Package org.rcsb.cif.schema.mm

Class StructConn

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

  • Constructor Details

  • Method Details

    • createDelegate

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

    • getConnTypeId

      public StrColumn getConnTypeId()
      This data item is a pointer to _struct_conn_type.id in the STRUCT_CONN_TYPE category.
      Returns:
      StrColumn

    • getDetails

      public StrColumn getDetails()
      A description of special aspects of the connection.
      Returns:
      StrColumn

    • getId

      public StrColumn getId()
      The value of _struct_conn.id must uniquely identify a record in the STRUCT_CONN list. Note that this item need not be a number; it can be any unique identifier.
      Returns:
      StrColumn

    • getPtnr1LabelAltId

      public StrColumn getPtnr1LabelAltId()
      A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category.
      Returns:
      StrColumn

    • getPtnr1LabelAsymId

      public StrColumn getPtnr1LabelAsymId()
      A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPtnr1LabelAtomId

      public StrColumn getPtnr1LabelAtomId()
      A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
      Returns:
      StrColumn

    • getPtnr1LabelCompId

      public StrColumn getPtnr1LabelCompId()
      A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPtnr1LabelSeqId

      public IntColumn getPtnr1LabelSeqId()
      A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
      Returns:
      IntColumn

    • getPtnr1AuthAsymId

      public StrColumn getPtnr1AuthAsymId()
      A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPtnr1AuthAtomId

      public StrColumn getPtnr1AuthAtomId()
      A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPtnr1AuthCompId

      public StrColumn getPtnr1AuthCompId()
      A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPtnr1AuthSeqId

      public IntColumn getPtnr1AuthSeqId()
      A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
      Returns:
      IntColumn

    • getPtnr1Role

      public StrColumn getPtnr1Role()
      The chemical or structural role of the first partner in the structure connection.
      Returns:
      StrColumn

    • getPtnr1Symmetry

      public StrColumn getPtnr1Symmetry()
      Describes the symmetry operation that should be applied to the atom set specified by _struct_conn.ptnr1_label* to generate the first partner in the structure connection.
      Returns:
      StrColumn

    • getPtnr2LabelAltId

      public StrColumn getPtnr2LabelAltId()
      A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_sites_alt.id in the ATOM_SITES_ALT category.
      Returns:
      StrColumn

    • getPtnr2LabelAsymId

      public StrColumn getPtnr2LabelAsymId()
      A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPtnr2LabelAtomId

      public StrColumn getPtnr2LabelAtomId()
      A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _chem_comp_atom.atom_id in the CHEM_COMP_ATOM category.
      Returns:
      StrColumn

    • getPtnr2LabelCompId

      public StrColumn getPtnr2LabelCompId()
      A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPtnr2LabelSeqId

      public IntColumn getPtnr2LabelSeqId()
      A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
      Returns:
      IntColumn

    • getPtnr2AuthAsymId

      public StrColumn getPtnr2AuthAsymId()
      A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPtnr2AuthAtomId

      public StrColumn getPtnr2AuthAtomId()
      A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPtnr2AuthCompId

      public StrColumn getPtnr2AuthCompId()
      A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPtnr2AuthSeqId

      public IntColumn getPtnr2AuthSeqId()
      A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
      Returns:
      IntColumn

    • getPtnr2Role

      public StrColumn getPtnr2Role()
      The chemical or structural role of the second partner in the structure connection.
      Returns:
      StrColumn

    • getPtnr2Symmetry

      public StrColumn getPtnr2Symmetry()
      Describes the symmetry operation that should be applied to the atom set specified by _struct_conn.ptnr2_label* to generate the second partner in the structure connection.
      Returns:
      StrColumn

    • getPdbxPtnr1PDBInsCode

      public StrColumn getPdbxPtnr1PDBInsCode()
      A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPdbxPtnr1AuthAltId

      public StrColumn getPdbxPtnr1AuthAltId()
      A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.pdbx_auth_alt_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPdbxPtnr1LabelAltId

      public StrColumn getPdbxPtnr1LabelAltId()
      A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPdbxPtnr1StandardCompId

      public StrColumn getPdbxPtnr1StandardCompId()
      A placeholder for the standard residue name found in the MODRES record of a PDB file.
      Returns:
      StrColumn

