Package org.rcsb.cif.schema.core

Class CifCoreBlock

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

  • Constructor Details

  • Method Details

    • getAliasedColumn

      public Column<?> getAliasedColumn​(String... aliases)

    • createDelegate

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

    • getCifCore

      public CifCore getCifCore()
      The CIF_CORE group contains the definitions of data items that are common to all domains of crystallographic studies.
      Returns:
      CifCore

    • getDiffraction

      public Diffraction getDiffraction()
      The DICTIONARY group encompassing the CORE DIFFRACTION data items defined and used with in the Crystallographic Information Framework (CIF).
      Returns:
      Diffraction

    • getDiffrn

      public Diffrn getDiffrn()
      The CATEGORY of data items used to describe the diffraction experiment.
      Returns:
      Diffrn

    • getDiffrnAttenuator

      public DiffrnAttenuator getDiffrnAttenuator()
      The CATEGORY of data items which specify the attenuators used in the diffraction source.
      Returns:
      DiffrnAttenuator

    • getDiffrnDetector

      public DiffrnDetector getDiffrnDetector()
      The CATEGORY of data items which specify the detectors used in the in the measurement of diffraction intensities.
      Returns:
      DiffrnDetector

    • getDiffrnMeasurement

      public DiffrnMeasurement getDiffrnMeasurement()
      The CATEGORY of data items which specify the details of the diffraction measurement.
      Returns:
      DiffrnMeasurement

    • getDiffrnOrient

      public DiffrnOrient getDiffrnOrient()
      The CATEGORY of data items which specify the orientation of the crystal axes to the diffractometer goniometer.
      Returns:
      DiffrnOrient

    • getDiffrnOrientMatrix

      public DiffrnOrientMatrix getDiffrnOrientMatrix()
      The CATEGORY of data items which specify the matrix specifying the orientation of the crystal axes to the diffractometer goniometer.
      Returns:
      DiffrnOrientMatrix

    • getDiffrnOrientRefln

      public DiffrnOrientRefln getDiffrnOrientRefln()
      The CATEGORY of data items which specify the reflections used to calculate the matrix which gives the orientation of the crystal axes to the diffractometer goniometer.
      Returns:
      DiffrnOrientRefln

    • getDiffrnRadiation

      public DiffrnRadiation getDiffrnRadiation()
      The CATEGORY of data items which specify the wavelength of the radiation used in measuring diffraction intensities. Items may be looped to identify and assign weights to distinct wavelength components from a polychromatic beam.
      Returns:
      DiffrnRadiation

    • getDiffrnRadiationWavelength

      public DiffrnRadiationWavelength getDiffrnRadiationWavelength()
      The CATEGORY of data items which specify the wavelength of the radiation used in measuring diffraction intensities. Items may be looped to identify and assign weights to distinct wavelength components from a polychromatic beam.
      Returns:
      DiffrnRadiationWavelength

    • getDiffrnRefln

      public DiffrnRefln getDiffrnRefln()
      The CATEGORY of data items which specify the reflection measurements, prior to data reduction and merging.
      Returns:
      DiffrnRefln

    • getDiffrnReflns

      public DiffrnReflns getDiffrnReflns()
      The CATEGORY of data items which specify the overall reflection measurement information.
      Returns:
      DiffrnReflns

    • getDiffrnReflnsClass

      public DiffrnReflnsClass getDiffrnReflnsClass()
      The CATEGORY of data items which specify different classes of reflections in the raw measured diffraction data.
      Returns:
      DiffrnReflnsClass

    • getDiffrnReflnsTransfMatrix

      public DiffrnReflnsTransfMatrix getDiffrnReflnsTransfMatrix()
      The CATEGORY of data items which specify the elements of the matrix used to transform the reflection indices _diffrn_refln.hkl into _refln.hkl. |11 12 13| (h k l) diffraction |21 22 23| = (h' k' l') |31 32 33|
      Returns:
      DiffrnReflnsTransfMatrix

    • getDiffrnScaleGroup

      public DiffrnScaleGroup getDiffrnScaleGroup()
      The CATEGORY of data items which specify the groups of reflections in the raw measured diffraction data with different relative scales.
      Returns:
      DiffrnScaleGroup

    • getDiffrnSource

      public DiffrnSource getDiffrnSource()
      The CATEGORY of data items which specify information about the radiation source.
      Returns:
      DiffrnSource

    • getDiffrnStandard

      public DiffrnStandard getDiffrnStandard()
      The CATEGORY of data items which specify information about the standard reflections used in the diffraction measurement process.
      Returns:
      DiffrnStandard

