Package org.rcsb.cif.schema.mm

Class MmCifBlock

java.lang.Object
org.rcsb.cif.schema.DelegatingBlock
org.rcsb.cif.schema.mm.MmCifBlock
All Implemented Interfaces:
Block
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class MmCifBlock
extends DelegatingBlock

  • Constructor Details

  • Method Details

    • createDelegate

      protected Category createDelegate​(String categoryName, Category category)
      Specified by:
      createDelegate in class DelegatingBlock

    • getAtomSite

      public AtomSite getAtomSite()
      Data items in the ATOM_SITE category record details about the atom sites in a macromolecular crystal structure, such as the positional coordinates, atomic displacement parameters, magnetic moments and directions. The data items for describing anisotropic atomic displacement factors are only used if the corresponding items are not given in the ATOM_SITE_ANISOTROP category.
      Returns:
      AtomSite

    • getAtomSiteAnisotrop

      public AtomSiteAnisotrop getAtomSiteAnisotrop()
      Data items in the ATOM_SITE_ANISOTROP category record details about anisotropic displacement parameters. If the ATOM_SITE_ANISOTROP category is used for storing these data, the corresponding ATOM_SITE data items are not used.
      Returns:
      AtomSiteAnisotrop

    • getAtomSites

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

    • getAtomSitesAlt

      public AtomSitesAlt getAtomSitesAlt()
      Data items in the ATOM_SITES_ALT category record details about the structural ensembles that should be generated from atom sites or groups of atom sites that are modelled in alternative conformations in this data block.
      Returns:
      AtomSitesAlt

    • getAtomSitesAltEns

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

    • getAtomSitesAltGen

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

    • getAtomSitesFootnote

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

    • getAtomType

      public AtomType getAtomType()
      Data items in the ATOM_TYPE category record details about the properties of the atoms that occupy the atom sites, such as the atomic scattering factors.
      Returns:
      AtomType

    • getAudit

      public Audit getAudit()
      Data items in the AUDIT category record details about the creation and subsequent updating of the data block. Note that these items apply only to the creation and updating of the data block, and should not be confused with the data items in the JOURNAL category that record different stages in the publication of the material in the data block.
      Returns:
      Audit

    • getAuditAuthor

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

    • getAuditConform

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

    • getAuditContactAuthor

      public AuditContactAuthor getAuditContactAuthor()
      Data items in the AUDIT_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the content of this data block.
      Returns:
      AuditContactAuthor

    • getCell

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

    • getCellMeasurement

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

    • getCellMeasurementRefln

      public CellMeasurementRefln getCellMeasurementRefln()
      Data items in the CELL_MEASUREMENT_REFLN category record details about the reflections used to determine the crystallographic cell parameters. The CELL_MEASUREMENT_REFLN data items would in general be used only for diffractometer data.
      Returns:
      CellMeasurementRefln

    • getChemComp

      public ChemComp getChemComp()
      Data items in the CHEM_COMP category give details about each of the chemical components from which the relevant chemical structures can be constructed, such as name, mass or charge. The related categories CHEM_COMP_ATOM, CHEM_COMP_BOND, CHEM_COMP_ANGLE etc. describe the detailed geometry of these chemical components.
      Returns:
      ChemComp

    • getChemCompAngle

      public ChemCompAngle getChemCompAngle()
      Data items in the CHEM_COMP_ANGLE category record details about angles in a chemical component. Angles are designated by three atoms, with the second atom forming the vertex of the angle. Target values may be specified as angles in degrees, as a distance between the first and third atoms, or both.
      Returns:
      ChemCompAngle

    • getChemCompAtom

      public ChemCompAtom getChemCompAtom()
      Data items in the CHEM_COMP_ATOM category record details about the atoms in a chemical component. Specifying the atomic coordinates for the components in this category is an alternative to specifying the structure of the component via bonds, angles, planes etc. in the appropriate CHEM_COMP subcategories.
      Returns:
      ChemCompAtom

    • getChemCompBond

      public ChemCompBond getChemCompBond()
      Data items in the CHEM_COMP_BOND category record details about the bonds between atoms in a chemical component. Target values may be specified as bond orders, as a distance between the two atoms, or both.
      Returns:
      ChemCompBond

    • getChemCompChir

      public ChemCompChir getChemCompChir()
      Data items in the CHEM_COMP_CHIR category provide details about the chiral centres in a chemical component. The atoms bonded to the chiral atom are specified in the CHEM_COMP_CHIR_ATOM category.
      Returns:
      ChemCompChir

    • getChemCompChirAtom

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

    • getChemCompLink

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

    • getChemCompPlane

      public ChemCompPlane getChemCompPlane()
      Data items in the CHEM_COMP_PLANE category provide identifiers for the planes in a chemical component. The atoms in the plane are specified in the CHEM_COMP_PLANE_ATOM category.
      Returns:
      ChemCompPlane

    • getChemCompPlaneAtom

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

    • getChemCompTor

      public ChemCompTor getChemCompTor()
      Data items in the CHEM_COMP_TOR category record details about the torsion angles in a chemical component. As torsion angles can have more than one target value, the target values are specified in the CHEM_COMP_TOR_VALUE category.
      Returns:
      ChemCompTor

    • getChemCompTorValue

      public ChemCompTorValue getChemCompTorValue()
      Data items in the CHEM_COMP_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_COMP_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both.
      Returns:
      ChemCompTorValue

    • getChemLink

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

    • getChemLinkAngle

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

    • getChemLinkBond

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

    • getChemLinkChir

      public ChemLinkChir getChemLinkChir()
      Data items in the CHEM_LINK_CHIR category provide details about the chiral centres in a link between two chemical components. The atoms bonded to the chiral atom are specified in the CHEM_LINK_CHIR_ATOM category.
      Returns:
      ChemLinkChir

    • getChemLinkChirAtom

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

    • getChemLinkPlane

      public ChemLinkPlane getChemLinkPlane()
      Data items in the CHEM_LINK_PLANE category provide identifiers for the planes in a link between two chemical components. The atoms in the plane are specified in the CHEM_LINK_PLANE_ATOM category.
      Returns:
      ChemLinkPlane

    • getChemLinkPlaneAtom

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

    • getChemLinkTor

      public ChemLinkTor getChemLinkTor()
      Data items in the CHEM_LINK_TOR category record details about the torsion angles in a link between two chemical components. As torsion angles can have more than one target value, the target values are specified in the CHEM_LINK_TOR_VALUE category.
      Returns:
      ChemLinkTor

    • getChemLinkTorValue

      public ChemLinkTorValue getChemLinkTorValue()
      Data items in the CHEM_LINK_TOR_VALUE category record details about the target values for the torsion angles enumerated in the CHEM_LINK_TOR list. Target values may be specified as angles in degrees, as a distance between the first and fourth atoms, or both.
      Returns:
      ChemLinkTorValue

    • getChemical

      public Chemical getChemical()
      Data items in the CHEMICAL category would not in general be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL category record details about the composition and chemical properties of the compounds. The formula data items must agree with those that specify the density, unit-cell and Z values.
      Returns:
      Chemical

    • getChemicalConnAtom

      public ChemicalConnAtom getChemicalConnAtom()
      Data items in the CHEMICAL_CONN_ATOM category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the two-dimensional (2D) chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_ATOM data items provide information about the chemical properties of the atoms in the structure. In cases where crystallographic and molecular symmetry elements coincide, they must also contain symmetry-generated atoms, so that the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND data items will always describe a complete chemical entity.
      Returns:
      ChemicalConnAtom

    • getChemicalConnBond

      public ChemicalConnBond getChemicalConnBond()
      Data items in the CHEMICAL_CONN_BOND category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_CONN_ATOM and CHEMICAL_CONN_BOND categories record details about the two-dimensional (2D) chemical structure of the molecular species. They allow a 2D chemical diagram to be reconstructed for use in a publication or in a database search for structural and substructural relationships. The CHEMICAL_CONN_BOND data items specify the connections between the atoms in the CHEMICAL_CONN_ATOM list and the nature of the chemical bond between these atoms.
      Returns:
      ChemicalConnBond

    • getChemicalFormula

      public ChemicalFormula getChemicalFormula()
      Data items in the CHEMICAL_FORMULA category would not, in general, be used in a macromolecular CIF. See instead the ENTITY data items. Data items in the CHEMICAL_FORMULA category specify the composition and chemical properties of the compound. The formula data items must agree with those that specify the density, unit-cell and Z values. The following rules apply to the construction of the data items _chemical_formula.analytical, _chemical_formula.structural and _chemical_formula.sum. For the data item _chemical_formula.moiety, the formula construction is broken up into residues or moieties, i.e. groups of atoms that form a molecular unit or molecular ion. The rules given below apply within each moiety but different requirements apply to the way that moieties are connected (see _chemical_formula.moiety). (1) Only recognized element symbols may be used. (2) Each element symbol is followed by a 'count' number. A count of '1' may be omitted. (3) A space or parenthesis must separate each cluster of (element symbol + count). (4) Where a group of elements is enclosed in parentheses, the multiplier for the group must follow the closing parenthesis. That is, all element and group multipliers are assumed to be printed as subscripted numbers. (An exception to this rule exists for _chemical_formula.moiety formulae where pre- and post-multipliers are permitted for molecular units.) (5) Unless the elements are ordered in a manner that corresponds to their chemical structure, as in _chemical_formula.structural, the order of the elements within any group or moiety should be: C, then H, then the other elements in alphabetical order of their symbol. This is the 'Hill' system used by Chemical Abstracts. This ordering is used in _chemical_formula.moiety and _chemical_formula.sum.
      Returns:
      ChemicalFormula

    • getCitation

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

    • getCitationAuthor

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

    • getCitationEditor

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

    • getComputing

      public Computing getComputing()
      Data items in the COMPUTING category record details about the computer programs used in the crystal structure analysis. Data items in this category would not, in general, be used in a macromolecular CIF. The category SOFTWARE, which allows a more detailed description of computer programs and their attributes to be given, would be used instead.
      Returns:
      Computing

    • getDatabase

      public Database getDatabase()
      Data items in the DATABASE category have been superseded by data items in the DATABASE_2 category. They are included here only for compliance with older CIFs.
      Returns:
      Database

    • getDatabase2

      public Database2 getDatabase2()
      Data items in the DATABASE_2 category record details about the database identifiers of the data block. These data items are assigned by database managers and should only appear in a data block if they originate from that source. The name of this category, DATABASE_2, arose because the category name DATABASE was already in use in the core CIF dictionary, but was used differently from the way it needed to be used in the mmCIF dictionary. Since CIF data names cannot be changed once they have been adopted, a new category had to be created.
      Returns:
      Database2

    • getDatabasePDBCaveat

      public DatabasePDBCaveat getDatabasePDBCaveat()
      Data items in the DATABASE_PDB_CAVEAT category record details about features of the data block flagged as 'caveats' by the Protein Data Bank (PDB). These data items are included only for consistency with PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file.
      Returns:
      DatabasePDBCaveat

    • getDatabasePDBMatrix

      public DatabasePDBMatrix getDatabasePDBMatrix()
      The DATABASE_PDB_MATRIX category provides placeholders for transformation matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file.
      Returns:
      DatabasePDBMatrix

    • getDatabasePDBRemark

      public DatabasePDBRemark getDatabasePDBRemark()
      Data items in the DATABASE_PDB_REMARK category record details about the data block as archived by the Protein Data Bank (PDB). Some data appearing in PDB REMARK records can be algorithmically extracted into the appropriate data items in the data block. These data items are included only for consistency with older PDB format files. They should appear in a data block only if that data block was created by reformatting a PDB format file. NOTE: These remark records in this category are not uniformly annotated by the PDB and may not be consistent with nomenclature or labeling used in the entry.
      Returns:
      DatabasePDBRemark

    • getDatabasePDBRev

      public DatabasePDBRev getDatabasePDBRev()
      Data items in the DATABASE_PDB_REV category record details about the history of the data block as archived by the Protein Data Bank (PDB). These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source.
      Returns:
      DatabasePDBRev

    • getDatabasePDBRevRecord

      public DatabasePDBRevRecord getDatabasePDBRevRecord()
      Data items in the DATABASE_PDB_REV_RECORD category record details about specific record types that were changed in a given revision of a PDB entry. These data items are assigned by the PDB database managers and should only appear in a data block if they originate from that source.
      Returns:
      DatabasePDBRevRecord

    • getDatabasePDBTvect

      public DatabasePDBTvect getDatabasePDBTvect()
      The DATABASE_PDB_TVECT category provides placeholders for the TVECT matrices and vectors used by the Protein Data Bank (PDB). These data items are included only for consistency with older PDB format files. They should appear in a data block only if the data block was created by reformatting a PDB format file.
      Returns:
      DatabasePDBTvect

    • getDiffrn

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

    • getDiffrnAttenuator

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

    • getDiffrnDetector

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

    • getDiffrnMeasurement

      public DiffrnMeasurement getDiffrnMeasurement()
      Data items in the DIFFRN_MEASUREMENT category record details about the device used to orient and/or position the crystal during data measurement and the manner in which the diffraction data were measured.
      Returns:
      DiffrnMeasurement

    • getDiffrnOrientMatrix

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

    • getDiffrnOrientRefln

      public DiffrnOrientRefln getDiffrnOrientRefln()
      Data items in the DIFFRN_ORIENT_REFLN category record details about the reflections that define the orientation matrix used in the measurement of the diffraction intensities.
      Returns:
      DiffrnOrientRefln