    • getPdbxPtnr2PDBInsCode

      public StrColumn getPdbxPtnr2PDBInsCode()
      A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPdbxPtnr2AuthAltId

      public StrColumn getPdbxPtnr2AuthAltId()
      A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.pdbx_auth_alt_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPdbxPtnr2LabelAltId

      public StrColumn getPdbxPtnr2LabelAltId()
      A component of the identifier for partner 2 of the structure connection. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPdbxPtnr3AuthAltId

      public StrColumn getPdbxPtnr3AuthAltId()
      A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.pdbx_auth_alt_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPdbxPtnr3AuthAsymId

      public StrColumn getPdbxPtnr3AuthAsymId()
      A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPdbxPtnr3AuthAtomId

      public StrColumn getPdbxPtnr3AuthAtomId()
      A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPdbxPtnr3AuthCompId

      public StrColumn getPdbxPtnr3AuthCompId()
      A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPdbxPtnr3PDBInsCode

      public StrColumn getPdbxPtnr3PDBInsCode()
      A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPdbxPtnr3AuthSeqId

      public StrColumn getPdbxPtnr3AuthSeqId()
      A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPdbxPtnr3LabelAltId

      public StrColumn getPdbxPtnr3LabelAltId()
      A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPdbxPtnr3LabelAsymId

      public StrColumn getPdbxPtnr3LabelAsymId()
      A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.label_asym_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPdbxPtnr3LabelAtomId

      public StrColumn getPdbxPtnr3LabelAtomId()
      A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.label_atom_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPdbxPtnr3LabelCompId

      public StrColumn getPdbxPtnr3LabelCompId()
      A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.label_comp_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPdbxPtnr3LabelSeqId

      public IntColumn getPdbxPtnr3LabelSeqId()
      A component of the identifier for partner 1 of the structure connection. This data item is a pointer to _atom_site.label_seq_id in the ATOM_SITE category.
      Returns:
      IntColumn

    • getPdbxPDBId

      public StrColumn getPdbxPDBId()
      A placeholder for the PDB id in the case the category is used to hold the information of the MODRES record of a PDB file.
      Returns:
      StrColumn

    • getPdbxDistValue

      public FloatColumn getPdbxDistValue()
      Distance value for this contact.
      Returns:
      FloatColumn

    • getPdbxValueOrder

      public StrColumn getPdbxValueOrder()
      The chemical bond order associated with the specified atoms in this contact.
      Returns:
      StrColumn

    • getPdbxLeavingAtomFlag

      public StrColumn getPdbxLeavingAtomFlag()
      This data item identifies if the linkage has displaced leaving atoms on both, one or none of the connected atoms forming the linkage. Leaving atoms are defined within their chemical defintions of each connected component.
      Returns:
      StrColumn

    • getPdbxPtnr1ModName

      public StrColumn getPdbxPtnr1ModName()
      The abbreviation of the modifier group.
      Returns:
      StrColumn

    • getPdbxPtnr1SugarName

      public StrColumn getPdbxPtnr1SugarName()
      The abbreviation of the sugar modifier in the case it is a conformer of deoxyribose or ribose.
      Returns:
      StrColumn

    • getPdbxPtnr1ReplacedAtom

      public StrColumn getPdbxPtnr1ReplacedAtom()
      The name of the atom which got replaced by the modifier.
      Returns:
      StrColumn

    • getPdbxPtnr3AuthInsCode

      public StrColumn getPdbxPtnr3AuthInsCode()
      A component of the identifier for partner 3 of the structure connection. This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPdbxPtnr1AtomStereoConfig

      public StrColumn getPdbxPtnr1AtomStereoConfig()
      The chiral configuration of the first atom making the linkage.
      Returns:
      StrColumn

    • getPdbxPtnr1LeavingAtomId

      public StrColumn getPdbxPtnr1LeavingAtomId()
      The leaving atom that is removed from first atom making the linkage.
      Returns:
      StrColumn

    • getPdbxPtnr2AtomStereoConfig

      public StrColumn getPdbxPtnr2AtomStereoConfig()
      The chiral configuration of the second atom making the linkage.
      Returns:
      StrColumn

    • getPdbxPtnr2LeavingAtomId

      public StrColumn getPdbxPtnr2LeavingAtomId()
      The leaving atom that is removed from second atom making the linkage.
      Returns:
      StrColumn

    • getPdbxRole

      public StrColumn getPdbxRole()
      The chemical or structural role of the interaction
      Returns:
      StrColumn