Class BondMaker

  • public class BondMaker
    extends Object
    Adds polymer bonds for peptides and nucleotides based on distance cutoffs and intra-group (residue) bonds based on data from the Chemical Component Dictionary to the Structure object. TODO the current implementation adds bonds to the first model only. This should be sufficient for homogeneous models, but here are a few inhomogeneous models in the PDB. A better handling of models should be considered in the future.
    Peter Rose, Ulysse Carion
    • Field Detail


        public static final Set<String> BOND_TYPES_TO_PARSE
        The types of bonds that are read from struct_conn (type specified in field conn_type_id)
    • Method Detail

      • makeBonds

        public void makeBonds()
        Creates bond objects and corresponding references in Atom objects:
      • peptide bonds: inferred from sequence and distances
      • nucleotide bonds: inferred from sequence and distances
      • intra-group (residue) bonds: read from the chemical component dictionary, via ChemCompProvider