    • getDiffrnRadiation

      public DiffrnRadiation getDiffrnRadiation()
      Data items in the DIFFRN_RADIATION category describe the radiation used in measuring the diffraction intensities, its collimation and monochromatization before the sample. Post-sample treatment of the beam is described by data items in the DIFFRN_DETECTOR category.
      Returns:
      DiffrnRadiation

    • getDiffrnRadiationWavelength

      public DiffrnRadiationWavelength getDiffrnRadiationWavelength()
      Data items in the DIFFRN_RADIATION_WAVELENGTH category describe the wavelength of the radiation used to measure the diffraction intensities. Items may be looped to identify and assign weights to distinct components of a polychromatic beam.
      Returns:
      DiffrnRadiationWavelength

    • getDiffrnRefln

      public DiffrnRefln getDiffrnRefln()
      Data items in the DIFFRN_REFLN category record details about the intensities in the diffraction data set identified by _diffrn_refln.diffrn_id. The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements in the particular diffraction data set identified by _diffrn_reflns.diffrn_id.
      Returns:
      DiffrnRefln

    • getDiffrnReflns

      public DiffrnReflns getDiffrnReflns()
      Data items in the DIFFRN_REFLNS category record details about the set of intensities measured in the diffraction experiment. The DIFFRN_REFLN data items refer to individual intensity measurements and must be included in looped lists. The DIFFRN_REFLNS data items specify the parameters that apply to all intensity measurements in a diffraction data set.
      Returns:
      DiffrnReflns

    • getDiffrnScaleGroup

      public DiffrnScaleGroup getDiffrnScaleGroup()
      Data items in the DIFFRN_SCALE_GROUP category record details of the scaling factors applied to place all intensities in the reflection lists on a common scale. Scaling groups might, for example, correspond to each film in a multi-film data set or each crystal in a multi-crystal data set.
      Returns:
      DiffrnScaleGroup

    • getDiffrnSource

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

    • getDiffrnStandardRefln

      public DiffrnStandardRefln getDiffrnStandardRefln()
      Data items in the DIFFRN_STANDARD_REFLN category record details about the reflections treated as standards during the measurement of a set of diffraction intensities. Note that these are the individual standard reflections, not the results of the analysis of the standard reflections.
      Returns:
      DiffrnStandardRefln

    • getDiffrnStandards

      public DiffrnStandards getDiffrnStandards()
      Data items in the DIFFRN_STANDARDS category record details about the set of standard reflections used to monitor intensity stability during the measurement of diffraction intensities. Note that these records describe properties common to the set of standard reflections, not the standard reflections themselves.
      Returns:
      DiffrnStandards

    • getEntity

      public Entity getEntity()
      Data items in the ENTITY category record details (such as chemical composition, name and source) about the molecular entities that are present in the crystallographic structure. Items in the various ENTITY subcategories provide a full chemical description of these molecular entities. Entities are of three types: polymer, non-polymer and water. Note that the water category includes only water; ordered solvent such as sulfate ion or acetone would be described as individual non-polymer entities. The ENTITY category is specific to macromolecular CIF applications and replaces the function of the CHEMICAL category in the CIF core. It is important to remember that the ENTITY data are not the result of the crystallographic experiment; those results are represented by the ATOM_SITE data items. ENTITY data items describe the chemistry of the molecules under investigation and can most usefully be thought of as the ideal groups to which the structure is restrained or constrained during refinement. It is also important to remember that entities do not correspond directly to the enumeration of the contents of the asymmetric unit. Entities are described only once, even in those structures that contain multiple observations of an entity. The STRUCT_ASYM data items, which reference the entity list, describe and label the contents of the asymmetric unit.
      Returns:
      Entity

    • getEntityKeywords

      public EntityKeywords getEntityKeywords()
      Data items in the ENTITY_KEYWORDS category specify keywords relevant to the molecular entities. Note that this list of keywords is separate from the list that is used for the STRUCT_BIOL data items and is intended to provide only the information that one would know about the molecular entity *if one did not know its structure*. Hence polypeptides are simply polypeptides, not cytokines or beta-alpha-barrels, and polyribonucleic acids are simply poly-RNA, not transfer- RNA.
      Returns:
      EntityKeywords

    • getEntityLink

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

    • getEntityNameCom

      public EntityNameCom getEntityNameCom()
      Data items in the ENTITY_NAME_COM category record the common name or names associated with the entity. In some cases, the entity name may not be the same as the name of the biological structure. For example, haemoglobin alpha chain would be the entity common name, not haemoglobin.
      Returns:
      EntityNameCom

    • getEntityNameSys

      public EntityNameSys getEntityNameSys()
      Data items in the ENTITY_NAME_SYS category record the systematic name or names associated with the entity and the system that was used to construct the systematic name. In some cases, the entity name may not be the same as the name of the biological structure.
      Returns:
      EntityNameSys

    • getEntityPoly

      public EntityPoly getEntityPoly()
      Data items in the ENTITY_POLY category record details about the polymer, such as the type of the polymer, the number of monomers and whether it has nonstandard features.
      Returns:
      EntityPoly

    • getEntityPolySeq

      public EntityPolySeq getEntityPolySeq()
      Data items in the ENTITY_POLY_SEQ category specify the sequence of monomers in a polymer. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID. The corresponding ATOM_SITE entries should reflect this heterogeneity.
      Returns:
      EntityPolySeq

    • getEntry

      public Entry getEntry()
      There is only one item in the ENTRY category, _entry.id. This data item gives a name to this entry and is indirectly a key to the categories (such as CELL, GEOM, EXPTL) that describe information pertinent to the entire data block.
      Returns:
      Entry

    • getEntryLink

      public EntryLink getEntryLink()
      Data items in the ENTRY_LINK category record the relationships between the current data block identified by _entry.id and other data blocks within the current file which may be referenced in the current data block.
      Returns:
      EntryLink

    • getExptl

      public Exptl getExptl()
      Data items in the EXPTL category record details about the experimental work prior to the intensity measurements and details about the absorption-correction technique employed.
      Returns:
      Exptl

    • getExptlCrystal

      public ExptlCrystal getExptlCrystal()
      Data items in the EXPTL_CRYSTAL category record the results of experimental measurements on the crystal or crystals used, such as shape, size or density.
      Returns:
      ExptlCrystal

    • getExptlCrystalFace

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

    • getExptlCrystalGrow

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

    • getExptlCrystalGrowComp

      public ExptlCrystalGrowComp getExptlCrystalGrowComp()
      Data items in the EXPTL_CRYSTAL_GROW_COMP category record details about the components of the solutions that were 'mixed' (by whatever means) to produce the crystal. In general, solution 1 is the solution that contains the molecule to be crystallized and solution 2 is the solution that contains the precipitant. However, the number of solutions required to describe the crystallization protocol is not limited to 2. Details of the crystallization protocol should be given in _exptl_crystal_grow_comp.details using the solutions described in EXPTL_CRYSTAL_GROW_COMP.
      Returns:
      ExptlCrystalGrowComp

    • getGeom

      public Geom getGeom()
      Data items in the GEOM and related (GEOM_ANGLE, GEOM_BOND, GEOM_CONTACT, GEOM_HBOND and GEOM_TORSION) categories record details about the molecular geometry as calculated from the contents of the ATOM, CELL and SYMMETRY data. Geometry data are therefore redundant, in that they can be calculated from other more fundamental quantities in the data block. However, they provide a check on the correctness of both sets of data and enable the most important geometric data to be identified for publication by setting the appropriate publication flag.
      Returns:
      Geom

    • getGeomAngle

      public GeomAngle getGeomAngle()
      Data items in the GEOM_ANGLE category record details about the bond angles as calculated from the contents of the ATOM, CELL and SYMMETRY data.
      Returns:
      GeomAngle

    • getGeomBond

      public GeomBond getGeomBond()
      Data items in the GEOM_BOND category record details about the bond lengths as calculated from the contents of the ATOM, CELL and SYMMETRY data.
      Returns:
      GeomBond

    • getGeomContact

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

    • getGeomHbond

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

    • getGeomTorsion

      public GeomTorsion getGeomTorsion()
      Data items in the GEOM_TORSION category record details about torsion angles as calculated from the contents of the ATOM, CELL and SYMMETRY data. The vector direction _geom_torsion.atom_site_id_2 to _geom_torsion.atom_site_id_3 is the viewing direction, and the torsion angle is the angle of twist required to superimpose the projection of the vector between site 2 and site 1 onto the projection of the vector between site 3 and site 4. Clockwise torsions are positive, anticlockwise torsions are negative. Ref: Klyne, W. & Prelog, V. (1960). Experientia, 16, 521-523.
      Returns:
      GeomTorsion

    • getJournal

      public Journal getJournal()
      Data items in the JOURNAL category record details about the book-keeping by the journal staff when processing a data block submitted for publication. The creator of a data block will not normally specify these data. The data names are not defined in the dictionary because they are for journal use only.
      Returns:
      Journal

    • getJournalIndex

      public JournalIndex getJournalIndex()
      Data items in the JOURNAL_INDEX category are used to list terms used to generate the journal indexes. The creator of a data block will not normally specify these data items.
      Returns:
      JournalIndex

    • getPhasing

      public Phasing getPhasing()
      Data items in the PHASING category record details about the phasing of the structure, listing the various methods used in the phasing process. Details about the application of each method are listed in the appropriate subcategories.
      Returns:
      Phasing

    • getPhasingAveraging

      public PhasingAveraging getPhasingAveraging()
      Data items in the PHASING_AVERAGING category record details about the phasing of the structure where methods involving averaging of multiple observations of the molecule in the asymmetric unit are involved.
      Returns:
      PhasingAveraging

    • getPhasingIsomorphous

      public PhasingIsomorphous getPhasingIsomorphous()
      Data items in the PHASING_ISOMORPHOUS category record details about the phasing of the structure where a model isomorphous to the structure being phased was used to generate the initial phases.
      Returns:
      PhasingIsomorphous

    • getPhasingMAD

      public PhasingMAD getPhasingMAD()
      Data items in the PHASING_MAD category record details about the phasing of the structure where methods involving multiple-wavelength anomalous-dispersion techniques are involved.
      Returns:
      PhasingMAD

    • getPhasingMADClust

      public PhasingMADClust getPhasingMADClust()
      Data items in the PHASING_MAD_CLUST category record details about a cluster of experiments that contributed to the generation of a set of phases.
      Returns:
      PhasingMADClust

    • getPhasingMADExpt

      public PhasingMADExpt getPhasingMADExpt()
      Data items in the PHASING_MAD_EXPT category record details about a MAD phasing experiment, such as the number of experiments that were clustered together to produce a set of phases or the statistics for those phases.
      Returns:
      PhasingMADExpt

    • getPhasingMADRatio

      public PhasingMADRatio getPhasingMADRatio()
      Data items in the PHASING_MAD_RATIO category record the ratios of phasing statistics between pairs of data sets in a MAD phasing experiment, in given shells of resolution.
      Returns:
      PhasingMADRatio

    • getPhasingMADSet

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

    • getPhasingMIR

      public PhasingMIR getPhasingMIR()
      Data items in the PHASING_MIR category record details about the phasing of the structure where methods involving isomorphous replacement are involved. All isomorphous-replacement-based techniques are covered by this category, including single isomorphous replacement (SIR), multiple isomorphous replacement (MIR) and single or multiple isomorphous replacement plus anomalous scattering (SIRAS, MIRAS).
      Returns:
      PhasingMIR

    • getPhasingMIRDer

      public PhasingMIRDer getPhasingMIRDer()
      Data items in the PHASING_MIR_DER category record details about individual derivatives used in the phasing of the structure when methods involving isomorphous replacement are involved. A derivative in this context does not necessarily equate with a data set; for instance, the same data set could be used to one resolution limit as an isomorphous scatterer and to a different resolution (and with a different sigma cutoff) as an anomalous scatterer. These would be treated as two distinct derivatives, although both derivatives would point to the same data sets via _phasing_MIR_der.der_set_id and _phasing_MIR_der.native_set_id.
      Returns:
      PhasingMIRDer

    • getPhasingMIRDerRefln

      public PhasingMIRDerRefln getPhasingMIRDerRefln()
      Data items in the PHASING_MIR_DER_REFLN category record details about the calculated structure factors obtained in an MIR phasing experiment. This list may contain information from a number of different derivatives; _phasing_MIR_der_refln.der_id indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.) It is not necessary for the data items describing the measured value of F to appear in this list, as they will be given in the PHASING_SET_REFLN category. However, these items can also be listed here for completeness.
      Returns:
      PhasingMIRDerRefln

    • getPhasingMIRDerShell

      public PhasingMIRDerShell getPhasingMIRDerShell()
      Data items in the PHASING_MIR_DER_SHELL category record statistics, broken down into shells of resolution, for an MIR phasing experiment. This list may contain information from a number of different derivatives; _phasing_MIR_der_shell.der_id indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.)
      Returns:
      PhasingMIRDerShell

    • getPhasingMIRDerSite

      public PhasingMIRDerSite getPhasingMIRDerSite()
      Data items in the PHASING_MIR_DER_SITE category record details about the heavy-atom sites in an MIR phasing experiment. This list may contain information from a number of different derivatives; _phasing_MIR_der_site.der_id indicates to which derivative a given record corresponds. (A derivative in this context does not necessarily equate with a data set; see the definition of the PHASING_MIR_DER category for a discussion of the meaning of derivative.)
      Returns:
      PhasingMIRDerSite

