Package org.biojava.nbio.structure.io
Class BondMaker
- java.lang.Object
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- org.biojava.nbio.structure.io.BondMaker
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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
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Field Summary
Fields Modifier and Type Field 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)
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Constructor Summary
Constructors Constructor Description BondMaker(Structure structure, FileParsingParameters params)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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 ofSSBondImpl
s parsed from a PDB/mmCIF file.void
formLinkRecordBond(PDBTemporaryStorageUtils.LinkRecord linkRecord)
Creates bond objects from a LinkRecord as parsed from a PDB filevoid
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, viaChemCompProvider
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Field Detail
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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)
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Constructor Detail
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BondMaker
public BondMaker(Structure structure, FileParsingParameters params)
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Method Detail
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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
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formDisulfideBonds
public void formDisulfideBonds(List<SSBondImpl> disulfideBonds)
Creates disulfide bond objects and references in the corresponding Atoms objects, given a list ofSSBondImpl
s parsed from a PDB/mmCIF file.- Parameters:
disulfideBonds
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formLinkRecordBond
public void formLinkRecordBond(PDBTemporaryStorageUtils.LinkRecord linkRecord)
Creates bond objects from a LinkRecord as parsed from a PDB file- Parameters:
linkRecord
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formBondsFromStructConn
public void formBondsFromStructConn(List<StructConn> structConn)
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