Class StructConn

  • All Implemented Interfaces:
    Category

    @Generated("org.rcsb.cif.generator.SchemaGenerator")
    public class StructConn
    extends BaseCategory
    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 Detail

      • StructConn

        public StructConn​(String name,
                          int rowCount,
                          Object[] encodedColumns)
      • StructConn

        public StructConn​(String name)
    • Method Detail

      • 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