    • getPhasingMIRShell

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

    • getPhasingSet

      public PhasingSet getPhasingSet()
      Data items in the PHASING_SET category record details about the data sets used in a phasing experiment. A given data set may be used in a number of different ways; for instance, a single data set could be used both as an isomorphous derivative and as a component of a multiple-wavelength calculation. This category establishes identifiers for each data set and permits the archiving of a subset of experimental information for each data set (cell constants, wavelength, temperature etc.). This and related categories of data items are provided so that derivative intensity and phase information can be stored in the same data block as the information for the refined structure. If all the possible experimental information for each data set (raw data sets, crystal growth conditions etc.) is to be archived, these data items should be recorded in a separate data block.
      Returns:
      PhasingSet

    • getPhasingSetRefln

      public PhasingSetRefln getPhasingSetRefln()
      Data items in the PHASING_SET_REFLN category record the values of the measured structure factors used in a phasing experiment. This list may contain information from a number of different data sets; _phasing_set_refln.set_id indicates the data set to which a given record corresponds.
      Returns:
      PhasingSetRefln

    • getPubl

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

    • getPublAuthor

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

    • getPublBody

      public PublBody getPublBody()
      Data items in the PUBL_BODY category permit the labelling of different text sections within the body of a paper. Note that these should not be used in a paper which has a standard format with sections tagged by specific data names (such as in Acta Crystallographica Section C). Typically, each journal will supply a list of the specific items it requires in its Notes for Authors.
      Returns:
      PublBody

    • getPublManuscriptIncl

      public PublManuscriptIncl getPublManuscriptIncl()
      Data items in the PUBL_MANUSCRIPT_INCL category allow the authors of a manuscript submitted for publication to list data names that should be added to the standard request list used by the journal printing software.
      Returns:
      PublManuscriptIncl

    • getRefine

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

    • getRefineAnalyze

      public RefineAnalyze getRefineAnalyze()
      Data items in the REFINE_ANALYZE category record details about the refined structure that are often used to analyze the refinement and assess its quality. A given computer program may or may not produce values corresponding to these data names.
      Returns:
      RefineAnalyze

    • getRefineBIso

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

    • getRefineFunctMinimized

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

    • getRefineHist

      public RefineHist getRefineHist()
      Data items in the REFINE_HIST category record details about the steps during the refinement of the structure. These data items are not meant to be as thorough a description of the refinement as is provided for the final model in other categories; rather, these data items provide a mechanism for sketching out the progress of the refinement, supported by a small set of representative statistics.
      Returns:
      RefineHist

    • getRefineLsRestr

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

    • getRefineLsRestrNcs

      public RefineLsRestrNcs getRefineLsRestrNcs()
      Data items in the REFINE_LS_RESTR_NCS category record details about the restraints applied to atom positions in domains related by noncrystallographic symmetry during least-squares refinement, and also about the deviation of the restrained atomic parameters at the end of the refinement. It is expected that these values will only be reported once for each set of restrained domains.
      Returns:
      RefineLsRestrNcs

    • getRefineLsRestrType

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

    • getRefineLsShell

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

    • getRefineOccupancy

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

    • getRefln

      public Refln getRefln()
      Data items in the REFLN category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped.
      Returns:
      Refln

    • getReflnSysAbs

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

    • getReflns

      public Reflns getReflns()
      Data items in the REFLNS category record details about the reflection data used to determine the ATOM_SITE data items. The REFLN data items refer to individual reflections and must be included in looped lists. The REFLNS data items specify the parameters that apply to all reflections. The REFLNS data items are not looped.
      Returns:
      Reflns

    • getReflnsScale

      public ReflnsScale getReflnsScale()
      Data items in the REFLNS_SCALE category record details about the structure-factor scales. They are referenced from within the REFLN list through _refln.scale_group_code.
      Returns:
      ReflnsScale

    • getReflnsShell

      public ReflnsShell getReflnsShell()
      Data items in the REFLNS_SHELL category record details about the reflection data used to determine the ATOM_SITE data items broken down into shells of resolution.
      Returns:
      ReflnsShell

    • getSoftware

      public Software getSoftware()
      Data items in the SOFTWARE category record details about the software used in the structure analysis, which implies any software used in the generation of any data items associated with the structure determination and structure representation. These data items allow computer programs to be referenced in more detail than data items in the COMPUTING category do.
      Returns:
      Software

    • getStruct

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

    • getStructAsym

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

    • getStructBiol

      public StructBiol getStructBiol()
      Data items in the STRUCT_BIOL category record details about the structural elements that form each structure of biological significance. A given crystal structure may contain many different biological structures. A given structural component in the asymmetric unit may be part of more than one biological unit. A given biological structure may involve crystallographic symmetry. For instance, in a structure of a lysozyme-FAB structure, the light- and heavy-chain components of the FAB could be one biological unit, while the two chains of the FAB and the lysozyme could constitute a second biological unit.
      Returns:
      StructBiol

    • getStructBiolGen

      public StructBiolGen getStructBiolGen()
      Data items in the STRUCT_BIOL_GEN category record details about the generation of each biological unit. The STRUCT_BIOL_GEN data items provide the specifications of the components that constitute that biological unit, which may include symmetry elements.
      Returns:
      StructBiolGen

    • getStructBiolKeywords

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

    • getStructBiolView

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

    • getStructConf

      public StructConf getStructConf()
      Data items in the STRUCT_CONF category record details about the backbone conformation of a segment of polymer. Data items in the STRUCT_CONF_TYPE category define the criteria used to identify the backbone conformations.
      Returns:
      StructConf

    • getStructConfType

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

    • getStructConn

      public StructConn getStructConn()
      Data items in the STRUCT_CONN category record details about the connections between portions of the structure. These can be hydrogen bonds, salt bridges, disulfide bridges and so on. The STRUCT_CONN_TYPE records define the criteria used to identify these connections.
      Returns:
      StructConn

    • getStructConnType

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

    • getStructKeywords

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

    • getStructMonDetails

      public StructMonDetails getStructMonDetails()
      Data items in the STRUCT_MON_DETAILS category record details about specifics of calculations summarized in data items in the STRUCT_MON_PROT and STRUCT_MON_NUCL categories. These can include the coefficients used in map calculations, the radii used for including points in a calculation and so on.
      Returns:
      StructMonDetails

    • getStructMonNucl

      public StructMonNucl getStructMonNucl()
      Data items in the STRUCT_MON_NUCL category record details about structural properties of a nucleic acid when analyzed at the monomer level. Analogous data items for proteins are given in the STRUCT_MON_PROT category. For items where the value of the property depends on the method employed to calculate it, details of the method of calculation are given using data items in the STRUCT_MON_DETAILS category.
      Returns:
      StructMonNucl

    • getStructMonProt

      public StructMonProt getStructMonProt()
      Data items in the STRUCT_MON_PROT category record details about structural properties of a protein when analyzed at the monomer level. Analogous data items for nucleic acids are given in the STRUCT_MON_NUCL category. For items where the value of the property depends on the method employed to calculate it, details of the method of calculation are given using data items in the STRUCT_MON_DETAILS category.
      Returns:
      StructMonProt

    • getStructMonProtCis

      public StructMonProtCis getStructMonProtCis()
      Data items in the STRUCT_MON_PROT_CIS category identify monomers that have been found to have the peptide bond in the cis conformation. The criterion used to select residues to be designated as containing cis peptide bonds is given in _struct_mon_details.prot_cis.
      Returns:
      StructMonProtCis

    • getStructNcsDom

      public StructNcsDom getStructNcsDom()
      Data items in the STRUCT_NCS_DOM category record information about the domains in an ensemble of domains related by one or more noncrystallographic symmetry operators. A domain need not correspond to a complete polypeptide chain; it can be composed of one or more segments in a single chain, or by segments from more than one chain.
      Returns:
      StructNcsDom

    • getStructNcsDomLim

      public StructNcsDomLim getStructNcsDomLim()
      Data items in the STRUCT_NCS_DOM_LIM category identify the start and end points of polypeptide chain segments that form all or part of a domain in an ensemble of domains related by noncrystallographic symmetry.
      Returns:
      StructNcsDomLim

    • getStructNcsEns

      public StructNcsEns getStructNcsEns()
      Data items in the STRUCT_NCS_ENS category record information about ensembles of domains related by noncrystallographic symmetry. The point group of the ensemble when taken as a whole may be specified, as well as any special aspects of the ensemble that require description.
      Returns:
      StructNcsEns

    • getStructNcsEnsGen

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

    • getStructNcsOper

      public StructNcsOper getStructNcsOper()
      Data items in the STRUCT_NCS_OPER category describe the noncrystallographic symmetry operations. Each operator is specified as a matrix and a subsequent translation vector. Operators need not represent proper rotations.
      Returns:
      StructNcsOper

    • getStructRef

      public StructRef getStructRef()
      Data items in the STRUCT_REF category allow the author of a data block to relate the entities or biological units described in the data block to information archived in external databases. For references to the sequence of a polymer, the value of the data item _struct_ref.seq_align is used to indicate whether the correspondence between the sequence of the entity or biological unit in the data block and the sequence in the referenced database entry is 'complete' or 'partial'. If this value is 'partial', the region (or regions) of the alignment may be delimited using data items in the STRUCT_REF_SEQ category. Similarly, the value of _struct_ref.seq_dif is used to indicate whether the two sequences contain point differences. If the value is 'yes', the differences may be identified and annotated using data items in the STRUCT_REF_SEQ_DIF category.
      Returns:
      StructRef

    • getStructRefSeq

      public StructRefSeq getStructRefSeq()
      Data items in the STRUCT_REF_SEQ category provide a mechanism for indicating and annotating a region (or regions) of alignment between the sequence of an entity or biological unit described in the data block and the sequence in the referenced database entry.
      Returns:
      StructRefSeq

    • getStructRefSeqDif

      public StructRefSeqDif getStructRefSeqDif()
      Data items in the STRUCT_REF_SEQ_DIF category provide a mechanism for indicating and annotating point differences between the sequence of the entity or biological unit described in the data block and the sequence of the referenced database entry.
      Returns:
      StructRefSeqDif

    • getStructSheet

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

    • getStructSheetHbond

      public StructSheetHbond getStructSheetHbond()
      Data items in the STRUCT_SHEET_HBOND category record details about the hydrogen bonding between residue ranges in a beta- sheet. It is necessary to treat hydrogen bonding independently of the designation of ranges, because the hydrogen bonding may begin in different places for the interactions of a given strand with the one preceding it and the one following it in the sheet.
      Returns:
      StructSheetHbond

    • getStructSheetOrder

      public StructSheetOrder getStructSheetOrder()
      Data items in the STRUCT_SHEET_ORDER category record details about the order of the residue ranges that form a beta-sheet. All order links are pairwise and the specified pairs are assumed to be adjacent to one another in the sheet. These data items are an alternative to the STRUCT_SHEET_TOPOLOGY data items and they allow all manner of sheets to be described.
      Returns:
      StructSheetOrder

    • getStructSheetRange

      public StructSheetRange getStructSheetRange()
      Data items in the STRUCT_SHEET_RANGE category record details about the residue ranges that form a beta-sheet. Residues are included in a range if they made beta-sheet-type hydrogen-bonding interactions with at least one adjacent strand and if there are at least two residues in the range.
      Returns:
      StructSheetRange

    • getStructSheetTopology

      public StructSheetTopology getStructSheetTopology()
      Data items in the STRUCT_SHEET_TOPOLOGY category record details about the topology of the residue ranges that form a beta-sheet. All topology links are pairwise and the specified pairs are assumed to be successive in the amino-acid sequence. These data items are useful in describing various simple and complex folds, but they become inadequate when the strands in the sheet come from more than one chain. The STRUCT_SHEET_ORDER data items can be used to describe single- and multiple-chain-containing sheets.
      Returns:
      StructSheetTopology

    • getStructSite

      public StructSite getStructSite()
      Data items in the STRUCT_SITE category record details about portions of the structure that contribute to structurally relevant sites (e.g. active sites, substrate-binding subsites, metal-coordination sites).
      Returns:
      StructSite

    • getStructSiteGen

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

    • getStructSiteKeywords

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

    • getStructSiteView

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

    • getSymmetry

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

    • getSymmetryEquiv

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

    • getAuditLink

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

    • getDiffrnReflnsClass

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

    • getRefineLsClass

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

    • getReflnsClass

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

    • getSpaceGroup

      public SpaceGroup getSpaceGroup()
      Contains all the data items that refer to the space group as a whole, such as its name or crystal system. They may be looped, for example, in a list of space groups and their properties. Only a subset of the SPACE_GROUP category items appear in this dictionary. The remainder are found in the symmetry CIF dictionary. Space-group types are identified by their number as given in International Tables for Crystallography Vol. A. Specific settings of the space groups can be identified either by their Hall symbol or by specifying their symmetry operations. The commonly used Hermann-Mauguin symbol determines the space-group type uniquely but several different Hermann-Mauguin symbols may refer to the same space-group type. A Hermann-Mauguin symbol contains information on the choice of the basis, but not on the choice of origin. Different formats for the Hermann-Mauguin symbol are found in the symmetry CIF dictionary.
      Returns:
      SpaceGroup

    • getSpaceGroupSymop

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

    • getValenceParam

      public ValenceParam getValenceParam()
      Data items in the VALENCE_PARAM category define the parameters used for calculating bond valences from bond lengths. In addition to the parameters, a pointer is given to the reference (in VALENCE_REF) from which the bond-valence parameters were taken.
      Returns:
      ValenceParam

