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The protein structure modules of BioJava.
/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
* Created on Mar. 6, 2014
*
*/
package org.biojava.nbio.structure.io;
import org.biojava.nbio.structure.*;
import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
import org.biojava.nbio.structure.io.mmcif.ChemCompProvider;
import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
import org.biojava.nbio.structure.io.mmcif.model.ChemCompBond;
import org.biojava.nbio.structure.io.mmcif.model.StructConn;
import org.biojava.nbio.structure.io.util.PDBTemporaryStorageUtils.LinkRecord;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
/**
* 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
* @author Ulysse Carion
*
*/
public class BondMaker {
private static final Logger logger = LoggerFactory.getLogger(BondMaker.class);
/**
* The types of bonds that are read from struct_conn (type specified in field conn_type_id)
*/
public static final Set BOND_TYPES_TO_PARSE;
static {
BOND_TYPES_TO_PARSE = new HashSet<>();
BOND_TYPES_TO_PARSE.add("disulf");
BOND_TYPES_TO_PARSE.add("covale");
BOND_TYPES_TO_PARSE.add("covale_base");
BOND_TYPES_TO_PARSE.add("covale_phosphate");
BOND_TYPES_TO_PARSE.add("covale_sugar");
BOND_TYPES_TO_PARSE.add("modres");
}
/**
* Maximum peptide (C - N) bond length considered for bond formation
*/
private static final double MAX_PEPTIDE_BOND_LENGTH = 1.8;
/**
* Maximum nucleotide (P - O3') bond length considered for bond formation
*/
private static final double MAX_NUCLEOTIDE_BOND_LENGTH = 2.1;
private Structure structure;
private FileParsingParameters params;
public BondMaker(Structure structure, FileParsingParameters params) {
this.structure = structure;
this.params = params;
}
/**
* 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 {@link ChemCompProvider}
*
*/
public void makeBonds() {
formPeptideBonds();
formNucleotideBonds();
formIntraResidueBonds();
trimBondLists();
}
private void formPeptideBonds() {
for (Chain chain : structure.getChains()) {
List groups = chain.getSeqResGroups();
for (int i = 0; i < groups.size() - 1; i++) {
if (!(groups.get(i) instanceof AminoAcidImpl)
|| !(groups.get(i + 1) instanceof AminoAcidImpl))
continue;
AminoAcidImpl tail = (AminoAcidImpl) groups.get(i);
AminoAcidImpl head = (AminoAcidImpl) groups.get(i + 1);
// atoms with no residue number don't have atom information
if (tail.getResidueNumber() == null
|| head.getResidueNumber() == null) {
continue;
}
Atom carboxylC;
Atom aminoN;
carboxylC = tail.getC();
aminoN = head.getN();
if (carboxylC == null || aminoN == null) {
// some structures may be incomplete and not store info
// about all of their atoms
continue;
}
if (Calc.getDistance(carboxylC, aminoN) < MAX_PEPTIDE_BOND_LENGTH) {
new BondImpl(carboxylC, aminoN, 1);
}
}
}
}
private void formNucleotideBonds() {
for (Chain chain : structure.getChains()) {
List groups = chain.getSeqResGroups();
for (int i = 0; i < groups.size() - 1; i++) {
if (!(groups.get(i) instanceof NucleotideImpl)
|| !(groups.get(i + 1) instanceof NucleotideImpl))
continue;
NucleotideImpl tail = (NucleotideImpl) groups.get(i);
NucleotideImpl head = (NucleotideImpl) groups.get(i + 1);
// atoms with no residue number don't have atom information
if (tail.getResidueNumber() == null
|| head.getResidueNumber() == null) {
continue;
}
Atom phosphorous = head.getP();
Atom oThreePrime = tail.getO3Prime();
if (phosphorous == null || oThreePrime == null) {
continue;
}
if (Calc.getDistance(phosphorous, oThreePrime) < MAX_NUCLEOTIDE_BOND_LENGTH) {
new BondImpl(phosphorous, oThreePrime, 1);
}
}
}
}
private void formIntraResidueBonds() {
for (Chain chain : structure.getChains()) {
List groups = chain.getAtomGroups();
for (Group mainGroup : groups) {
// atoms with no residue number don't have atom information
if (mainGroup.getResidueNumber() == null) {
continue;
}
// Now add support for altLocGroup
List totList = new ArrayList();
totList.add(mainGroup);
for(Group altLoc: mainGroup.getAltLocs()){
totList.add(altLoc);
}
// Now iterate through this list
for(Group group : totList){
ChemComp aminoChemComp = ChemCompGroupFactory.getChemComp(group
.getPDBName());
for (ChemCompBond chemCompBond : aminoChemComp.getBonds()) {
Atom a = group.getAtom(chemCompBond.getAtom_id_1());
Atom b = group.getAtom(chemCompBond.getAtom_id_2());
if ( a != null && b != null){
int bondOrder = chemCompBond.getNumericalBondOrder();
new BondImpl(a, b, bondOrder);
} else {
// Some of the atoms were missing. That's fine, there's
// nothing to do in this case.