    • getDiffrnStandardRefln

      public DiffrnStandardRefln getDiffrnStandardRefln()
      The CATEGORY of data items which specify the "standard" reflections measured repeatedly to monitor variations in intensity due to source flux, environment conditions or crystal quality.
      Returns:
      DiffrnStandardRefln

    • getRefln

      public Refln getRefln()
      The CATEGORY of data items used to describe the reflection data used in the refinement of a crystallographic structure model.
      Returns:
      Refln

    • getReflns

      public Reflns getReflns()
      The CATEGORY of data items used to specify parameters for the complete set of reflections used in the structure refinement process. Note that these parameters are often similar measures to those defined in the DIFFRN categories, but differ in that the parameters refer to the reduced/transformed reflections which have been used to refine the atom site data in the ATOM_SITE category. The DIFFRN definitions refer to the diffraction measurements and the raw reflection data.
      Returns:
      Reflns

    • getReflnsClass

      public ReflnsClass getReflnsClass()
      The CATEGORY of data items which specify the properties of reflections in specific classes of reflections.
      Returns:
      ReflnsClass

    • getReflnsScale

      public ReflnsScale getReflnsScale()
      The CATEGORY of data items which specify the scales needed to place measured structure factor coefficients on the same absolute scale.
      Returns:
      ReflnsScale

    • getReflnsShell

      public ReflnsShell getReflnsShell()
      The CATEGORY of data items which specify the information about reflections divided into shells bounded by d resolution limits.
      Returns:
      ReflnsShell

    • getExptl

      public Exptl getExptl()
      The CATEGORY of data items used to specify the experimental work prior to diffraction measurements. These include crystallization crystal measurements and absorption-correction techniques used..
      Returns:
      Exptl

    • getCell

      public Cell getCell()
      The CATEGORY of data items used to describe the parameters of the crystal unit cell and their measurement.
      Returns:
      Cell

    • getCellMeasurement

      public CellMeasurement getCellMeasurement()
      The CATEGORY of data items used to describe the angles between the axes in the crystal unit cell.
      Returns:
      CellMeasurement

    • getCellMeasurementRefln

      public CellMeasurementRefln getCellMeasurementRefln()
      The CATEGORY of data items used to describe the reflection data used in the measurement of the crystal unit cell.
      Returns:
      CellMeasurementRefln

    • getChemical

      public Chemical getChemical()
      The CATEGORY of data items which describe the composition and chemical properties of the compound under study. The formula data items must be consistent with the density, unit-cell and Z values.
      Returns:
      Chemical

    • getChemicalConnAtom

      public ChemicalConnAtom getChemicalConnAtom()
      The CATEGORY of data items which describe the 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. In particular, 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 as to describe a complete chemical entity.
      Returns:
      ChemicalConnAtom

    • getChemicalConnBond

      public ChemicalConnBond getChemicalConnBond()
      The CATEGORY of data items which specify the connections between the atoms sites in the chemical_conn_atom list and the nature of the chemical bond between these atoms. These are 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.
      Returns:
      ChemicalConnBond

    • getChemicalFormula

      public ChemicalFormula getChemicalFormula()
      The CATEGORY of data items which 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, *.structural and *.sum. For the data item *.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 parentheses. That is, all element and group multipliers are assumed to be printed as subscripted numbers. [An exception to this rule exists for *.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 depends on whether or not carbon is present. If carbon is present, the order should be: C, then H, then the other elements in alphabetical order of their symbol. If carbon is not present, the elements are listed purely in alphabetic 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. _chemical_formula.iupac '[Mo (C O)4 (C18 H33 P)2]' _chemical_formula.moiety 'C40 H66 Mo O4 P2' _chemical_formula.structural '((C O)4 (P (C6 H11)3)2)Mo' _chemical_formula.sum 'C40 H66 Mo O4 P2' _chemical_formula.weight 768.81
      Returns:
      ChemicalFormula

    • getExptlAbsorpt

      public ExptlAbsorpt getExptlAbsorpt()
      The CATEGORY of data items used to specify the experimental details of the absorption measurements and corrections to the diffraction data.
      Returns:
      ExptlAbsorpt

    • getExptlCrystal

      public ExptlCrystal getExptlCrystal()
      The CATEGORY of data items used to specify information about crystals used in the diffraction measurements.
      Returns:
      ExptlCrystal

