block
        Returns:
        IhmMultiStateModeling
      • getIhmOrderedEnsemble

        public IhmOrderedEnsemble getIhmOrderedEnsemble()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmOrderedEnsemble in interface Block
        Returns:
        IhmOrderedEnsemble
      • getIhmModelingPostProcess

        public IhmModelingPostProcess getIhmModelingPostProcess()
        Description copied from interface: Block
        Data items in the IHM_MODELING_POST_PROCESS category records the details of the post processing of the models/results of the modeling protocol.
        Specified by:
        getIhmModelingPostProcess in interface Block
        Returns:
        IhmModelingPostProcess
      • getIhmEnsembleInfo

        public IhmEnsembleInfo getIhmEnsembleInfo()
        Description copied from interface: Block
        Data items in the IHM_ENSEMBLE_INFO category records the details of the model clusters or ensembles obtained after sampling.
        Specified by:
        getIhmEnsembleInfo in interface Block
        Returns:
        IhmEnsembleInfo
      • getIhmModelList

        public IhmModelList getIhmModelList()
        Description copied from interface: Block
        Data items in the IHM_MODEL_LIST category record the details of the models being deposited.
        Specified by:
        getIhmModelList in interface Block
        Returns:
        IhmModelList
      • getIhmModelRepresentative

        public IhmModelRepresentative getIhmModelRepresentative()
        Description copied from interface: Block
        Data items in the IHM_MODEL_REPRESENTATIVE category record the details of the representative model in an ensemble or cluster.
        Specified by:
        getIhmModelRepresentative in interface Block
        Returns:
        IhmModelRepresentative
      • getIhmDatasetList

        public IhmDatasetList getIhmDatasetList()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmDatasetList in interface Block
        Returns:
        IhmDatasetList
      • getIhmDatasetGroup

        public IhmDatasetGroup getIhmDatasetGroup()
        Description copied from interface: Block
        Category provides a mechanism to group datasets.
        Specified by:
        getIhmDatasetGroup in interface Block
        Returns:
        IhmDatasetGroup
      • getIhmRelatedDatasets

        public IhmRelatedDatasets getIhmRelatedDatasets()
        Description copied from interface: Block
        Category holds information about related datasets, where one is derived from the other.
        Specified by:
        getIhmRelatedDatasets in interface Block
        Returns:
        IhmRelatedDatasets
      • getIhmDatasetRelatedDbReference

        public IhmDatasetRelatedDbReference getIhmDatasetRelatedDbReference()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmDatasetRelatedDbReference in interface Block
        Returns:
        IhmDatasetRelatedDbReference
      • getIhmExternalReferenceInfo

        public IhmExternalReferenceInfo getIhmExternalReferenceInfo()
        Description copied from interface: Block
        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).
        Specified by:
        getIhmExternalReferenceInfo in interface Block
        Returns:
        IhmExternalReferenceInfo
      • getIhmExternalFiles

        public IhmExternalFiles getIhmExternalFiles()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmExternalFiles in interface Block
        Returns:
        IhmExternalFiles
      • getIhmDatasetExternalReference

        public IhmDatasetExternalReference getIhmDatasetExternalReference()
        Description copied from interface: Block
        Category provides additional details regarding input data hosted externally at other resources.
        Specified by:
        getIhmDatasetExternalReference in interface Block
        Returns:
        IhmDatasetExternalReference
      • getIhmLocalizationDensityFiles

        public IhmLocalizationDensityFiles getIhmLocalizationDensityFiles()
        Description copied from interface: Block
        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.).
        Specified by:
        getIhmLocalizationDensityFiles in interface Block
        Returns:
        IhmLocalizationDensityFiles
      • getIhmPredictedContactRestraint

        public IhmPredictedContactRestraint getIhmPredictedContactRestraint()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmPredictedContactRestraint in interface Block
        Returns:
        IhmPredictedContactRestraint
      • getIhmHydroxylRadicalFpRestraint

        public IhmHydroxylRadicalFpRestraint getIhmHydroxylRadicalFpRestraint()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmHydroxylRadicalFpRestraint in interface Block
        Returns:
        IhmHydroxylRadicalFpRestraint
      • getIhmCrossLinkList

        public IhmCrossLinkList getIhmCrossLinkList()
        Description copied from interface: Block
        Data items in the IHM_CROSS_LINK_LIST category records the list of spatial restraints derived from chemical crosslinking experiment.
        Specified by:
        getIhmCrossLinkList in interface Block
        Returns:
        IhmCrossLinkList
      • getIhmCrossLinkRestraint