}
}
}
}
}
}
private void trimBondLists() {
for (Chain chain : structure.getChains()) {
for (Group group : chain.getAtomGroups()) {
for (Atom atom : group.getAtoms()) {
if (atom.getBonds()!=null && atom.getBonds().size() > 0) {
((ArrayList) atom.getBonds()).trimToSize();
}
}
}
}
}
/**
* Creates disulfide bond objects and references in the corresponding Atoms objects, given
* a list of {@link SSBondImpl}s parsed from a PDB/mmCIF file.
* @param disulfideBonds
*/
public void formDisulfideBonds(List disulfideBonds) {
List bonds = new ArrayList<>();
for (SSBondImpl disulfideBond : disulfideBonds) {
Bond bond = formDisulfideBond(disulfideBond);
if (bond!=null) bonds.add(bond);
}
structure.setSSBonds(bonds);
}
private Bond formDisulfideBond(SSBondImpl disulfideBond) {
try {
Atom a = getAtomFromRecord("SG", "", "CYS",
disulfideBond.getChainID1(), disulfideBond.getResnum1(),
disulfideBond.getInsCode1());
Atom b = getAtomFromRecord("SG", "", "CYS",
disulfideBond.getChainID2(), disulfideBond.getResnum2(),
disulfideBond.getInsCode2());
Bond ssbond = new BondImpl(a, b, 1);
structure.addSSBond(ssbond);
return ssbond;
} catch (StructureException e) {
// Note, in Calpha only mode the CYS SG's are not present.
if (! params.isParseCAOnly()) {
logger.warn("Could not find atoms specified in SSBOND record: {}",disulfideBond.toString());
} else {
logger.debug("Could not find atoms specified in SSBOND record while parsing in parseCAonly mode.");
}
return null;
}
}
/**
* Creates bond objects from a LinkRecord as parsed from a PDB file
* @param linkRecord
*/
public void formLinkRecordBond(LinkRecord linkRecord) {
// only work with atoms that aren't alternate locations
if (linkRecord.getAltLoc1().equals(" ")
|| linkRecord.getAltLoc2().equals(" "))
return;
try {
Atom a = getAtomFromRecord(linkRecord.getName1(),
linkRecord.getAltLoc1(), linkRecord.getResName1(),
linkRecord.getChainID1(), linkRecord.getResSeq1(),
linkRecord.getiCode1());
Atom b = getAtomFromRecord(linkRecord.getName2(),
linkRecord.getAltLoc2(), linkRecord.getResName2(),
linkRecord.getChainID2(), linkRecord.getResSeq2(),
linkRecord.getiCode2());
// TODO determine what the actual bond order of this bond is; for
// now, we're assuming they're single bonds
new BondImpl(a, b, 1);
} catch (StructureException e) {
// Note, in Calpha only mode the link atoms may not be present.
if (! params.isParseCAOnly()) {
logger.warn("Could not find atoms specified in LINK record: {}",linkRecord.toString());
} else {
logger.debug("Could not find atoms specified in LINK record while parsing in parseCAonly mode.");
}
}
}
public void formBondsFromStructConn(List structConn) {
final String symop = "1_555"; // For now - accept bonds within origin asymmetric unit.