    • getValenceRef

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

    • getPdbxAudit

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

    • getPdbxVersion

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

    • getPdbxAuditAuthor

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

    • getPdbxDatabaseMessage

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

    • getPdbxDatabasePDBObsSpr

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

    • getPdbxDatabaseProc

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

    • getPdbxDatabaseRemark

      public PdbxDatabaseRemark getPdbxDatabaseRemark()
      Data items in the PDBX_DATABASE_REMARK category record keep additional information about the entry. They are mostly used to create 'non-standard' PDB REMARK annotations (6-99).
      Returns:
      PdbxDatabaseRemark

    • getPdbxDatabaseStatus

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

    • getPdbxEntityName

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

    • getPdbxPrereleaseSeq

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

    • getPdbxPolySeqScheme

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

    • getPdbxNonpolyScheme

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

    • getPdbxRefine

      public PdbxRefine getPdbxRefine()
      Data items in the PDBX_REFINE category record details about additional structure refinement parameters which are needed to complete legacy REMARK 3 refinement templates in PDB format files.
      Returns:
      PdbxRefine

    • getPdbxStructSheetHbond

      public PdbxStructSheetHbond getPdbxStructSheetHbond()
      Data items in the PDBX_STRUCT_SHEET_HBOND category record details about the hydrogen bonding between residue ranges in a beta sheet. This category is provided for cases where only a single hydrogen bond is used to register the two residue ranges. Category STRUCT_SHEET_HBOND should be used when the initial and terminal hydrogen bonds for strand pair are known.
      Returns:
      PdbxStructSheetHbond

    • getPdbxXplorFile

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

    • getPdbxRefineAuxFile

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

    • getPdbxDatabaseRelated

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

    • getPdbxEntityAssembly

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

    • getPdbxExptlCrystalGrowComp

      public PdbxExptlCrystalGrowComp getPdbxExptlCrystalGrowComp()
      Data items in the PDBX_EXPTL_CRYSTAL_GROW_COMP category record details about the components of the solutions that were 'mixed' to produce the crystal.
      Returns:
      PdbxExptlCrystalGrowComp

    • getPdbxExptlCrystalGrowSol

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

    • getPdbxExptlCrystalCryoTreatment

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

    • getPdbxRefineTls

      public PdbxRefineTls getPdbxRefineTls()
      Data items in the REFINE_TLS category record details about TLS parameters used in structure refinement. Note that the intention is primarily to describe directly refined TLS parameters, although other methods of obtaining TLS parameters may be covered, see item _pdbx_refine_tls.method
      Returns:
      PdbxRefineTls

    • getPdbxRefineTlsGroup

      public PdbxRefineTlsGroup getPdbxRefineTlsGroup()
      Data items in the PDBX_REFINE_TLS_GROUP category record details about a fragment of a TLS group. Properties of the TLS group are recorded in PDBX_REFINE_TLS
      Returns:
      PdbxRefineTlsGroup

    • getPdbxContactAuthor

      public PdbxContactAuthor getPdbxContactAuthor()
      Data items in the PDBX_CONTACT_AUTHOR category record details about the name and address of the author to be contacted concerning the contents of this data block. This category atomizes information to a greater degree than the standard AUDIT_CONTACT_AUTHOR category.
      Returns:
      PdbxContactAuthor

    • getPdbxSGProject

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

    • getPdbxAtomSiteAnisoTls

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

    • getPdbxNmrDetails

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

    • getPdbxNmrSampleDetails

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

    • getPdbxNmrExptlSample

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

    • getPdbxNmrExptlSampleConditions

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

    • getPdbxNmrSpectrometer

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

    • getPdbxNmrExptl

      public PdbxNmrExptl getPdbxNmrExptl()
      In this section, enter information on those experiments that were used to generate constraint data. For each NMR experiment indicate which sample and which sample conditions were used for the experiment.
      Returns:
      PdbxNmrExptl

    • getPdbxNmrSoftware

      public PdbxNmrSoftware getPdbxNmrSoftware()
      Description of the software that was used for data collection, data processing, data analysis, structure calculations and refinement. The description should include the name of the software, the author of the software and the version used.
      Returns:
      PdbxNmrSoftware

    • getPdbxNmrConstraints

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

    • getPdbxNmrEnsemble

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

    • getPdbxNmrEnsembleRms

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

    • getPdbxNmrRepresentative

      public PdbxNmrRepresentative getPdbxNmrRepresentative()
      An average structure is often calculated in addition to the ensemble, or one of the ensemble is selected as a representative structure. This section describes selection of the representative structure.
      Returns:
      PdbxNmrRepresentative

    • getPdbxNmrRefine

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

    • getPdbxNmrForceConstants

      public PdbxNmrForceConstants getPdbxNmrForceConstants()
      The final force constants, including units, employed for the various experimental constraints, covalent geometry constraints, and the non-bonded interaction terms in the target function used for simulated annealing.
      Returns:
      PdbxNmrForceConstants

    • getNdbStructConfNa

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

    • getNdbStructFeatureNa

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

    • getNdbStructNaBasePair

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

    • getNdbStructNaBasePairStep

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

    • getNdbOriginalNdbCoordinates

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

    • getPdbxEntityNonpoly

      public PdbxEntityNonpoly getPdbxEntityNonpoly()
      Returns:
      PdbxEntityNonpoly

    • getPdbxPhasingDm

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

    • getPdbxPhasingDmShell

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

    • getPdbxPhasingMADShell

      public PdbxPhasingMADShell getPdbxPhasingMADShell()
      Data items in the PDBX_PHASING_MAD_SHELL category record details about the phasing of the structure, when methods involving multiple anomalous dispersion techniques are involved (note: the values are overall, but broken down into shells of resolution)
      Returns:
      PdbxPhasingMADShell

    • getPdbxPhasingMADSet

      public PdbxPhasingMADSet getPdbxPhasingMADSet()
      Record details about each phasing set: (Note: the phasing set is different from data set. for example: if there are three data sets, the inflection point (IP), the peak (PK) and the high remote (HR), the combination of the phasing set will be IP_iso, PK_iso (the isomorphous repleacement with HR as 'native'), IP_ano, PK_ano and HR_ano (the anomalous difference with itself). Therefore, there are five set used for phasing.
      Returns:
      PdbxPhasingMADSet

    • getPdbxPhasingMADSetShell

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

    • getPdbxPhasingMADSetSite

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

    • getPdbxPhasingMR

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

    • getPdbxRefineComponent

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

    • getPdbxEntityProdProtocol

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

    • getPdbxEntitySrcGenProdOther

      public PdbxEntitySrcGenProdOther getPdbxEntitySrcGenProdOther()
      This category contains details for process steps that are not explicitly catered for elsewhere. It provides some basic details as well as placeholders for a list of parameters and values (the category PDBX_ENTITY_SRC_GEN_PROD_OTHER_PARAMETER). Note that processes that have been modelled explicitly should not be represented using this category.
      Returns:
      PdbxEntitySrcGenProdOther

    • getPdbxEntitySrcGenProdOtherParameter

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

    • getPdbxEntitySrcGenProdPcr

      public PdbxEntitySrcGenProdPcr getPdbxEntitySrcGenProdPcr()
      This category contains details for the PCR steps used in the overall protein production process. The PCR is assumed to be applied to the result of the previous production step, or the gene source if this is the first production step.
      Returns:
      PdbxEntitySrcGenProdPcr

    • getPdbxEntitySrcGenProdDigest

      public PdbxEntitySrcGenProdDigest getPdbxEntitySrcGenProdDigest()
      This category contains details for the DIGEST steps used in the overall protein production process. The digestion is assumed to be applied to the result of the previous production step, or the gene source if this is the first production step.
      Returns:
      PdbxEntitySrcGenProdDigest

    • getPdbxEntitySrcGenClone

      public PdbxEntitySrcGenClone getPdbxEntitySrcGenClone()
      This category contains details for the cloning steps used in the overall protein production process. Each row in PDBX_ENTITY_SRC_GEN_CLONE should have an equivalent row in either PDBX_ENTITY_SRC_GEN_CLONE_LIGATION or PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION. If only summary information is provided data in the later two categories may be omitted.
      Returns:
      PdbxEntitySrcGenClone

    • getPdbxEntitySrcGenCloneLigation

      public PdbxEntitySrcGenCloneLigation getPdbxEntitySrcGenCloneLigation()
      This category contains details for the ligation-based cloning steps used in the overall protein production process. _pdbx_entity_src_gen_clone_ligation.clone_step_id in this category must point at a defined _pdbx_entity_src_gen_clone.step_id. The details in PDBX_ENTITY_SRC_GEN_CLONE_LIGATION extend the details in PDBX_ENTITY_SRC_GEN_CLONE to cover ligation dependent cloning steps.
      Returns:
      PdbxEntitySrcGenCloneLigation

    • getPdbxEntitySrcGenCloneRecombination

      public PdbxEntitySrcGenCloneRecombination getPdbxEntitySrcGenCloneRecombination()
      This category contains details for the recombination-based cloning steps used in the overall protein production process. It is assumed that these reactions will use commercially available kits. _pdbx_entity_src_gen_clone_recombination.clone_step_id in this category must point at a defined _pdbx_entity_src_gen_clone.step_id. The details in PDBX_ENTITY_SRC_GEN_CLONE_RECOMBINATION extend the details in PDBX_ENTITY_SRC_GEN_CLONE to cover recombination dependent cloning steps.
      Returns:
      PdbxEntitySrcGenCloneRecombination

    • getPdbxEntitySrcGenExpress

      public PdbxEntitySrcGenExpress getPdbxEntitySrcGenExpress()
      This category contains details for the EXPRESSION steps used in the overall protein production process. It is hoped that this category will cover all forms of cell-based expression by reading induction as induction/transformation/transfection.
      Returns:
      PdbxEntitySrcGenExpress

    • getPdbxEntitySrcGenExpressTimepoint

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

    • getPdbxEntitySrcGenLysis

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

    • getPdbxEntitySrcGenRefold

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

    • getPdbxEntitySrcGenProteolysis

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

    • getPdbxEntitySrcGenChrom

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

    • getPdbxEntitySrcGenFract

      public PdbxEntitySrcGenFract getPdbxEntitySrcGenFract()
      This category contains details for the fraction steps used in the overall protein production process. Examples of fractionation steps are centrifugation and magnetic bead pull-down purification.
      Returns:
      PdbxEntitySrcGenFract

    • getPdbxEntitySrcGenPure

      public PdbxEntitySrcGenPure getPdbxEntitySrcGenPure()
      This category contains details for the final purified protein product. Note that this category does not contain the amino acid sequence of the protein. The sequence will be found in the ENTITY_POLY_SEQ entry with matching entity_id. Only one PDBX_ENTITY_SRC_GEN_PURE category is allowed per entity, hence there is no step_id for this category.
      Returns:
      PdbxEntitySrcGenPure

    • getPdbxEntitySrcGenCharacter

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

    • getPdbxConstruct

      public PdbxConstruct getPdbxConstruct()
      Data items in the PDBX_CONSTRUCT category specify a sequence of nucleic acids or amino acids. It is a catch-all that may be used to provide details of sequences known to be relevant to the project as well as primers, plasmids, proteins and such like that are either used or produced during the protein production process. Molecules described here are not necessarily complete, so for instance it would be possible to include either a complete plasmid or just its insert. This category may be considered as an abbreviated form of _entity where the molecules described are not required to appear in the final co-ordinates. Note that the details provided here all pertain to a single entry as defined at deposition. It is anticipated that _pdbx_construct.id would also be composed of a sequence that is unique within a given site prefixed by a code that identifies that site and would, therefore, be GLOBALLY unique. Thus this category could also be used locally to store details about the different constructs used during protein production without reference to the entry_id (which only becomes a meaningful concept during deposition).
      Returns:
      PdbxConstruct

    • getPdbxConstructFeature

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

    • getPdbxRobotSystem

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

    • getPdbxBuffer

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

    • getPdbxBufferComponents

      public PdbxBufferComponents getPdbxBufferComponents()
      Constituents of buffer in sample
      Returns:
      PdbxBufferComponents

    • getPdbxDomain

      public PdbxDomain getPdbxDomain()
      Data items in the PDBX_DOMAIN category record information about domain definitions. A domain need not correspond to a completely polypeptide chain; it can be composed of one or more segments in a single chain, or by segments from more than one chain.
      Returns:
      PdbxDomain

    • getPdbxDomainRange

      public PdbxDomainRange getPdbxDomainRange()
      Data items in the PDBX_DOMAIN_RANGE category identify the beginning and ending points of polypeptide chain segments that form all or part of a domain.
      Returns:
      PdbxDomainRange

    • getPdbxSequenceRange

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

    • getPdbxFeatureEntry

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

    • getPdbxFeatureDomain

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

    • getPdbxFeatureSequenceRange

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

    • getPdbxFeatureAssembly

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

    • getPdbxFeatureMonomer

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

    • getPdbxExptlPd

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

    • getPdbxReflnsTwin

      public PdbxReflnsTwin getPdbxReflnsTwin()
      Details decribing crystallographic twinning.
      Returns:
      PdbxReflnsTwin

    • getPdbxStructInfo

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

    • getPdbxReRefinement

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

    • getPdbxStructAssemblyProp

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

    • getPdbxStructRefSeqFeature

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

    • getPdbxStructRefSeqFeatureProp

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

    • getPdbxStructChemCompDiagnostics

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

    • getPdbxChemCompSynonyms

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

    • getPdbxChemCompFeature

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

    • getPdbxCoordinateModel

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

    • getPdbxStructChemCompFeature

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

    • getPdbxDiffrnReflnsShell

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

    • getPdbxBondDistanceLimits

      public PdbxBondDistanceLimits getPdbxBondDistanceLimits()
      This category provides a table of upper and lower distance limits used as criteria in determining covalent bonds. The table is organized by atom type pairs.
      Returns:
      PdbxBondDistanceLimits