    • getExptlCrystalAppearance

      public ExptlCrystalAppearance getExptlCrystalAppearance()
      The CATEGORY of ENUMERATION items used to specify information about the crystal colour and appearance.
      Returns:
      ExptlCrystalAppearance

    • getExptlCrystalFace

      public ExptlCrystalFace getExptlCrystalFace()
      The CATEGORY of data items which specify the dimensions of the crystal used in the diffraction measurements.
      Returns:
      ExptlCrystalFace

    • getSpaceGroup

      public SpaceGroup getSpaceGroup()
      The CATEGORY of data items used to specify space group information about the crystal used in the diffraction measurements. Space-group types are identified by their number as listed in International Tables for Crystallography Volume A, or by their Schoenflies symbol. Specific settings of the space groups can be identified by their Hall symbol, by specifying their symmetry operations or generators, or by giving the transformation that relates the specific setting to the reference setting based on International Tables Volume A and stored in this dictionary. 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. Ref: International Tables for Crystallography (2002). Volume A, Space-group symmetry, edited by Th. Hahn, 5th ed. Dordrecht: Kluwer Academic Publishers.
      Returns:
      SpaceGroup

    • getSpaceGroupGenerator

      public SpaceGroupGenerator getSpaceGroupGenerator()
      The CATEGORY of data items used to list generators for the space group
      Returns:
      SpaceGroupGenerator

    • getSpaceGroupSymop

      public SpaceGroupSymop getSpaceGroupSymop()
      The CATEGORY of data items used to describe symmetry equivalent sites in the crystal unit cell.
      Returns:
      SpaceGroupSymop

    • getSpaceGroupWyckoff

      public SpaceGroupWyckoff getSpaceGroupWyckoff()
      Contains information about Wyckoff positions of a space group. Only one site can be given for each special position but the remainder can be generated by applying the symmetry operations stored in _space_group_symop.operation_xyz.
      Returns:
      SpaceGroupWyckoff

    • getFunction

      public Function getFunction()
      The crystallographic functions the invoked in the definition methods of CORE STRUCTURE data items defined and used with in the Crystallographic Information Framework (CIF).
      Returns:
      Function

    • getModel

      public Model getModel()
      Items in the MODEL Category specify data for the crystal structure postulated and modelled from the atomic coordinates derived and refined from the diffraction information. The structural model is described principally in terms of the geometry of the 'connected' atom sites and the crystal symmetry in which they reside.
      Returns:
      Model

    • getGeom

      public Geom getGeom()
      The CATEGORY of data items used to specify the geometry of the structural model as derived from the atomic sites. The geometry is expressed in terms of the interatomic angles (GEOM_ANGLE data), covalent bond distances (GEOM_BOND data), contact distances (GEOM_CONTACT data), hydrogen bonds (GEOM_HBOND data) and torsion geometry (GEOM_TORSION data). Geometry data are usually redundant, in that they can be calculated from other more fundamental quantities in the data block. However, they serve the dual purposes of providing a check on the correctness of both sets of data and of enabling the most important geometric data to be identified for publication by setting the appropriate publication flag.
      Returns:
      Geom

    • getGeomAngle

      public GeomAngle getGeomAngle()
      The CATEGORY of data items used to specify the geometry angles in the structural model as derived from the atomic sites.
      Returns:
      GeomAngle

    • getGeomBond

      public GeomBond getGeomBond()
      The CATEGORY of data items used to specify the geometry bonds in the structural model as derived from the atomic sites.
      Returns:
      GeomBond

    • getGeomContact

      public GeomContact getGeomContact()
      The CATEGORY of data items used to specify the interatomic contact distances in the structural model.
      Returns:
      GeomContact

    • getGeomHbond

      public GeomHbond getGeomHbond()
      The CATEGORY of data items used to specify the hydrogen bond distances in the structural model as derived from atomic sites.
      Returns:
      GeomHbond

    • getGeomTorsion

      public GeomTorsion getGeomTorsion()
      The CATEGORY of data items used to specify the torsion angles in the structural model as derived from the atomic sites.
      Returns:
      GeomTorsion

    • getModelSite

      public ModelSite getModelSite()
      The CATEGORY of data items used to describe atomic sites and connections in the proposed atomic model.
      Returns:
      ModelSite

    • getValence

      public Valence getValence()
      The CATEGORY of items used to specify bond valence parameters used to calculate bond valences from bond lengths.
      Returns:
      Valence

    • getValenceParam

      public ValenceParam getValenceParam()
      The CATEGORY of items for listing bond valences.
      Returns:
      ValenceParam