List ssbonds = new ArrayList<>();
for (StructConn conn : structConn) {
if (!BOND_TYPES_TO_PARSE.contains(conn.getConn_type_id())) continue;
String chainId1;
String chainId2;
if(params.isUseInternalChainId()){
chainId1 = conn.getPtnr1_label_asym_id();
chainId2 = conn.getPtnr2_label_asym_id();
}
else{
chainId1 = conn.getPtnr1_auth_asym_id();
chainId2 = conn.getPtnr2_auth_asym_id();
}
String insCode1 = "";
if (!conn.getPdbx_ptnr1_PDB_ins_code().equals("?")) insCode1 = conn.getPdbx_ptnr1_PDB_ins_code();
String insCode2 = "";
if (!conn.getPdbx_ptnr2_PDB_ins_code().equals("?")) insCode2 = conn.getPdbx_ptnr2_PDB_ins_code();
String seqId1 = conn.getPtnr1_auth_seq_id();
String seqId2 = conn.getPtnr2_auth_seq_id();
String resName1 = conn.getPtnr1_label_comp_id();
String resName2 = conn.getPtnr2_label_comp_id();
String atomName1 = conn.getPtnr1_label_atom_id();
String atomName2 = conn.getPtnr2_label_atom_id();
String altLoc1 = "";
if (!conn.getPdbx_ptnr1_label_alt_id().equals("?")) altLoc1 = conn.getPdbx_ptnr1_label_alt_id();
String altLoc2 = "";
if (!conn.getPdbx_ptnr2_label_alt_id().equals("?")) altLoc2 = conn.getPdbx_ptnr2_label_alt_id();
// TODO: when issue 220 is implemented, add robust symmetry handling to allow bonds between symmetry-related molecules.
if (!conn.getPtnr1_symmetry().equals(symop) || !conn.getPtnr2_symmetry().equals(symop) ) {
logger.info("Skipping bond between atoms {}(residue {}{}) and {}(residue {}{}) belonging to different symmetry partners, because it is not supported yet",
atomName1, seqId1, insCode1, atomName2, seqId2, insCode2);
continue;
}
String altLocStr1 = altLoc1.isEmpty()? "" : "(alt loc "+altLoc1+")";
String altLocStr2 = altLoc2.isEmpty()? "" : "(alt loc "+altLoc2+")";
Atom a1 = null;
Atom a2 = null;
try {
a1 = getAtomFromRecord(atomName1, altLoc1, resName1, chainId1, seqId1, insCode1);
} catch (StructureException e) {
logger.warn("Could not find atom specified in struct_conn record: {}{}({}) in chain {}, atom {} {}", seqId1, insCode1, resName1, chainId1, atomName1, altLocStr1);
continue;
}
try {
a2 = getAtomFromRecord(atomName2, altLoc2, resName2, chainId2, seqId2, insCode2);
} catch (StructureException e) {
logger.warn("Could not find atom specified in struct_conn record: {}{}({}) in chain {}, atom {} {}", seqId2, insCode2, resName2, chainId2, atomName2, altLocStr2);
continue;
}
if (a1==null) {
// we couldn't find the atom, something must be wrong with the file
logger.warn("Could not find atom {} {} from residue {}{}({}) in chain {} to create bond specified in struct_conn", atomName1, altLocStr1, seqId1, insCode1, resName1, chainId1);
continue;
}
if (a2==null) {
// we couldn't find the atom, something must be wrong with the file
logger.warn("Could not find atom {} {} from residue {}{}({}) in chain {} to create bond specified in struct_conn", atomName2, altLocStr2, seqId2, insCode2, resName2, chainId2);
continue;
}
// assuming order 1 for all bonds, no information is provided by struct_conn
Bond bond = new BondImpl(a1, a2, 1);
if (conn.getConn_type_id().equals("disulf")) {
ssbonds.add(bond);
}
}
// only for ss bonds we add a specific map in structure, all the rests are linked only from Atom.getBonds
structure.setSSBonds(ssbonds);
}
private Atom getAtomFromRecord(String name, String altLoc, String resName, String chainID, String resSeq, String iCode)
throws StructureException {
if (iCode==null || iCode.isEmpty()) {
iCode = " "; // an insertion code of ' ' is ignored
}
Chain chain = structure.getChainByPDB(chainID);
ResidueNumber resNum = new ResidueNumber(chainID, Integer.parseInt(resSeq), iCode.charAt(0));
Group group = chain.getGroupByPDB(resNum);
Group g = group;
// there is an alternate location
if (!altLoc.isEmpty()) {
g = group.getAltLocGroup(altLoc.charAt(0));
if (g==null)
throw new StructureException("Could not find altLoc code "+altLoc+" in group "+resSeq+iCode+" of chain "+ chainID);
}
return g.getAtom(name);
}
}
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