    • getPdbxSolnScatter

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

    • getPdbxSolnScatterModel

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

    • getPdbxChemCompDescriptor

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

    • getPdbxChemCompIdentifier

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

    • getPdbxChemCompImport

      public PdbxChemCompImport getPdbxChemCompImport()
      Data items in the PDBX_CHEM_COMP_IMPORT category identify existing chemical components to be imported into the current component definition. Components in this list can be edited by instructions in categories pdbx_chem_comp_atom_edit and pdbx_chem_comp_bond_edit.
      Returns:
      PdbxChemCompImport

    • getPdbxChemCompAtomEdit

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

    • getPdbxChemCompBondEdit

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

    • getPdbxChemCompAudit

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

    • getPdbxValidateCloseContact

      public PdbxValidateCloseContact getPdbxValidateCloseContact()
      Data items in the PDBX_VALIDATE_CLOSE_CONTACT category list the atoms within the entry that are in close contact with regard the distances expected from either covalent bonding or closest approach by van der Waals contacts. Contacts within the asymmetric unit are considered. For those contacts not involving hydrogen a limit of 2.2 Angstroms is used. For contacts involving a hydrogen atom a cutoff of 1.6 Angstroms is used.
      Returns:
      PdbxValidateCloseContact

    • getPdbxValidateSymmContact

      public PdbxValidateSymmContact getPdbxValidateSymmContact()
      Data items in the PDBX_VALIDATE_SYMM_CONTACT category list the atoms within the entry that are in close contact with regard the distances expected from either covalent bonding or closest approach by van der Waals contacts. Contacts with for symmetry related contacts are considered. For those contacts not involving hydrogen a limit of 2.2 Angstroms is used. For contacts involving a hydrogen atom a cutoff of 1.6Angstrom is used.
      Returns:
      PdbxValidateSymmContact

    • getPdbxValidateRmsdBond

      public PdbxValidateRmsdBond getPdbxValidateRmsdBond()
      Data items in the PDBX_VALIDATE_RMSD_BOND category list the covalent bonds that have values which deviate from expected values by more than 6*rmsd.
      Returns:
      PdbxValidateRmsdBond

    • getPdbxValidateRmsdAngle

      public PdbxValidateRmsdAngle getPdbxValidateRmsdAngle()
      Data items in the PDBX_VALIDATE_RMSD_ANGLE category list the the covalent bond angles found in an entry that have values which deviate from expected values by more than 6*rmsd for the particular entry from the expected standard value
      Returns:
      PdbxValidateRmsdAngle

    • getPdbxValidateTorsion

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

    • getPdbxValidatePeptideOmega

      public PdbxValidatePeptideOmega getPdbxValidatePeptideOmega()
      Data items in the PDBX_VALIDATE_PEPTIDE_OMEGA category list the residues that contain peptide bonds deviate significantly from both cis and trans conformation. cis bonds, if any, are listed on cispep records. trans is defined as 180 +/- 30 and cis is defined as 0 +/- 30 degrees.
      Returns:
      PdbxValidatePeptideOmega

    • getPdbxValidateChiral

      public PdbxValidateChiral getPdbxValidateChiral()
      Data items in the PDBX_VALIDATE_CHIRAL category list the residues that contain unexpected configuration of chiral centers. IMPROPER HA N C CB chirality CA IMPROPER HB1 HB2 CA CG stereo CB as this number approaches (+) or (-) 180.0, then the error in predicting the true chirality of the center increases. Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. HERE improper C---N----CA---CB done expected answer is around -120 mean -122.52 D-amino acid is +120.0
      Returns:
      PdbxValidateChiral

    • getPdbxValidatePlanes

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

    • getPdbxValidatePlanesAtom

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

    • getPdbxValidateMainChainPlane

      public PdbxValidateMainChainPlane getPdbxValidateMainChainPlane()
      Data items in the PDBX_VALIDATE_MAIN_CHAIN_PLANE category list the residues that contain unexpected deviations from planes for main chain atoms as defined by the improper torsion angle describing planarity: PLANARITY = C(i-1) - CA(i-1) - N(i) - O(i-1) ==> planar < 5 as a pseudo torsion
      Returns:
      PdbxValidateMainChainPlane

    • getPdbxStructConnAngle

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

    • getPdbxUnobsOrZeroOccResidues

      public PdbxUnobsOrZeroOccResidues getPdbxUnobsOrZeroOccResidues()
      Data items in the PDBX_UNOBS_OR_ZERO_OCC_RESIDUES category list the residues within the entry that are not observed or have zero occupancy.
      Returns:
      PdbxUnobsOrZeroOccResidues

    • getPdbxUnobsOrZeroOccAtoms

      public PdbxUnobsOrZeroOccAtoms getPdbxUnobsOrZeroOccAtoms()
      Data items in the PDBX_UNOBS_OR_ZERO_OCC_ATOMS category list the atoms within the entry that are either unobserved or have zero occupancy/
      Returns:
      PdbxUnobsOrZeroOccAtoms

    • getPdbxEntryDetails

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

    • getPdbxStructModResidue

      public PdbxStructModResidue getPdbxStructModResidue()
      Data items in the PDBX_STRUCT_MOD_RESIDUE category list the modified polymer components in the entry and provide some details describing the nature of the modification.
      Returns:
      PdbxStructModResidue

    • getPdbxStructRefSeqInsertion

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

    • getPdbxStructRefSeqDeletion

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

    • getPdbxRemediationAtomSiteMapping

      public PdbxRemediationAtomSiteMapping getPdbxRemediationAtomSiteMapping()
      Data items in the PDBX_REMEDIATION_ATOM_SITE_MAPPING category records mapping information between selected molecular entities that have been chemically redefined. The prior and current atom nomenclature is tabulated in this category.
      Returns:
      PdbxRemediationAtomSiteMapping

    • getPdbxValidatePolymerLinkage

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

    • getPdbxHelicalSymmetry

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

    • getPdbxPointSymmetry

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

    • getPdbxStructEntityInst

      public PdbxStructEntityInst getPdbxStructEntityInst()
      Data items in the PDBX_STRUCT_ENTITY_INST category record details about the structural elements in the deposited entry. The entity instance is a method neutral identifier for the observed molecular entities in the deposited coordinate set.
      Returns:
      PdbxStructEntityInst

    • getPdbxStructOperList

      public PdbxStructOperList getPdbxStructOperList()
      Data items in the PDBX_STRUCT_OPER_LIST category describe Cartesian rotation and translation operations required to generate or transform the coordinates deposited with this entry.
      Returns:
      PdbxStructOperList

    • getPdbxStructAssembly

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

    • getPdbxStructAssemblyGen

      public PdbxStructAssemblyGen getPdbxStructAssemblyGen()
      Data items in the PDBX_STRUCT_ASSEMBLY_GEN category record details about the generation of each macromolecular assemblies. The PDBX_STRUCT_ASSEMBLY_GEN data items provide the specifications of the components that constitute that assembly in terms of cartesian transformations.
      Returns:
      PdbxStructAssemblyGen

    • getPdbxStructAsymGen

      public PdbxStructAsymGen getPdbxStructAsymGen()
      Data items in the PDBX_STRUCT_ASYM_GEN category record details about the generation of the crystallographic asymmetric unit. The PDBX_STRUCT_ASYM_GEN data items provide the specifications of the components that constitute the asymmetric unit in terms of cartesian transformations of deposited coordinates.
      Returns:
      PdbxStructAsymGen

    • getPdbxStructMsymGen

      public PdbxStructMsymGen getPdbxStructMsymGen()
      Data items in the PDBX_STRUCT_MSYM_GEN category record details about the generation of the minimal asymmetric unit. For instance, this category can be used to provide this information for helical and point symmetry systems. The PDBX_STRUCT_MSYM_GEN data items provide the specifications of the components that constitute the asymmetric unit in terms of cartesian transformations of deposited coordinates.
      Returns:
      PdbxStructMsymGen

    • getPdbxStructLegacyOperList

      public PdbxStructLegacyOperList getPdbxStructLegacyOperList()
      Data items in the PDBX_STRUCT_LEGACY_OPER_LIST category describe Cartesian rotation and translation operations required to generate or transform the coordinates deposited with this entry. This category provides a container for matrices used to construct icosahedral assemblies in legacy entries.
      Returns:
      PdbxStructLegacyOperList

    • getPdbxChemCompAtomFeature

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

    • getPdbxReferenceMoleculeFamily

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

    • getPdbxReferenceMoleculeList

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

    • getPdbxReferenceMolecule

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

    • getPdbxReferenceEntityList

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

    • getPdbxReferenceEntityNonpoly

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

    • getPdbxReferenceEntityLink

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

    • getPdbxReferenceEntityPolyLink

      public PdbxReferenceEntityPolyLink getPdbxReferenceEntityPolyLink()
      Data items in the PDBX_REFERENCE_ENTITY_POLY_LINK category give details about polymer linkages including both standard and non-standard linkages between polymer componnents.
      Returns:
      PdbxReferenceEntityPolyLink

    • getPdbxReferenceEntityPoly

      public PdbxReferenceEntityPoly getPdbxReferenceEntityPoly()
      Data items in the PDBX_REFERENCE_ENTITY_POLY category record details about the polymer, such as the type of the polymer, the number of monomers and whether it has nonstandard features.
      Returns:
      PdbxReferenceEntityPoly

    • getPdbxReferenceEntityPolySeq

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

    • getPdbxReferenceEntitySequence

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

    • getPdbxReferenceEntitySrcNat

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

    • getPdbxReferenceMoleculeDetails

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

    • getPdbxReferenceMoleculeSynonyms

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

    • getPdbxReferenceEntitySubcomponents

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

    • getPdbxReferenceMoleculeAnnotation

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

    • getPdbxReferenceMoleculeFeatures

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

    • getPdbxReferenceMoleculeRelatedStructures

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

    • getPdbxStructGroupList

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

    • getPdbxStructGroupComponents

      public PdbxStructGroupComponents getPdbxStructGroupComponents()
      Data items in the PDBX_STRUCT_GROUP_COMPONENTS category list component-level group assignments within the entry. Groups are defined and described in category PDBX_STRUCT_GROUP_LIST.
      Returns:
      PdbxStructGroupComponents

    • getPdbxStructGroupComponentRange

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

    • getPdbxPrdAudit

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

    • getPdbxFamilyPrdAudit

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

    • getPdbxMolecule

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

    • getPdbxMoleculeFeatures

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

    • getPdbxFamilyGroupIndex

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

    • getPdbxDistantSolventAtoms

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

    • getPdbxStructSpecialSymmetry

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

    • getPdbxReferencePublicationList

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

    • getPdbxNmrAssignedChemShiftList

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

    • getPdbxNmrChemShiftExperiment

      public PdbxNmrChemShiftExperiment getPdbxNmrChemShiftExperiment()
      Items in the chem_shift_experiment category provide pointers to the NMR experiments and samples used to collect the data for a set of reported assigned chemical shifts.
      Returns:
      PdbxNmrChemShiftExperiment

    • getPdbxNmrChemShiftRef

      public PdbxNmrChemShiftRef getPdbxNmrChemShiftRef()
      Items in the pdbx_nmr_chem_shift_ref category provide the chemical shift referencing values used in assigning the chemical shift positions for peaks in spectral peak lists and assigned atom chemical shifts.
      Returns:
      PdbxNmrChemShiftRef

    • getPdbxNmrChemShiftReference

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

    • getPdbxNmrChemShiftSoftware

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

    • getPdbxNmrConstraintFile

      public PdbxNmrConstraintFile getPdbxNmrConstraintFile()
      Items in the pdbx_nmr_constraint_file category record the name of the constraint file, the software used to calculate conformers with the constraint file, and the characteristics of the constraints in the constraint file.
      Returns:
      PdbxNmrConstraintFile

    • getPdbxNmrSoftwareTask

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

    • getPdbxNmrSpectralDim

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

    • getPdbxNmrSpectralPeakList

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

    • getPdbxNmrSpectralPeakSoftware

      public PdbxNmrSpectralPeakSoftware getPdbxNmrSpectralPeakSoftware()
      Items in the pdbx_nmr_spectral_peak_software category provide pointers to the software category and methods category where descriptions of software applications and methods can be found.
      Returns:
      PdbxNmrSpectralPeakSoftware

    • getPdbxNmrSystematicChemShiftOffset

      public PdbxNmrSystematicChemShiftOffset getPdbxNmrSystematicChemShiftOffset()
      Items in the pdbx_nmr_systematic_chem_shift_offset category define chemical shift offsets that systematically affect all chemical shifts in a set of assigned chemical shifts for a specific nuclei.
      Returns:
      PdbxNmrSystematicChemShiftOffset

    • getPdbxNmrUpload

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

    • getPdbxAuditSupport

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

    • getPdbxChemCompSubcomponentStructConn

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

    • getPdbxChemCompSubcomponentEntityList

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

    • getEntitySrcNat

      public EntitySrcNat getEntitySrcNat()
      Data items in the ENTITY_SRC_NAT category record details of the source from which the entity was obtained in cases where the entity was isolated directly from a natural tissue.
      Returns:
      EntitySrcNat

    • getEntitySrcGen

      public EntitySrcGen getEntitySrcGen()
      Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated. The following are treated separately: items pertaining to the tissue from which the gene was obtained, items pertaining to the host organism for gene expression and items pertaining to the actual producing organism (plasmid).
      Returns:
      EntitySrcGen