    • getValenceRef

      public ValenceRef getValenceRef()
      The CATEGORY of items for listing valence references.
      Returns:
      ValenceRef

    • getPublication

      public Publication getPublication()
      The DICTIONARY group encompassing the CORE PUBLICATION data items defined and used with in the Crystallographic Information Framework (CIF).
      Returns:
      Publication

    • getAudit

      public Audit getAudit()
      The CATEGORY of data items used to record details about the creation and subsequent updating of the data block.
      Returns:
      Audit

    • getAuditAuthor

      public AuditAuthor getAuditAuthor()
      The CATEGORY of data items used for author(s) details.
      Returns:
      AuditAuthor

    • getAuditConform

      public AuditConform getAuditConform()
      The CATEGORY of data items used describe dictionary versions by which data names in the current data block are conformant.
      Returns:
      AuditConform

    • getAuditContactAuthor

      public AuditContactAuthor getAuditContactAuthor()
      The CATEGORY of data items used for contact author(s) details.
      Returns:
      AuditContactAuthor

    • getAuditLink

      public AuditLink getAuditLink()
      The CATEGORY of data items used to record details about the relationships between data blocks in the current CIF.
      Returns:
      AuditLink

    • 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()
      Category of items describing citation author(s) details.
      Returns:
      CitationAuthor

    • getCitationEditor

      public CitationEditor getCitationEditor()
      Category of items describing citation editor(s) details.
      Returns:
      CitationEditor

    • getComputing

      public Computing getComputing()
      The CATEGORY of data items used to record details of the computer programs used in the crystal structure analysis.
      Returns:
      Computing

    • getDatabase

      public Database getDatabase()
      The CATEGORY of data items recording database deposition.
      Returns:
      Database

    • getDatabaseCode

      public DatabaseCode getDatabaseCode()
      The CATEGORY of data items recording database deposition. These data items are assigned by database managers and should only appear in a CIF if they originate from that source.
      Returns:
      DatabaseCode

    • getDatabaseRelated

      public DatabaseRelated getDatabaseRelated()
      A category of items recording entries in databases that describe the same or related data. Databases wishing to insert their own canonical codes when archiving and delivering data blocks should use items from the DATABASE category.
      Returns:
      DatabaseRelated

    • getDisplay

      public Display getDisplay()
      The CATEGORY of data items used to enumerate the display parameters used in the discipline.
      Returns:
      Display

    • getDisplayColour

      public DisplayColour getDisplayColour()
      The CATEGORY of data items used to enumerate the display colour codes used in the discipline.
      Returns:
      DisplayColour

    • getJournal

      public Journal getJournal()
      Category of items recording details about the book-keeping by the journal staff when processing a CIF submitted for publication. The creator of a CIF will not normally specify these data items.
      Returns:
      Journal

    • getJournalCoeditor

      public JournalCoeditor getJournalCoeditor()
      Category of items recording co-editor details.
      Returns:
      JournalCoeditor

    • getJournalDate

      public JournalDate getJournalDate()
      Category of items recording dates of publication processing.
      Returns:
      JournalDate

    • getJournalIndex

      public JournalIndex getJournalIndex()
      Category of items describing publication indices.
      Returns:
      JournalIndex

    • getJournalTecheditor

      public JournalTecheditor getJournalTecheditor()
      Category of items recording details of the technical editor processing this publication.
      Returns:
      JournalTecheditor

    • getPubl

      public Publ getPubl()
      Data items in the PUBL category are used when submitting a manuscript for publication. They refer either to the paper as a whole, or to specific named elements within a paper (such as the title and abstract, or the Comment and Experimental sections of Acta Crystallographica Section C). The data items in the PUBL_BODY category should be used for the textual content of other submissions. Typically, each journal will supply a list of the specific items it requires in its Notes for Authors.
      Returns:
      Publ

    • getPublAuthor

      public PublAuthor getPublAuthor()
      Category of data items recording the author information.
      Returns:
      PublAuthor

    • getPublBody

      public PublBody getPublBody()
      Data items in the PUBL_BODY category permit labelling of different text sections within the body of a submitted 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

    • getPublContactAuthor

      public PublContactAuthor getPublContactAuthor()
      Category of items describing contact author(s) details.
      Returns:
      PublContactAuthor

    • getPublManuscript

      public PublManuscript getPublManuscript()
      Category of items describing the publication manuscript.
      Returns:
      PublManuscript

