Package org.rcsb.cif.schema.mm

Class ChemComp

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.ChemComp
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class ChemComp
extends DelegatingCategory
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.

  • Constructor Details

  • Method Details

    • createDelegate

      protected Column createDelegate​(String columnName, Column column)
      Overrides:
      createDelegate in class DelegatingCategory

    • getFormula

      public StrColumn getFormula()
      The formula for the chemical component. Formulae are written according to the following rules: (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), but in general parentheses are not used. (4) The order of elements depends on whether carbon is present or not. 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.
      Returns:
      StrColumn

    • getFormulaWeight

      public FloatColumn getFormulaWeight()
      Formula mass in daltons of the chemical component.
      Returns:
      FloatColumn

    • getId

      public StrColumn getId()
      The value of _chem_comp.id must uniquely identify each item in the CHEM_COMP list. For protein polymer entities, this is the three-letter code for the amino acid. For nucleic acid polymer entities, this is the one-letter code for the base.
      Returns:
      StrColumn

    • getModelDetails

      public StrColumn getModelDetails()
      A description of special aspects of the generation of the coordinates for the model of the component.
      Returns:
      StrColumn

    • getModelErf

      public StrColumn getModelErf()
      A pointer to an external reference file from which the atomic description of the component is taken.
      Returns:
      StrColumn

    • getModelSource

      public StrColumn getModelSource()
      The source of the coordinates for the model of the component.
      Returns:
      StrColumn

    • getMonNstdClass

      public StrColumn getMonNstdClass()
      A description of the class of a nonstandard monomer if the nonstandard monomer represents a modification of a standard monomer.
      Returns:
      StrColumn

    • getMonNstdDetails

      public StrColumn getMonNstdDetails()
      A description of special details of a nonstandard monomer.
      Returns:
      StrColumn

    • getMonNstdFlag

      public StrColumn getMonNstdFlag()
      'yes' indicates that this is a 'standard' monomer, 'no' indicates that it is 'nonstandard'. Nonstandard monomers should be described in more detail using the _chem_comp.mon_nstd_parent, _chem_comp.mon_nstd_class and _chem_comp.mon_nstd_details data items.
      Returns:
      StrColumn

    • getMonNstdParent

      public StrColumn getMonNstdParent()
      The name of the parent monomer of the nonstandard monomer, if the nonstandard monomer represents a modification of a standard monomer.
      Returns:
      StrColumn

    • getMonNstdParentCompId

      public StrColumn getMonNstdParentCompId()
      The identifier for the parent component of the nonstandard component. May be be a comma separated list if this component is derived from multiple components. Items in this indirectly point to _chem_comp.id in the CHEM_COMP category.
      Returns:
      StrColumn

    • getName

      public StrColumn getName()
      The full name of the component.
      Returns:
      StrColumn

    • getNumberAtomsAll

      public IntColumn getNumberAtomsAll()
      The total number of atoms in the component.
      Returns:
      IntColumn

    • getNumberAtomsNh

      public IntColumn getNumberAtomsNh()
      The number of non-hydrogen atoms in the component.
      Returns:
      IntColumn

    • getOneLetterCode

      public StrColumn getOneLetterCode()
      For standard polymer components, the one-letter code for the component. For non-standard polymer components, the one-letter code for parent component if this exists; otherwise, the one-letter code should be given as 'X'. Components that derived from multiple parents components are described by a sequence of one-letter-codes.
      Returns:
      StrColumn

    • getThreeLetterCode

      public StrColumn getThreeLetterCode()
      For standard polymer components, the common three-letter code for the component. Non-standard polymer components and non-polymer components are also assigned three-letter-codes. For ambiguous polymer components three-letter code should be given as 'UNK'. Ambiguous ions are assigned the code 'UNX'. Ambiguous non-polymer components are assigned the code 'UNL'.
      Returns:
      StrColumn

    • getType

      public StrColumn getType()
      For standard polymer components, the type of the monomer. Note that monomers that will form polymers are of three types: linking monomers, monomers with some type of N-terminal (or 5') cap and monomers with some type of C-terminal (or 3') cap.
      Returns:
      StrColumn

    • getPdbxSynonyms

      public StrColumn getPdbxSynonyms()
      Synonym list for the component.
      Returns:
      StrColumn

    • getPdbxModificationDetails

      public StrColumn getPdbxModificationDetails()
      For nonstandard components a text description of modification of the parent component.
      Returns:
      StrColumn