        public IhmCrossLinkRestraint getIhmCrossLinkRestraint()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmCrossLinkRestraint in interface Block
        Returns:
        IhmCrossLinkRestraint
      • getIhmCrossLinkResult

        public IhmCrossLinkResult getIhmCrossLinkResult()
        Description copied from interface: Block
        Data items in the IHM_CROSS_LINK_RESULT category records the results of the crosslinking restraints in the IHM modeling.
        Specified by:
        getIhmCrossLinkResult in interface Block
        Returns:
        IhmCrossLinkResult
      • getIhmCrossLinkResultParameters

        public IhmCrossLinkResultParameters getIhmCrossLinkResultParameters()
        Description copied from interface: Block
        Data items in the IHM_CROSS_LINK_RESULT_PARAMETERS category records the results of the crosslinking restraint parameters in the IHM modeling.
        Specified by:
        getIhmCrossLinkResultParameters in interface Block
        Returns:
        IhmCrossLinkResultParameters
      • getIhm2demClassAverageRestraint

        public Ihm2demClassAverageRestraint getIhm2demClassAverageRestraint()
        Description copied from interface: Block
        Data items in the IHM_2DEM_CLASS_AVERAGE_RESTRAINT category records the details of the 2DEM class averages used in the IHM modeling.
        Specified by:
        getIhm2demClassAverageRestraint in interface Block
        Returns:
        Ihm2demClassAverageRestraint
      • getIhm2demClassAverageFitting

        public Ihm2demClassAverageFitting getIhm2demClassAverageFitting()
        Description copied from interface: Block
        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.
        Specified by:
        getIhm2demClassAverageFitting in interface Block
        Returns:
        Ihm2demClassAverageFitting
      • getIhm3demRestraint

        public Ihm3demRestraint getIhm3demRestraint()
        Description copied from interface: Block
        Data items in the IHM_3DEM_RESTRAINT category records the details of the 3DEM maps used as restraints in the IHM modeling.
        Specified by:
        getIhm3demRestraint in interface Block
        Returns:
        Ihm3demRestraint
      • getIhmSasRestraint

        public IhmSasRestraint getIhmSasRestraint()
        Description copied from interface: Block
        Data items in the IHM_SAS_RESTRAINT category records the details of the SAS data used as restraints in the IHM modeling.
        Specified by:
        getIhmSasRestraint in interface Block
        Returns:
        IhmSasRestraint
      • getIhmStartingModelCoord

        public IhmStartingModelCoord getIhmStartingModelCoord()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmStartingModelCoord in interface Block
        Returns:
        IhmStartingModelCoord
      • getIhmSphereObjSite

        public IhmSphereObjSite getIhmSphereObjSite()
        Description copied from interface: Block
        Data items in the IHM_SPHERE_OBJ_SITE category records the details of the spherical objects modeled in the integrative structural model.
        Specified by:
        getIhmSphereObjSite in interface Block
        Returns:
        IhmSphereObjSite
      • getIhmGaussianObjSite

        public IhmGaussianObjSite getIhmGaussianObjSite()
        Description copied from interface: Block
        Data items in the IHM_GAUSSIAN_OBJ_SITE category records the details of the gaussian objects modeled in the integrative structural model.
        Specified by:
        getIhmGaussianObjSite in interface Block
        Returns:
        IhmGaussianObjSite
      • getIhmGaussianObjEnsemble

        public IhmGaussianObjEnsemble getIhmGaussianObjEnsemble()
        Description copied from interface: Block
        Data items in the IHM_GAUSSIAN_OBJ_ENSEMBLE category records the details of the gaussian objects representing an ensemble or cluster of models.
        Specified by:
        getIhmGaussianObjEnsemble in interface Block
        Returns:
        IhmGaussianObjEnsemble
      • getIhmResiduesNotModeled

        public IhmResiduesNotModeled getIhmResiduesNotModeled()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmResiduesNotModeled in interface Block
        Returns:
        IhmResiduesNotModeled
      • getIhmFeatureList

        public IhmFeatureList getIhmFeatureList()
        Description copied from interface: Block
        IHM_FEATURE_LIST is the high level category that provides defintions to select atoms/residues from polymeric and non-polymeric entities.
        Specified by:
        getIhmFeatureList in interface Block
        Returns:
        IhmFeatureList
      • getIhmPseudoSiteFeature

        public IhmPseudoSiteFeature getIhmPseudoSiteFeature()
        Description copied from interface: Block
        Data items in the IHM_PSEUDO_SITE_FEATURE category records the details of pseudo positions for the features listed in IHM_FEATURE_LIST.
        Specified by:
        getIhmPseudoSiteFeature in interface Block
        Returns:
        IhmPseudoSiteFeature
      • getIhmPolyAtomFeature