    • getPdbxEntitySrcSyn

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

    • getPdbxEntityPolyCompLinkList

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

    • getPdbxLinkedEntity

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

    • getPdbxLinkedEntityInstanceList

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

    • getPdbxLinkedEntityList

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

    • getPdbxLinkedEntityLinkList

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

    • getPdbxEntityBranchDescriptor

      public PdbxEntityBranchDescriptor getPdbxEntityBranchDescriptor()
      Data items in the PDBX_ENTITY_BRANCH_DESCRIPTOR category provide string descriptors of entity chemical structure.
      Returns:
      PdbxEntityBranchDescriptor

    • getPdbxReferenceLinkedEntity

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

    • getPdbxReferenceLinkedEntityCompList

      public PdbxReferenceLinkedEntityCompList getPdbxReferenceLinkedEntityCompList()
      Data items in the pdbx_reference_linked_entity_comp_list category lists the constituents of common observed interaction patterns described in the pdbx_reference_linked_entity category.
      Returns:
      PdbxReferenceLinkedEntityCompList

    • getPdbxReferenceLinkedEntityCompLink

      public PdbxReferenceLinkedEntityCompLink getPdbxReferenceLinkedEntityCompLink()
      Data items in the pdbx_reference_linked_entity_comp_link category enumerate inter-entity linkages between the components of common observed interaction patterns described in the pdbx_reference_linked_entity category.
      Returns:
      PdbxReferenceLinkedEntityCompLink

    • getPdbxReferenceLinkedEntityLink

      public PdbxReferenceLinkedEntityLink getPdbxReferenceLinkedEntityLink()
      Data items in the pdbx_reference_linked_entity_link category enumerate linkages between the entities in common observed interaction patterns described in the pdbx_reference_linked_entity category.
      Returns:
      PdbxReferenceLinkedEntityLink

    • getPdbxRelatedExpDataSet

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

    • getPdbxDatabaseStatusHistory

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

    • getEmAssembly

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

    • getEmEntityAssembly

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

    • getEmVirusEntity

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

    • getEmSamplePreparation

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

    • getEmSampleSupport

      public EmSampleSupport getEmSampleSupport()
      Data items in the EM_SAMPLE_SUPPORT category record details of the electron microscope grid type, grid support film and pretreatment of whole before sample is applied
      Returns:
      EmSampleSupport

    • getEmBuffer

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

    • getEmVitrification

      public EmVitrification getEmVitrification()
      Data items in the EM_VITRIFICATION category record details about the method and cryogen used in rapid freezing of the sample on the grid prior to its insertion in the electron microscope
      Returns:
      EmVitrification

    • getEmImaging

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

    • getEmDetector

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

    • getEmImageScans

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

    • getEm2dProjectionSelection

      public Em2dProjectionSelection getEm2dProjectionSelection()
      Data items in the EM_2D_PROJECTION_SELECTION category record details of images from scanned micrographs and the number of particles selected from a scanned set of micrographs.
      Returns:
      Em2dProjectionSelection

    • getEm3dReconstruction

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

    • getEm3dFitting

      public Em3dFitting getEm3dFitting()
      Data items in the 3D_FITTING category record details of the method of fitting atomic coordinates from a PDB file into a 3d-em volume map file
      Returns:
      Em3dFitting

    • getEm3dFittingList

      public Em3dFittingList getEm3dFittingList()
      Data items in the 3D_FITTING_LIST category lists the methods of fitting atomic coordinates from a PDB file into a 3d-em volume map file
      Returns:
      Em3dFittingList

    • getEmHelicalEntity

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

    • getEmExperiment

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

    • getEmSingleParticleEntity

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

    • getEmAdmin

      public EmAdmin getEmAdmin()
      Administration-related data items
      Returns:
      EmAdmin

    • getEmAuthorList

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

    • getEmDbReference

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

    • getEmDbReferenceAuxiliary

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

    • getEmDepui

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

    • getEmObsolete

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

    • getEmSupersede

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

    • getEmEntityAssemblyMolwt

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

    • getEmEntityAssemblyNaturalsource

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

    • getEmEntityAssemblyRecombinant

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

    • getEmVirusNaturalHost

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

    • getEmVirusShell

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

    • getEmSpecimen

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

    • getEmEmbedding

      public EmEmbedding getEmEmbedding()
      Sugar embedding category
      Returns:
      EmEmbedding

    • getEmFiducialMarkers

      public EmFiducialMarkers getEmFiducialMarkers()
      Description of fiducial markers.
      Returns:
      EmFiducialMarkers

    • getEmFocusedIonBeam

      public EmFocusedIonBeam getEmFocusedIonBeam()
      Description of sectioning by focused_ion_beam
      Returns:
      EmFocusedIonBeam

    • getEmGridPretreatment

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

    • getEmUltramicrotomy

      public EmUltramicrotomy getEmUltramicrotomy()
      Description of sectioning by ultramicrotomy
      Returns:
      EmUltramicrotomy

    • getEmHighPressureFreezing

      public EmHighPressureFreezing getEmHighPressureFreezing()
      Description of high pressure freezing
      Returns:
      EmHighPressureFreezing

    • getEmShadowing

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

    • getEmTomographySpecimen

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

    • getEmCrystalFormation

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

    • getEmStaining

      public EmStaining getEmStaining()
      Staining category
      Returns:
      EmStaining

    • getEmSupportFilm

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

    • getEmBufferComponent

      public EmBufferComponent getEmBufferComponent()
      Buffer category
      Returns:
      EmBufferComponent

    • getEmDiffraction

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

    • getEmDiffractionShell

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

    • getEmDiffractionStats

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

    • getEmTomography

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

    • getEmImageRecording

      public EmImageRecording getEmImageRecording()
      Data items in the EM_IMAGE_RECORDING category record details of the image recording (either film/microdensitometer or electronic detector) and parameters for image digitization.
      Returns:
      EmImageRecording

    • getEmImagingOptics

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

    • getEmFinalClassification

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

    • getEmStartModel

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

    • getEmSoftware

      public EmSoftware getEmSoftware()
      Description of the software that was used for data collection, data processing, data analysis, structure calculations and refinement. The description should include the name of the software, the author of the software and the version used.
      Returns:
      EmSoftware

    • getEmEulerAngleAssignment

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

    • getEmCtfCorrection

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

    • getEmVolumeSelection

      public EmVolumeSelection getEmVolumeSelection()
      Volume selection in image processing
      Returns:
      EmVolumeSelection

    • getEm3dCrystalEntity

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

    • getEm2dCrystalEntity

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

    • getEmImageProcessing

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

    • getEmParticleSelection

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

    • getEmMap

      public EmMap getEmMap()
      Data items in the EMD_MAP category record parameters of the CCP4 binary-format map file header (see ftp://ftp.wwpdb.org/pub/emdb/doc/map_format/EMDB_mapFormat_v1.0.pdf), parameters derived from the map header, pixel size, contour level, and annotation details from the depositor. The map is a three-dimensional array of data-values of the same data-type. Important parameters are data-type and array size in three dimensions (i.e. the number of columns, rows and sections). Columns are the fastest changing, followed by rows and sections.
      Returns:
      EmMap

    • getEmFscCurve

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

    • getEmInterpretFigure

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

    • getEmLayerLines

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

    • getEmStructureFactors

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

    • getEmDepositorInfo

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

    • getEmMapDepositorInfo

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

    • getEmMaskDepositorInfo

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

    • getEmFigureDepositorInfo

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

    • getEmLayerLinesDepositorInfo

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

    • getEmStructureFactorsDepositorInfo

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

    • getPdbxSeqMapDepositorInfo

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

    • getPdbxChemCompDepositorInfo

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

    • getPdbxStructRefSeqDepositorInfo

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

    • getPdbxStructRefSeqDifDepositorInfo

      public PdbxStructRefSeqDifDepositorInfo getPdbxStructRefSeqDifDepositorInfo()
      Data items in the PDBX_STRUCT_REF_SEQ_DIF_DEPOSITOR_INFO category capture depositor provided information related to the archival cateogory STRUCT_REF_SEQ_DIF.
      Returns:
      PdbxStructRefSeqDifDepositorInfo

    • getPdbxStructAssemblyPropDepositorInfo

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

    • getPdbxStructAssemblyDepositorInfo

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

    • getPdbxStructAssemblyGenDepositorInfo

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

    • getPdbxStructOperListDepositorInfo

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

    • getPdbxPointSymmetryDepositorInfo

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

    • getPdbxHelicalSymmetryDepositorInfo

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

    • getPdbxStructAssemblyAuthEvidenceDepositorInfo

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

    • getPdbxSolventAtomSiteMapping

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

    • getPdbxMoleculeFeaturesDepositorInfo

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

    • getPdbxChemCompInstanceDepositorInfo

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

    • getPdbxDepuiStatusFlags

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

    • getPdbxDepuiUpload

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

    • getPdbxDepuiValidationStatusFlags

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

    • getPdbxChemCompUploadDepositorInfo

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

    • getPdbxDepuiEntityStatusFlags

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

    • getPdbxDepuiEntityFeatures

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

    • getPdbxDepositionMessageInfo

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

    • getPdbxDepositionMessageFileReference

      public PdbxDepositionMessageFileReference getPdbxDepositionMessageFileReference()
      Data items in the PDBX_DEPOSITION_MESSAGE_FILE_REFERENCE category record details of files references associated with messages defined in the PDBX_DEPOSITION_MESSAGE_INFO data category.
      Returns:
      PdbxDepositionMessageFileReference

    • getPdbxDepuiEntryDetails

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

    • getPdbxDataProcessingStatus

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

    • getPdbxEntityInstanceFeature

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

    • getPdbxEntitySrcGenDepositorInfo

      public PdbxEntitySrcGenDepositorInfo getPdbxEntitySrcGenDepositorInfo()
      Data items in the PDBX_ENTITY_SRC_GEN_DEPOSITOR_INFO category record details of the source from which the entity was obtained in cases where the source was genetically manipulated. The following are treated separately: items pertaining to the tissue from which the gene was obtained, items pertaining to the host organism for gene expression and items pertaining to the actual producing organism (plasmid).
      Returns:
      PdbxEntitySrcGenDepositorInfo

    • getPdbxChemCompModel

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

    • getPdbxChemCompModelAtom

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

    • getPdbxChemCompModelBond

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

    • getPdbxChemCompModelFeature

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

    • getPdbxChemCompModelDescriptor

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

    • getPdbxChemCompModelAudit

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

    • getPdbxChemCompModelReference

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

    • getPdbxViewCategoryGroup

      public PdbxViewCategoryGroup getPdbxViewCategoryGroup()
      Data items in the PDBX_VIEW_CATEGORY_GROUP identify collections of related mmCIF categories. Views provide a vehicle for presenting different logical arrangements of dictionary contents.
      Returns:
      PdbxViewCategoryGroup

    • getPdbxViewCategory

      public PdbxViewCategory getPdbxViewCategory()
      Data items in the PDBX_VIEW_CATEGORY specify the categories belonging to a category view group. An alias name for the the mmCIF category may also be specified for the each category in the view.
      Returns:
      PdbxViewCategory

    • getPdbxViewItem

      public PdbxViewItem getPdbxViewItem()
      Data items in the PDBX_VIEW_ITEM specify the mmCIF data items belonging to a view category. An alias name for the the mmCIF item may be specified for the each item in the view category. The role of the item in the view category can be designated as mandatory, optional, or hidden.
      Returns:
      PdbxViewItem

    • getPdbxCoord

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

    • getPdbxConnect

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

    • getPdbxConnectType

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

    • getPdbxConnectModification

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

    • getPdbxConnectAtom

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

    • getPdbxDatabasePDBMaster

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

    • getPdbxDatabasePdbOmit

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

    • getPdbxDbref

      public PdbxDbref getPdbxDbref()
      These records are used in the DBREF record of a PDB file and are used as place holders for NDB ID's in PDB files.
      Returns:
      PdbxDbref

    • getPdbxDrugInfo

      public PdbxDrugInfo getPdbxDrugInfo()
      Data items in the PDBX_DRUG_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated.
      Returns:
      PdbxDrugInfo

    • getPdbxInhibitorInfo

      public PdbxInhibitorInfo getPdbxInhibitorInfo()
      Data items in the PDBX_INHIBITOR_INFO category are still used until the 'entity' categories are entered into the database, even though the inhibitor is repeated.
      Returns:
      PdbxInhibitorInfo

    • getPdbxIonInfo

      public PdbxIonInfo getPdbxIonInfo()
      Data items in the PDBX_ION_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated.
      Returns:
      PdbxIonInfo

    • getPdbxHybrid

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

    • getPdbxNaStrandInfo

      public PdbxNaStrandInfo getPdbxNaStrandInfo()
      Data items in the PDBX_NA_STRAND_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated.
      Returns:
      PdbxNaStrandInfo

    • getPdbxNonstandardList

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

    • getPdbxPdbCompnd

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

    • getPdbxPdbSource

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

    • getPdbxProteinInfo

      public PdbxProteinInfo getPdbxProteinInfo()
      Data items in the PDBX_PROTEIN_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated.
      Returns:
      PdbxProteinInfo

    • getPdbxSolventInfo

      public PdbxSolventInfo getPdbxSolventInfo()
      Data items in the PDBX_SOLVENT_INFO category are still used until the 'entity' categories are entered into the database, even though the information is repeated.
      Returns:
      PdbxSolventInfo

