Package org.rcsb.cif.schema.mm

Class PdbxValidateChiral

java.lang.Object
org.rcsb.cif.schema.DelegatingCategory
org.rcsb.cif.schema.mm.PdbxValidateChiral
All Implemented Interfaces:
Category
@Generated("org.rcsb.cif.schema.generator.SchemaGenerator")
public class PdbxValidateChiral
extends DelegatingCategory
Data items in the PDBX_VALIDATE_CHIRAL category list the residues that contain unexpected configuration of chiral centers. IMPROPER HA N C CB chirality CA IMPROPER HB1 HB2 CA CG stereo CB as this number approaches (+) or (-) 180.0, then the error in predicting the true chirality of the center increases. Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. HERE improper C---N----CA---CB done expected answer is around -120 mean -122.52 D-amino acid is +120.0

  • Constructor Details

  • Method Details

    • createDelegate

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

    • getId

      public IntColumn getId()
      The value of _pdbx_validate_chiral.id must uniquely identify each item in the PDBX_VALIDATE_CHIRAL list. This is an integer serial number.
      Returns:
      IntColumn

    • getPDBModelNum

      public IntColumn getPDBModelNum()
      The model number for the given residue This data item is a pointer to _atom_site.pdbx_PDB_model_num in the ATOM_SITE category.
      Returns:
      IntColumn

    • getAuthAsymId

      public StrColumn getAuthAsymId()
      Part of the identifier of the residue This data item is a pointer to _atom_site.auth_asym_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getAuthAtomId

      public StrColumn getAuthAtomId()
      Part of the identifier of the residue This data item is a pointer to _atom_site.auth_atom_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getLabelAltId

      public StrColumn getLabelAltId()
      Part of the identifier of the residue This data item is a pointer to _atom_site.label_alt_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getAuthCompId

      public StrColumn getAuthCompId()
      Part of the identifier of the residue This data item is a pointer to _atom_site.auth_comp_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getAuthSeqId

      public StrColumn getAuthSeqId()
      Part of the identifier of the residue This data item is a pointer to _atom_site.auth_seq_id in the ATOM_SITE category.
      Returns:
      StrColumn

    • getPDBInsCode

      public StrColumn getPDBInsCode()
      Optional identifier of the residue This data item is a pointer to _atom_site.pdbx_PDB_ins_code in the ATOM_SITE category.
      Returns:
      StrColumn

    • getOmega

      public FloatColumn getOmega()
      The value of the OMEGA angle for the peptide linkage between the two defined residues
      Returns:
      FloatColumn

    • getDetails

      public StrColumn getDetails()
      A description of the outlier angle e.g. ALPHA-CARBON
      Returns:
      StrColumn