    • getPdbxComponentNo

      public IntColumn getPdbxComponentNo()
      A serial number used by PDB in the FORMUL record.
      Returns:
      IntColumn

    • getPdbxType

      public StrColumn getPdbxType()
      A preliminary classification used by PDB.
      Returns:
      StrColumn

    • getPdbxAmbiguousFlag

      public StrColumn getPdbxAmbiguousFlag()
      A preliminary classification used by PDB to indicate that the chemistry of this component while described as clearly as possible is still ambiguous. Software tools may not be able to process this component definition.
      Returns:
      StrColumn

    • getPdbxReplacedBy

      public StrColumn getPdbxReplacedBy()
      Identifies the _chem_comp.id of the component that has replaced this component.
      Returns:
      StrColumn

    • getPdbxReplaces

      public StrColumn getPdbxReplaces()
      Identifies the _chem_comp.id's of the components which have been replaced by this component. Multiple id codes should be separated by commas.
      Returns:
      StrColumn

    • getPdbxFormalCharge

      public IntColumn getPdbxFormalCharge()
      The net integer charge assigned to this component. This is the formal charge assignment normally found in chemical diagrams.
      Returns:
      IntColumn

    • getPdbxSubcomponentList

      public StrColumn getPdbxSubcomponentList()
      The list of subcomponents contained in this component.
      Returns:
      StrColumn

    • getPdbxModelCoordinatesDetails

      public StrColumn getPdbxModelCoordinatesDetails()
      This data item provides additional details about the model coordinates in the component definition.
      Returns:
      StrColumn

    • getPdbxModelCoordinatesDbCode

      public StrColumn getPdbxModelCoordinatesDbCode()
      This data item identifies the PDB database code from which the heavy atom model coordinates were obtained.
      Returns:
      StrColumn

    • getPdbxIdealCoordinatesDetails

      public StrColumn getPdbxIdealCoordinatesDetails()
      This data item identifies the source of the ideal coordinates in the component definition.
      Returns:
      StrColumn

    • getPdbxIdealCoordinatesMissingFlag

      public StrColumn getPdbxIdealCoordinatesMissingFlag()
      This data item identifies if ideal coordinates are missing in this definition.
      Returns:
      StrColumn

    • getPdbxModelCoordinatesMissingFlag

      public StrColumn getPdbxModelCoordinatesMissingFlag()
      This data item identifies if model coordinates are missing in this definition.
      Returns:
      StrColumn

    • getPdbxInitialDate

      public StrColumn getPdbxInitialDate()
      Date component was added to database.
      Returns:
      StrColumn

    • getPdbxModifiedDate

      public StrColumn getPdbxModifiedDate()
      Date component was last modified.
      Returns:
      StrColumn

    • getPdbxReleaseStatus

      public StrColumn getPdbxReleaseStatus()
      This data item holds the current release status for the component.
      Returns:
      StrColumn

    • getPdbxProcessingSite

      public StrColumn getPdbxProcessingSite()
      This data item identifies the deposition site that processed this chemical component defintion.
      Returns:
      StrColumn

    • getPdbxNumberSubcomponents

      public IntColumn getPdbxNumberSubcomponents()
      The number of subcomponents represented in this component.
      Returns:
      IntColumn

    • getPdbxClass1

      public StrColumn getPdbxClass1()
      Internal classifier used to organize ligand dictionary (broad chemical class).
      Returns:
      StrColumn

    • getPdbxClass2

      public StrColumn getPdbxClass2()
      Internal classifier used to organize ligand dictionary (notable chemical features).
      Returns:
      StrColumn

    • getPdbxCompType

      public StrColumn getPdbxCompType()
      A type classification of this chemical component.
      Returns:
      StrColumn

    • getPdbxReservedName

      public StrColumn getPdbxReservedName()
      Previous chemical name used for this component if a name correction has been made.
      Returns:
      StrColumn

    • getPdbxStatus

      public StrColumn getPdbxStatus()
      Release status of component
      Returns:
      StrColumn

    • getPdbxTypeModified

      public IntColumn getPdbxTypeModified()
      Modification flag.
      Returns:
      IntColumn

    • getPdbxCasnum

      public StrColumn getPdbxCasnum()
      Chemical Abstract Service identifier.
      Returns:
      StrColumn

    • getPdbxSmiles

      public StrColumn getPdbxSmiles()
      SMILES code for component.
      Returns:
      StrColumn

    • getPdbxNscnum

      public StrColumn getPdbxNscnum()
      NSC identifier for component.
      Returns:
      StrColumn