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 Summary

Fields

Modifier and Type	Field and Description
static Set<String>	BOND_TYPES_TO_PARSE The types of bonds that are read from struct_conn (type specified in field conn_type_id)

Constructor Summary

Constructors

Constructor and Description
BondMaker(Structure structure, FileParsingParameters params)

Method Summary

Modifier and Type	Method and Description
void	formBondsFromStructConn(List<StructConn> structConn)
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.
void	formLinkRecordBond(PDBTemporaryStorageUtils.LinkRecord linkRecord) Creates bond objects from a LinkRecord as parsed from a PDB file
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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

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 Detail

BondMaker

public BondMaker(Structure structure,
                 FileParsingParameters params)

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

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)