    • getPublManuscriptInclExtra

      public PublManuscriptInclExtra getPublManuscriptInclExtra()
      Category of data items that allow the authors of a manuscript to submit for publication data names that should be added to the standard request list employed by journal printing software. Although these fields are primarily intended to identify CIF data items that the author wishes to include in a published paper, they can also be used to identify data names created so that non-CIF items can be included in the publication. Note that *.item names MUST be enclosed in single quotes.
      Returns:
      PublManuscriptInclExtra

    • getPublRequested

      public PublRequested getPublRequested()
      CATEGORY of data items that enable the author to make specific requests to the journal office for processing.
      Returns:
      PublRequested

    • getPublSection

      public PublSection getPublSection()
      Manuscript section data if submitted in parts. see also _publ_manuscript.text and _publ_manuscript.processed. The _publ_section.exptl_prep, _publ_section.exptl_refinement and _publ_section.exptl_solution items are preferred for separating the chemical preparation, refinement and structure solution aspects of the experimental description.
      Returns:
      PublSection

    • getStructure

      public Structure getStructure()
      The DICTIONARY group encompassing the CORE STRUCTURE data items defined and used with in the Crystallographic Information Framework (CIF).
      Returns:
      Structure

    • getAtom

      public Atom getAtom()
      The CATEGORY of data items used to describe atomic information used in crystallographic structure studies.
      Returns:
      Atom

    • getAtomSite

      public AtomSite getAtomSite()
      The CATEGORY of data items used to describe atom site information used in crystallographic structure studies.
      Returns:
      AtomSite

    • getAtomSiteAniso

      public AtomSiteAniso getAtomSiteAniso()
      The CATEGORY of data items used to describe the anisotropic thermal parameters of the atomic sites in a crystal structure.
      Returns:
      AtomSiteAniso

    • getAtomSites

      public AtomSites getAtomSites()
      The CATEGORY of data items used to describe information which applies to all atom sites in a crystal structure.
      Returns:
      AtomSites

    • getAtomSitesCartnTransform

      public AtomSitesCartnTransform getAtomSitesCartnTransform()
      The CATEGORY of data items used to describe the matrix elements used to transform Cartesion coordinates into fractional coordinates of all atom sites in a crystal structure.
      Returns:
      AtomSitesCartnTransform

    • getAtomSitesFractTransform

      public AtomSitesFractTransform getAtomSitesFractTransform()
      The CATEGORY of data items used to describe the matrix elements used to transform Cartesion coordinates into fractional coordinates of all atom sites in a crystal structure.
      Returns:
      AtomSitesFractTransform

    • getAtomType

      public AtomType getAtomType()
      The CATEGORY of data items used to describe atomic type information used in crystallographic structure studies.
      Returns:
      AtomType

    • getAtomTypeScat

      public AtomTypeScat getAtomTypeScat()
      The CATEGORY of data items used to describe atomic scattering information used in crystallographic structure studies.
      Returns:
      AtomTypeScat

    • getRefine

      public Refine getRefine()
      The CATEGORY of data items used to specify information about the refinement of the structural model.
      Returns:
      Refine

    • getRefineDiff

      public RefineDiff getRefineDiff()
      The CATEGORY of data items which specify the electron density limits in a difference Fourier map after the structure has been refined. The rms value is with respect to the arithmetic mean density, and is derived from summations over each grid point in the asymmetric unit of the cell.
      Returns:
      RefineDiff

    • getRefineLs

      public RefineLs getRefineLs()
      The CATEGORY of data items used to specify information about the refinement of the structural model.
      Returns:
      RefineLs

    • getRefineLsClass

      public RefineLsClass getRefineLsClass()
      The CATEGORY of data items used to specify information about the refinement of the structural model.
      Returns:
      RefineLsClass

    • getSymmetry

      public Symmetry getSymmetry()
      Returns:
      Symmetry

    • getDiffrnStandards

      public DiffrnStandards getDiffrnStandards()
      Returns:
      DiffrnStandards

    • getCellAngle

      public CellAngle getCellAngle()
      Returns:
      CellAngle

    • getChemCompBond

      public ChemCompBond getChemCompBond()
      Returns:
      ChemCompBond

    • getSymmetryEquiv

      public SymmetryEquiv getSymmetryEquiv()
      Returns:
      SymmetryEquiv

    • getPublManuscriptIncl

      public PublManuscriptIncl getPublManuscriptIncl()
      Returns:
      PublManuscriptIncl

    • getAtomSiteAnisotrop

      public AtomSiteAnisotrop getAtomSiteAnisotrop()
      Returns:
      AtomSiteAnisotrop