    • getPdbxSource

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

    • getPdbxStructBiolFunc

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

    • getPdbxStructPackGen

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

    • getPdbxTrnaInfo

      public PdbxTrnaInfo getPdbxTrnaInfo()
      Data items in the PDBX_TRNA_INFO category are still used until the 'entity' categories are entered into the database, even though the T-RNA is repeated.
      Returns:
      PdbxTrnaInfo

    • getPdbxUnpair

      public PdbxUnpair getPdbxUnpair()
      These records give information about residues which do not pair (h-bond) in the asymmetric unit. The records about Watson-Crick base pairing depend on these records.
      Returns:
      PdbxUnpair

    • getPdbxRefineLsRestrNcs

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

    • getPdbxStructNcsVirusGen

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

    • getPdbxSequenceAnnotation

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

    • getPdbxPostProcessDetails

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

    • getPdbxPostProcessStatus

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

    • getPdbxStructLink

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

    • getPdbxMissingResidueList

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

    • getPdbxDataProcessingCell

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

    • getPdbxDataProcessingReflns

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

    • getPdbxDataProcessingDetector

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

    • getPdbxChemCompNonstandard

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

    • getPdbxEntityPolyProteinClass

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

    • getPdbxEntityNameTaxonomyTree

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

    • getPdbxEntityNameTaxonomy

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

    • getPdbxEntityNameInstance

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

    • getPdbxTableinfo

      public PdbxTableinfo getPdbxTableinfo()
      Returns:
      PdbxTableinfo

    • getPdbxColumninfo

      public PdbxColumninfo getPdbxColumninfo()
      Returns:
      PdbxColumninfo

    • getPdbxValAngle

      public PdbxValAngle getPdbxValAngle()
      The PDBX_VAL_ANGLE category lists the covalent bond angles in this entry deviating by greater than 6*sigma from standard values. This is a completely derived category. Do not edit.
      Returns:
      PdbxValAngle

    • getPdbxValBond

      public PdbxValBond getPdbxValBond()
      The PDBX_VAL_BOND category lists the covalent bond angles in this entry deviating by greater than 6*sigma from standard values. This is a completely derived category. Do not edit.
      Returns:
      PdbxValBond

    • getPdbxValContact

      public PdbxValContact getPdbxValContact()
      The PDBX_VAL_CONTACT category lists non-bonded atoms within the assymetric unit of the entry that are in close contact. For those contacts not involving hydrogen a limit of 2.2 Angstroms is used. For contacts involving a hydrogen atom a cutoff of 1.6 Angstrom is used. This is a completely derived category. Do not edit.
      Returns:
      PdbxValContact

    • getPdbxValSymContact

      public PdbxValSymContact getPdbxValSymContact()
      The PDBX_VAL_SYM_CONTACT category lists symmetry related contacts amoung non-bonded atoms. For those contacts not involving hydrogen a limit of 2.2 Angstroms is used. For contacts involving a hydrogen atom a cutoff of 1.6 Angstrom is used. This is a completely derived category. Do not edit.
      Returns:
      PdbxValSymContact

    • getPdbxRmchOutlier

      public PdbxRmchOutlier getPdbxRmchOutlier()
      Data items in the PDBX_RMCH_OUTLIER category list the residues with torsion angles outside the expected Ramachandran regions. This is a completely derived category. Do not edit.
      Returns:
      PdbxRmchOutlier

    • getPdbxMissingAtomPoly

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

    • getPdbxMissingAtomNonpoly

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

    • getPdbxValChiral

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

    • getPdbxAtlas

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

    • getPdbxSummaryFlags

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

    • getPdbxEntityFuncBindMode

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

    • getPdbxEntityFuncEnzyme

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

    • getPdbxEntityFuncRegulatory

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

    • getPdbxEntityFuncStructural

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

    • getPdbxEntityFuncOther

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

    • getPdbxEntityPolyDomain

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

    • getPdbxNaStructKeywds

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

    • getPdbxEntityPolyNaType

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

    • getPdbxEntityPolyNaNonstandard

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

    • getPdbxVirtualAngle

      public PdbxVirtualAngle getPdbxVirtualAngle()
      Data items in the PDBX_VIRTUAL_ANGLE category record details about the molecular virtual angles, as calculated from the contents of the ATOM, CELL, and SYMMETRY data.
      Returns:
      PdbxVirtualAngle

    • getPdbxVirtualBond

      public PdbxVirtualBond getPdbxVirtualBond()
      Data items in the PDBX_VIRTUAL_BOND category record details about virtual bonds, as calculated from the contents of the ATOM, CELL, and SYMMETRY data.
      Returns:
      PdbxVirtualBond

    • getPdbxVirtualTorsion

      public PdbxVirtualTorsion getPdbxVirtualTorsion()
      Data items in the PDBX_VIRTUAL_TORSION category record details about virtual torsion angles, as calculated from the contents of the ATOM, CELL, and SYMMETRY data.
      Returns:
      PdbxVirtualTorsion

    • getPdbxSequencePattern

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

    • getPdbxStereochemistry

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

    • getPdbxRmsDevsCovalent

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

    • getPdbxRmsDevsCovByMonomer

      public PdbxRmsDevsCovByMonomer getPdbxRmsDevsCovByMonomer()
      Data items in the PDBX_RMS_DEVS_COV_BY_MONOMER record the RMS deviations covalent geometry for each momoner relative to small molecule crystal standards.
      Returns:
      PdbxRmsDevsCovByMonomer

    • getPdbxSugarPhosphateGeometry

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

    • getPdbxNmrComputing

      public PdbxNmrComputing getPdbxNmrComputing()
      The table in this section is used to describe the software that was used for data collection, data processing, data analysis, structure calculations and refinement. The description should include both the name of the software and the version used.
      Returns:
      PdbxNmrComputing

    • getPdbxAuditConformExtension

      public PdbxAuditConformExtension getPdbxAuditConformExtension()
      Data items in the PDBX_AUDIT_CONFORM_EXTENSION category describe extension dictionary versions against which the data names appearing the current data block are conformant.
      Returns:
      PdbxAuditConformExtension

    • getPdbxDccMapman

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

    • getPdbxDccRsccMapman

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

    • getPdbxDccRsccMapmanOverall

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

    • getPdbxDccDensity

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

    • getPdbxDccGeometry

      public PdbxDccGeometry getPdbxDccGeometry()
      Data items in the category record the overall deviations about geometry (such as bond length, angle, dihedral, chirality, planarity). These data are calculated with the phenix module model_vs_data.
      Returns:
      PdbxDccGeometry

    • getPdbxDccDensityCorr

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

    • getPdbxDccMap

      public PdbxDccMap getPdbxDccMap()
      Data items in the category record residual map properties such as Real Space electron density Correlation Coefficient (RSCC), real space R factors (RSR) and the Zscores for each residue, the main/side chains.
      Returns:
      PdbxDccMap

    • getPdbxDepositGroup

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

    • getPdbxDepositGroupIndex

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

    • getPdbxStructAssemblyAuthEvidence

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

    • getPdbxStructAssemblyAuthClassification

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

    • getPdbxCrystalAlignment

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

    • getPdbxAuditRevisionHistory

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

    • getPdbxAuditRevisionGroup

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

    • getPdbxAuditRevisionCategory

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

    • getPdbxAuditRevisionDetails

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

    • getPdbxAuditRevisionItem

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

    • getPdbxSupportingExpDataSet

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

    • getPdbxSerialCrystallographyMeasurement

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

    • getPdbxSerialCrystallographySampleDelivery

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

    • getPdbxSerialCrystallographySampleDeliveryInjection

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

    • getPdbxSerialCrystallographySampleDeliveryFixedTarget

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

    • getPdbxSerialCrystallographyDataReduction

      public PdbxSerialCrystallographyDataReduction getPdbxSerialCrystallographyDataReduction()
      Data items in the PDBX_SERIAL_CRYSTALLOGRAPHY_DATA_REDUCTION category record details about data processing that are unique to XFEL experiments. These will compliment data recorded in category pdbx_diffrn_merge_stat.
      Returns:
      PdbxSerialCrystallographyDataReduction

    • getPdbxEntityBranchList

      public PdbxEntityBranchList getPdbxEntityBranchList()
      Data items in the PDBX_ENTITY_BRANCH_LIST category specify the list of monomers in a branched entity. Allowance is made for the possibility of microheterogeneity in a sample by allowing a given sequence number to be correlated with more than one monomer ID. The corresponding ATOM_SITE entries should reflect this heterogeneity.
      Returns:
      PdbxEntityBranchList

    • getPdbxEntityBranchLink

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

    • getPdbxEntityBranch

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

    • getPdbxBranchScheme

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

    • getPdbxChemCompRelated

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

    • getPdbxChemCompAtomRelated

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

    • getIhmEntityPolySegment

      public IhmEntityPolySegment getIhmEntityPolySegment()
      Data items in the IHM_ENTITY_POLY_SEGMENT category identifies segments of polymeric entities.
      Returns:
      IhmEntityPolySegment

    • getIhmStartingModelDetails

      public IhmStartingModelDetails getIhmStartingModelDetails()
      Data items in the IHM_STARTING_MODEL_DETAILS category records the details about structural models used as starting inputs in the integrative model building process.
      Returns:
      IhmStartingModelDetails

    • getIhmStartingComparativeModels

      public IhmStartingComparativeModels getIhmStartingComparativeModels()
      Data items in the IHM_STARTING_COMPARATIVE_MODELS category records additional details about comparative models used as starting inputs in the integrative model building process.
      Returns:
      IhmStartingComparativeModels

    • getIhmStartingComputationalModels

      public IhmStartingComputationalModels getIhmStartingComputationalModels()
      Data items in the IHM_STARTING_COMPUTATIONAL_MODELS category records additional details about computational models used as starting inputs in the integrative model building process.
      Returns:
      IhmStartingComputationalModels

    • getIhmStartingModelSeqDif

      public IhmStartingModelSeqDif getIhmStartingModelSeqDif()
      Data items in the IHM_STARTING_MODEL_SEQ_DIF category provide a mechanism for indicating and annotating point differences between the sequence of the entity or biological unit described in the data block and the sequence of the starting model used in the integrative modeling referenced from a database. The point differences may be due to point mutations introduced in the starting model or the presence of modified amino acid residues.
      Returns:
      IhmStartingModelSeqDif

    • getIhmModelRepresentation

      public IhmModelRepresentation getIhmModelRepresentation()
      Data items in the IHM_MODEL_REPRESENTATION category lists the various mono or multi-scale model representations used in the integrative modeling study.
      Returns:
      IhmModelRepresentation

    • getIhmModelRepresentationDetails

      public IhmModelRepresentationDetails getIhmModelRepresentationDetails()
      Data items in the IHM_MODEL_REPRESENTATION_DETAILS category records the details about the architecture and representation of structural models involved in the integrative modeling study.
      Returns:
      IhmModelRepresentationDetails

    • getIhmStructAssemblyDetails

      public IhmStructAssemblyDetails getIhmStructAssemblyDetails()
      Data items in the IHM_STRUCT_ASSEMBLY_DETAILS category records the details of the structural assemblies and used in the integrative modeling.
      Returns:
      IhmStructAssemblyDetails

    • getIhmStructAssembly

      public IhmStructAssembly getIhmStructAssembly()
      Data items in the IHM_STRUCT_ASSEMBLY category lists all the structural assemblies used in the integrative modeling study.
      Returns:
      IhmStructAssembly

    • getIhmStructAssemblyClass

      public IhmStructAssemblyClass getIhmStructAssemblyClass()
      Data items in the IHM_STRUCT_ASSEMBLY_CLASS category lists all the structural assembly classes relevant to the entry. This category provides a mechanism to define classes of the structural assemblies.
      Returns:
      IhmStructAssemblyClass

    • getIhmStructAssemblyClassLink

      public IhmStructAssemblyClassLink getIhmStructAssemblyClassLink()
      Data items in the IHM_STRUCT_ASSEMBLY_CLASS_LINK category provides details regarding the structural assembly classes. This category provides a mechanism to identify the classes to which structural assemblies belong.
      Returns:
      IhmStructAssemblyClassLink

    • getIhmModelingProtocol

      public IhmModelingProtocol getIhmModelingProtocol()
      Data items in the IHM_MODELING_PROTOCOL category lists all modeling protocols used in the integrative modeling study.
      Returns:
      IhmModelingProtocol

    • getIhmModelingProtocolDetails

      public IhmModelingProtocolDetails getIhmModelingProtocolDetails()
      Data items in the IHM_MODELING_PROTOCOL_DETAILS category records the step-wise details of the integrative modeling workflow.
      Returns:
      IhmModelingProtocolDetails

    • getIhmMultiStateModeling

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

    • getIhmMultiStateModelGroupLink

      public IhmMultiStateModelGroupLink getIhmMultiStateModelGroupLink()
      IHM_MULTI_STATE_MODEL_GROUP_LINK category provides the list of models groups corresponding to a particular state.
      Returns:
      IhmMultiStateModelGroupLink

    • getIhmOrderedEnsemble

      public IhmOrderedEnsemble getIhmOrderedEnsemble()
      Data items in the IHM_ORDERED_ENSEMBLE category records the details of the ensembles ordered by time or other order. Ordered ensembles are described as directed graphs with edges between nodes representing models or model groups.
      Returns:
      IhmOrderedEnsemble

    • getIhmModelingPostProcess

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

    • getIhmEnsembleInfo

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

    • getIhmEnsembleSubSample

      public IhmEnsembleSubSample getIhmEnsembleSubSample()
      Data items in the IHM_ENSEMBLE_SUB_SAMPLE category records the details of the sub samples within the ensembles.
      Returns:
      IhmEnsembleSubSample