        public IhmPolyAtomFeature getIhmPolyAtomFeature()
        Description copied from interface: Block
        Data items in the IHM_POLY_ATOM_FEATURE category provides the defintions required to select specific atoms.
        Specified by:
        getIhmPolyAtomFeature in interface Block
        Returns:
        IhmPolyAtomFeature
      • getIhmPolyResidueFeature

        public IhmPolyResidueFeature getIhmPolyResidueFeature()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmPolyResidueFeature in interface Block
        Returns:
        IhmPolyResidueFeature
      • getIhmNonPolyFeature

        public IhmNonPolyFeature getIhmNonPolyFeature()
        Description copied from interface: Block
        Data items in the IHM_NON_POLY_FEATURE category provides the defintions required to select a non-polymeric (ligand) feature.
        Specified by:
        getIhmNonPolyFeature in interface Block
        Returns:
        IhmNonPolyFeature
      • getIhmInterfaceResidueFeature

        public IhmInterfaceResidueFeature getIhmInterfaceResidueFeature()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmInterfaceResidueFeature in interface Block
        Returns:
        IhmInterfaceResidueFeature
      • getIhmDerivedDistanceRestraint

        public IhmDerivedDistanceRestraint getIhmDerivedDistanceRestraint()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmDerivedDistanceRestraint in interface Block
        Returns:
        IhmDerivedDistanceRestraint
      • getIhmGeometricObjectList

        public IhmGeometricObjectList getIhmGeometricObjectList()
        Description copied from interface: Block
        Data items in the IHM_GEOMETRIC_OBJECT_LIST category records the list of geometric objects used as restraints in the integrative modeling study.
        Specified by:
        getIhmGeometricObjectList in interface Block
        Returns:
        IhmGeometricObjectList
      • getIhmGeometricObjectCenter

        public IhmGeometricObjectCenter getIhmGeometricObjectCenter()
        Description copied from interface: Block
        Data items in the IHM_GEOMETRIC_OBJECT_CENTER category records the center of geometric objects used as restraints in the integrative modeling study.
        Specified by:
        getIhmGeometricObjectCenter in interface Block
        Returns:
        IhmGeometricObjectCenter
      • getIhmGeometricObjectTransformation

        public IhmGeometricObjectTransformation getIhmGeometricObjectTransformation()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmGeometricObjectTransformation in interface Block
        Returns:
        IhmGeometricObjectTransformation
      • getIhmGeometricObjectSphere

        public IhmGeometricObjectSphere getIhmGeometricObjectSphere()
        Description copied from interface: Block
        Data items in the IHM_GEOMETRIC_OBJECT_SPHERE category records the parameters of a sphere.
        Specified by:
        getIhmGeometricObjectSphere in interface Block
        Returns:
        IhmGeometricObjectSphere
      • getIhmGeometricObjectTorus

        public IhmGeometricObjectTorus getIhmGeometricObjectTorus()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmGeometricObjectTorus in interface Block
        Returns:
        IhmGeometricObjectTorus
      • getIhmGeometricObjectHalfTorus

        public IhmGeometricObjectHalfTorus getIhmGeometricObjectHalfTorus()
        Description copied from interface: Block
        Data items in the IHM_GEOMETRIC_OBJECT_HALF_TORUS category records the parameters of half-torus that represents a membrane.
        Specified by:
        getIhmGeometricObjectHalfTorus in interface Block
        Returns:
        IhmGeometricObjectHalfTorus
      • getIhmGeometricObjectAxis

        public IhmGeometricObjectAxis getIhmGeometricObjectAxis()
        Description copied from interface: Block
        Data items in the IHM_GEOMETRIC_OBJECT_AXIS category records the details of an axis used in a spatial restraint.
        Specified by:
        getIhmGeometricObjectAxis in interface Block
        Returns:
        IhmGeometricObjectAxis
      • getIhmGeometricObjectPlane

        public IhmGeometricObjectPlane getIhmGeometricObjectPlane()
        Description copied from interface: Block
        Data items in the IHM_GEOMETRIC_OBJECT_PLANE category records the details of a plane used in a spatial restraint.
        Specified by:
        getIhmGeometricObjectPlane in interface Block
        Returns:
        IhmGeometricObjectPlane
      • getIhmGeometricObjectDistanceRestraint

        public IhmGeometricObjectDistanceRestraint getIhmGeometricObjectDistanceRestraint()
        Description copied from interface: Block
        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.
        Specified by:
        getIhmGeometricObjectDistanceRestraint in interface Block
        Returns:
        IhmGeometricObjectDistanceRestraint