Package org.rcsb.cif.schema.mm

Class IhmCrossLinkRestraint

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

  • Constructor Details

  • Method Details

    • createDelegate

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

    • getId

      public IntColumn getId()
      A unique identifier for the cross link record.
      Returns:
      IntColumn

    • getGroupId

      public IntColumn getGroupId()
      An identifier for a set of ambiguous cross-links. Handles implementation uncertainties related to multiple copies of subunit. This data item is a pointer to _ihm_cross_link_list.id in the IHM_CROSS_LINK_LIST category.
      Returns:
      IntColumn

    • getEntityId1

      public StrColumn getEntityId1()
      The entity identifier for the first monomer partner in the cross link This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category and the _ihm_cross_link_restraint.entity_id_1 in the IHM_CROSS_LINK_RESTRAINT category.
      Returns:
      StrColumn

    • getEntityId2

      public StrColumn getEntityId2()
      The entity identifier for the second monomer partner in the cross link This data item is a pointer to _entity_poly_seq.entity_id in the ENTITY_POLY_SEQ category and the _ihm_cross_link_restraint.entity_id_2 in the IHM_CROSS_LINK_RESTRAINT category.
      Returns:
      StrColumn

    • getAsymId1

      public StrColumn getAsymId1()
      An asym/strand identifier for the first monomer partner in the cross-link. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
      Returns:
      StrColumn

    • getAsymId2

      public StrColumn getAsymId2()
      An asym/strand identifier for the second monomer partner in the cross-link. This data item is a pointer to _struct_asym.id in the STRUCT_ASYM category.
      Returns:
      StrColumn

    • getCompId1

      public StrColumn getCompId1()
      The component identifier for the first monomer partner in the cross link. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category and the _ihm_cross_link_restraint.comp_id_1 in the IHM_CROSS_LINK_RESTRAINT category.
      Returns:
      StrColumn

    • getCompId2

      public StrColumn getCompId2()
      The component identifier for the second monomer partner in the cross link. This data item is a pointer to _entity_poly_seq.mon_id in the ENTITY_POLY_SEQ category and the _ihm_cross_link_restraint.comp_id_2 in the IHM_CROSS_LINK_RESTRAINT category.
      Returns:
      StrColumn

    • getSeqId1

      public IntColumn getSeqId1()
      The sequence index for the first monomer partner in the cross link. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category and the _ihm_cross_link_restraint.seq_id_1 in the IHM_CROSS_LINK_RESTRAINT category.
      Returns:
      IntColumn

    • getSeqId2

      public IntColumn getSeqId2()
      The sequence index for the second monomer partner in the cross link. This data item is a pointer to _entity_poly_seq.num in the ENTITY_POLY_SEQ category and the _ihm_cross_link_restraint.seq_id_2 in the IHM_CROSS_LINK_RESTRAINT category.
      Returns:
      IntColumn

    • getAtomId1

      public StrColumn getAtomId1()
      The atom identifier for the first monomer partner in the cross link. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
      Returns:
      StrColumn

    • getAtomId2

      public StrColumn getAtomId2()
      The atom identifier for the second monomer partner in the cross link. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
      Returns:
      StrColumn

    • getRestraintType

      public StrColumn getRestraintType()
      The type of the cross link restraint applied.
      Returns:
      StrColumn

    • getConditionalCrosslinkFlag

      public StrColumn getConditionalCrosslinkFlag()
      The cross link conditionality.
      Returns:
      StrColumn

    • getModelGranularity

      public StrColumn getModelGranularity()
      The coarse-graining information for the crosslink implementation.
      Returns:
      StrColumn

    • getDistanceThreshold

      public FloatColumn getDistanceThreshold()
      The distance threshold applied to this crosslink in the integrative modeling task.
      Returns:
      FloatColumn

    • getPsi

      public FloatColumn getPsi()
      The uncertainty in the crosslinking experimental data; may be approximated to the false positive rate.
      Returns:
      FloatColumn

    • getSigma1

      public FloatColumn getSigma1()
      The uncertainty in the position of residue 1 in the crosslink arising due to the multi-scale nature of the model represention.
      Returns:
      FloatColumn

    • getSigma2

      public FloatColumn getSigma2()
      The uncertainty in the position of residue 2 in the crosslink arising due to the multi-scale nature of the model represention.
      Returns:
      FloatColumn

    • getPseudoSiteFlag

      public StrColumn getPseudoSiteFlag()
      A flag indicating if the cross link involves a pseudo site that is not part of the model representation and hence will not be part of the model. However, it can be part of the input restraints.
      Returns:
      StrColumn