    • getIhmModelList

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

    • getIhmModelGroup

      public IhmModelGroup getIhmModelGroup()
      IHM_MODEL_GROUP category defines collections or groups of integrative structural models.
      Returns:
      IhmModelGroup

    • getIhmModelGroupLink

      public IhmModelGroupLink getIhmModelGroupLink()
      IHM_MODEL_GROUP_LINK category provides the list of models present in a particular model group.
      Returns:
      IhmModelGroupLink

    • getIhmModelRepresentative

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

    • getIhmDatasetList

      public IhmDatasetList getIhmDatasetList()
      Category holds the list of all datasets used in the IHM modeling. These can be datasets archived in other related databases such as BMRB, EMDB, EMPIAR, SASBDB, PRIDE etc., or can be hosted in other places such as the authors website, github etc. These datasets are elaborated in detail in the IHM_DATASET_RELATED_DB_REFERENCE and/or the IHM_DATASET_EXTERNAL_REFERENCE categories. This category holds the list of all datasets used.
      Returns:
      IhmDatasetList

    • getIhmDatasetGroup

      public IhmDatasetGroup getIhmDatasetGroup()
      Category to define groups or collections of input datasets.
      Returns:
      IhmDatasetGroup

    • getIhmDatasetGroupLink

      public IhmDatasetGroupLink getIhmDatasetGroupLink()
      IHM_DATASET_GROUP_LINK category provides the list of datasets present in a particular group.
      Returns:
      IhmDatasetGroupLink

    • getIhmRelatedDatasets

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

    • getIhmDataTransformation

      public IhmDataTransformation getIhmDataTransformation()
      Data items in the IHM_DATA_TRANSFORMATION category records the details of the rotation matrix and translation vector that can be applied to transform the data.
      Returns:
      IhmDataTransformation

    • getIhmDatasetRelatedDbReference

      public IhmDatasetRelatedDbReference getIhmDatasetRelatedDbReference()
      Category holds information related to data sources for the entry. These can be datasets archived in other related databases such as BMRB, EMDB, EMPIAR, SASBDB, PRIDE etc.
      Returns:
      IhmDatasetRelatedDbReference

    • getIhmExternalReferenceInfo

      public IhmExternalReferenceInfo getIhmExternalReferenceInfo()
      Category holds links to other external data sources for the I/H model entry. Input datasets held in other databases such as EMDB, BMRB, SASBDB etc. are referenced in the IHM_DATASET_RELATED_DB_REFERENCE category. This data category, along with IHM_EXTERNAL_FILES category, holds information regarding other non-database external data sources, such as DOIs (digital object identifiers) or supplementary files stored locally. The DOIs can either lead to the external data file(s) directly (as in case of DOIs provided by the PDB) or might lead to an HTML landing page (as provided by Zenodo). In the latter case, additional URL (Uniform Resource Locator) information is required to retrieve the external data file(s).
      Returns:
      IhmExternalReferenceInfo

    • getIhmExternalFiles

      public IhmExternalFiles getIhmExternalFiles()
      Category provides details regarding external files. The IHM_EXTERNAL_REFERENCE_INFO category captures the top-level details regarding external data sources. This category captures the specific details regarding externally stored files related to the particular I/H model entry.
      Returns:
      IhmExternalFiles

    • getIhmDatasetExternalReference

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

    • getIhmLocalizationDensityFiles

      public IhmLocalizationDensityFiles getIhmLocalizationDensityFiles()
      Data items in the IHM_LOCALIZATION_DENSITY_FILES category records the details of files that provide information regarding localization densities of ensembles. These may be stored externally as local files or linked via DOI and can be in any accepted format that provides volume information (CCP4, MRC, etc.).
      Returns:
      IhmLocalizationDensityFiles

    • getIhmPredictedContactRestraint

      public IhmPredictedContactRestraint getIhmPredictedContactRestraint()
      Data items in the IHM_PREDICTED_CONTACT_RESTRAINT category records the list of predicted contacts used in the integrative modeling experiment. This has been adapted from the widely used CASP RR format (http://www.predictioncenter.org/casp8/index.cgi?page=format#RR). These contacts may be derived from various computational tools. The software information can be provided in the SOFTWARE category.
      Returns:
      IhmPredictedContactRestraint

    • getIhmHydroxylRadicalFpRestraint

      public IhmHydroxylRadicalFpRestraint getIhmHydroxylRadicalFpRestraint()
      Data items in the IHM_HYDROXYL_RADICAL_FP_RESTRAINT category records the restraints derived from hydroxyl radical footprinting experiment. These restraints provide information regarding solvent accessible surface area of residues.
      Returns:
      IhmHydroxylRadicalFpRestraint

    • getIhmChemicalComponentDescriptor

      public IhmChemicalComponentDescriptor getIhmChemicalComponentDescriptor()
      Data items in the IHM_CHEMICAL_COMPONENT_DESCRIPTOR category records the details of the chemical descriptors of various non-polymeric chemical components (fluorescent probes, crosslinking agents etc.) used in the experiments.
      Returns:
      IhmChemicalComponentDescriptor

    • getIhmProbeList

      public IhmProbeList getIhmProbeList()
      Data items in the IHM_PROBE_LIST category records the list of probes used in the experiment.
      Returns:
      IhmProbeList

    • getIhmPolyProbePosition

      public IhmPolyProbePosition getIhmPolyProbePosition()
      Data items in the IHM_POLY_PROBE_POSITION category identifies specific residue positions in the polymeric entity where probes are covalently attached.
      Returns:
      IhmPolyProbePosition

    • getIhmPolyProbeConjugate

      public IhmPolyProbeConjugate getIhmPolyProbeConjugate()
      Data items in the IHM_POLY_PROBE_CONJUGATE category records the details of the probes that are covalenty attached to residues in the polymeric entities.
      Returns:
      IhmPolyProbeConjugate

    • getIhmLigandProbe

      public IhmLigandProbe getIhmLigandProbe()
      Data items in the IHM_LIGAND_PROBE category identifies non-polymeric entities (ligands) that are used as probes.
      Returns:
      IhmLigandProbe

    • getIhmEprRestraint

      public IhmEprRestraint getIhmEprRestraint()
      Data items in the IHM_EPR_RESTRAINT category records the details of the EPR data used as restraints in the IHM modeling.
      Returns:
      IhmEprRestraint

    • getIhmCrossLinkList

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

    • getIhmCrossLinkRestraint

      public IhmCrossLinkRestraint getIhmCrossLinkRestraint()
      Data items in the IHM_CROSS_LINK_RESTRAINT category enumerates the implementation details of the chemical crosslinking restraints in the integrative modeling. This category holds the details of how the experimentally derived crosslinks are applied in the modeling.
      Returns:
      IhmCrossLinkRestraint

    • getIhmCrossLinkPseudoSite

      public IhmCrossLinkPseudoSite getIhmCrossLinkPseudoSite()
      Data items in the IHM_CROSS_LINK_PSEUDO_SITE category records the details of the pseudo sites involved in the cross links.
      Returns:
      IhmCrossLinkPseudoSite

    • getIhmCrossLinkResult

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

    • getIhmCrossLinkResultParameters

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

    • getIhm2demClassAverageRestraint

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

    • getIhm2demClassAverageFitting

      public Ihm2demClassAverageFitting getIhm2demClassAverageFitting()
      Data items in the IHM_2DEM_CLASS_AVERAGE_FITTING category records the details of the fitting of the model to the 2DEM class averages used in the IHM modeling. The following conventions are recommended while generating the rotation matrix and translation vector for transformation. - The model is rotated and translated to fit to the 2DEM image. - The 2DEM image should be in the XY plane. - The lower left image corner (image pixel index 0,0) should be at x,y,z = (0,0,0). - The 2D image is scaled by the _ihm_2dem_class_average_restraint.pixel_size_width and _ihm_2dem_class_average_restraint.pixel_size_height from the IHM_2DEM_CLASS_AVERAGE_RESTRAINT table. - The transformation is applied after the scaling and hence the translation vector should account for the scaling. - There are no specifications for Z translations i.e., how far the image should be from the model while projecting. It may be set to zero.
      Returns:
      Ihm2demClassAverageFitting

    • getIhm3demRestraint

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

    • getIhmSasRestraint

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

    • getIhmHdxRestraint

      public IhmHdxRestraint getIhmHdxRestraint()
      Data items in the IHM_HDX_RESTRAINT category captures the details of restraints derived from Hydrogen-Deuterium Exchange experiments.
      Returns:
      IhmHdxRestraint

    • getIhmStartingModelCoord

      public IhmStartingModelCoord getIhmStartingModelCoord()
      Data items in the IHM_STARTING_MODEL_COORD category records the coordinates for structural templates used as starting inputs in the integrative model building tasks.
      Returns:
      IhmStartingModelCoord

    • getIhmSphereObjSite

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

    • getIhmGaussianObjSite

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

    • getIhmGaussianObjEnsemble

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

    • getIhmPseudoSite

      public IhmPseudoSite getIhmPseudoSite()
      Data items in the IHM_PSEUDO_SITE_FEATURE category records the details of pseudo sites that may be used in the restraints or model representation.
      Returns:
      IhmPseudoSite

    • getIhmResiduesNotModeled

      public IhmResiduesNotModeled getIhmResiduesNotModeled()
      Data items in the IHM_RESIDUES_NOT_MODELED category record the details of the residues that are defined in the IHM_STRUCT_ASSEMBLY category but are missing in the three-dimensional model (ATOM_SITE, IHM_SPHERE_OBJ_SITE, IHM_GAUSSIAN_OBJ_SITE categories) i.e., residues in the assembly that are not modeled.
      Returns:
      IhmResiduesNotModeled

    • getIhmFeatureList

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

    • getIhmPseudoSiteFeature

      public IhmPseudoSiteFeature getIhmPseudoSiteFeature()
      Data items in the IHM_PSEUDO_SITE_FEATURE category records the details of pseudo site features listed in IHM_FEATURE_LIST.
      Returns:
      IhmPseudoSiteFeature

    • getIhmPolyAtomFeature

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

    • getIhmPolyResidueFeature

      public IhmPolyResidueFeature getIhmPolyResidueFeature()
      Data items in the IHM_POLY_RESIDUE_FEATURE category provides the defintions required to select a specific residue or a set of residues that may or may not be in a contiguous range.
      Returns:
      IhmPolyResidueFeature

    • getIhmNonPolyFeature

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

    • getIhmInterfaceResidueFeature

      public IhmInterfaceResidueFeature getIhmInterfaceResidueFeature()
      Data items in the IHM_INTERFACE_RESIDUE_FEATURE category captures the details of residues that are identified to be at the binding interface from experiments. This information is used by modeling software such as HADDOCK to create a set of ambiguous distance restraints at the binding interface between the molecular entities involved.
      Returns:
      IhmInterfaceResidueFeature

    • getIhmDerivedDistanceRestraint

      public IhmDerivedDistanceRestraint getIhmDerivedDistanceRestraint()
      Data items in the IHM_DERIVED_DISTANCE_RESTRAINT category records the list of distance restraints used in the integrative modeling experiment. These distance redistance restraints may be derived from various kinds of experiments.
      Returns:
      IhmDerivedDistanceRestraint

    • getIhmDerivedAngleRestraint

      public IhmDerivedAngleRestraint getIhmDerivedAngleRestraint()
      Data items in the IHM_DERIVED_ANGLE_RESTRAINT category records the list of angle restraints used in the integrative modeling experiment. These angle restraints may be derived from various kinds of experiments.
      Returns:
      IhmDerivedAngleRestraint

    • getIhmDerivedDihedralRestraint

      public IhmDerivedDihedralRestraint getIhmDerivedDihedralRestraint()
      Data items in the IHM_DERIVED_DIHEDRAL_RESTRAINT category records the list of dihedral restraints used in the integrative modeling experiment. These dihedral restraints may be derived from various kinds of experiments.
      Returns:
      IhmDerivedDihedralRestraint

    • getIhmGeometricObjectList

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

    • getIhmGeometricObjectCenter

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

    • getIhmGeometricObjectTransformation

      public IhmGeometricObjectTransformation getIhmGeometricObjectTransformation()
      Data items in the IHM_GEOMETRIC_OBJECT_TRANSFORMATION category records the details of the rotation matrix and translation vector applied for transforming the geometric object. If no transformation is provide, identity transformation is assumed.
      Returns:
      IhmGeometricObjectTransformation

    • getIhmGeometricObjectSphere

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

    • getIhmGeometricObjectTorus

      public IhmGeometricObjectTorus getIhmGeometricObjectTorus()
      Data items in the IHM_GEOMETRIC_OBJECT_TORUS category records the parameters of a torus. By definition, the base plane of the torus is the XY plane. The `ihm_geometric_object_transformation` category can be used to generate transformations to any other plane.
      Returns:
      IhmGeometricObjectTorus

    • getIhmGeometricObjectHalfTorus

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

    • getIhmGeometricObjectAxis

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

    • getIhmGeometricObjectPlane

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

    • getIhmGeometricObjectDistanceRestraint

      public IhmGeometricObjectDistanceRestraint getIhmGeometricObjectDistanceRestraint()
      Data items in the IHM_GEOMETRIC_OBJECT_DISTANCE_RESTRAINT category records the details of distance restraints involving geometric objects. If the geometric object involved is a plane, then the distance is along the normal following the right-hand rule. So for the xy plane, distance is along the z axis in the positive direction, 'above' the plane such that negative distances corresponded to positions below the plane.
      Returns:
      IhmGeometricObjectDistanceRestraint