Package org.biojava.nbio.structure.io

Class BondMaker

java.lang.Object
org.biojava.nbio.structure.io.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.
Author:
Peter Rose, Ulysse Carion

  • Field Details

    • BOND_TYPES_TO_PARSE

      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)

  • Constructor Details

  • Method Details

    • 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

    • formDisulfideBonds

      public void formDisulfideBonds(List<SSBondImpl> disulfideBonds)
      Creates disulfide bond objects and references in the corresponding Atoms objects, given a list of SSBondImpls parsed from a PDB/mmCIF file.
      Parameters:
      disulfideBonds -

    • formLinkRecordBond

      public void formLinkRecordBond(PDBTemporaryStorageUtils.LinkRecord linkRecord)
      Creates bond objects from a LinkRecord as parsed from a PDB file
      Parameters:
      linkRecord -

    • formBondsFromStructConn

      public void formBondsFromStructConn(List<StructConn> structConn)