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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 12.03.2004
* @author Andreas Prlic
*
*/
package org.biojava.nbio.structure;
import org.biojava.nbio.structure.io.FileConvert;
import org.biojava.nbio.structure.io.mmcif.ChemCompGroupFactory;
import org.biojava.nbio.structure.io.mmcif.chem.PolymerType;
import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.template.Sequence;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.Serializable;
import java.util.*;
/**
* A Chain in a PDB file. It contains several groups which can be of
* one of the types defined in the {@link GroupType} constants.
*
* @author Andreas Prlic
* @author Jules Jacobsen
* @since 1.4
*/
public class ChainImpl implements Chain, Serializable {
private final static Logger logger = LoggerFactory.getLogger(ChainImpl.class);
private static final long serialVersionUID = 1990171805277911840L;
/**
* The default chain identifier used to be an empty space
*/
public static String DEFAULT_CHAIN_ID = "A";
private String swissprot_id ;
private String chainID ; // the chain identifier as in PDB files
private List groups;
private List seqResGroups;
private Long id;
private EntityInfo mol;
private Structure parent;
private Map pdbResnumMap;
private String internalChainID; // the chain identifier used in mmCIF files
private List seqMisMatches = null;
/**
* Constructs a ChainImpl object.
*/
public ChainImpl() {
super();
chainID = DEFAULT_CHAIN_ID;
groups = new ArrayList() ;
seqResGroups = new ArrayList();
pdbResnumMap = new HashMap();
internalChainID = null;
}
/** {@inheritDoc}
*
*/
@Override
public Long getId() {
return id;
}
/** {@inheritDoc}
*
*/
@Override
public void setId(Long id) {
this.id = id;
}
/** {@inheritDoc}
*
*/
@Override
@Deprecated
public void setParent(Structure parent) {
setStructure(parent);
}
/** {@inheritDoc}
*
*/
@Override
public void setStructure(Structure parent){
this.parent = parent;
}
/** Returns the parent Structure of this chain.
*
* @return the parent Structure object
*/
@Override
public Structure getStructure() {
return parent;
}
/** Returns the parent Structure of this chain.
*
* @return the parent Structure object
* @deprecated use getStructure instead.
*/
@Override
@Deprecated
public Structure getParent() {
return getStructure();
}
/** Returns an identical copy of this Chain .
* @return an identical copy of this Chain
*/
@Override
public Object clone() {
// go through all groups and add to new Chain.
ChainImpl n = new ChainImpl();
// copy chain data:
n.setChainID( getChainID());
n.setSwissprotId ( getSwissprotId());
// NOTE the EntityInfo will be reset at the parent level (Structure) if cloning is happening from parent level
// here we don't deep-copy it and just keep the same reference, in case the cloning is happening at the Chain level only
n.setEntityInfo(this.mol);
n.setInternalChainID(internalChainID);
for (Group group : groups) {
Group g = (Group) group.clone();
n.addGroup(g);
g.setChain(n);
}
if (seqResGroups!=null){
List tmpSeqRes = new ArrayList();
// cloning seqres and atom groups is ugly, due to their
// nested relationship (some of the atoms can be in the seqres, but not all)
for (Group seqResGroup : seqResGroups) {
int i = findMathingGroupIndex(groups, seqResGroup);
Group g = null;
if (i!=-1) {
// group found in atom groups, we get the equivalent reference from the newly cloned atom groups
g = n.getAtomGroup(i);
} else {
// group not found in atom groups, we clone the seqres group
g = (Group) seqResGroup.clone();
}
g.setChain(n);
tmpSeqRes.add(g);
}
n.setSeqResGroups(tmpSeqRes);
}
return n ;
}
private static int findMathingGroupIndex(List atomGroups, Group g) {
int i = 0;
for (Group atomGroup: atomGroups) {
if (g==atomGroup) return i;
i++;
}
return -1;
}
/** {@inheritDoc}
*
*/
@Override
public void setEntityInfo(EntityInfo mol) {
this.mol = mol;
}
/** {@inheritDoc}
*
*/
@Override
public EntityInfo getEntityInfo() {
return this.mol;
}
/** set the Swissprot id of this chains .
* @param sp_id a String specifying the swissprot id value
* @see #getSwissprotId
*/
@Override
public void setSwissprotId(String sp_id){
swissprot_id = sp_id ;
}
/** get the Swissprot id of this chains .
* @return a String representing the swissprot id value
* @see #setSwissprotId
*/
@Override
public String getSwissprotId() {
return swissprot_id ;
}
/** {@inheritDoc}
*
*/
@Override
public void addGroup(Group group) {
group.setChain(this);
// Set the altlocs chain as well
for(Group g : group.getAltLocs()) {
g.setChain(this);
}
groups.add(group);
// store the position internally for quick access of this group
String pdbResnum = null ;
ResidueNumber resNum = group.getResidueNumber();
if ( resNum != null)
pdbResnum = resNum.toString();
if ( pdbResnum != null) {
Integer pos = groups.size() - 1;
// ARGH sometimes numbering in PDB files is confusing.
// e.g. PDB: 1sfe
/*
* ATOM 620 N GLY 93 -24.320 -6.591 4.210 1.00 46.82 N
* ATOM 621 CA GLY 93 -24.960 -6.849 5.497 1.00 47.35 C
* ATOM 622 C GLY 93 -26.076 -5.873 5.804 1.00 47.24 C
* ATOM 623 O GLY 93 -26.382 -4.986 5.006 1.00 47.56 O
* and ...
* HETATM 1348 O HOH 92 -21.853 -16.886 19.138 1.00 66.92 O
* HETATM 1349 O HOH 93 -26.126 1.226 29.069 1.00 71.69 O
* HETATM 1350 O HOH 94 -22.250 -18.060 -6.401 1.00 61.97 O
*/
// this check is to give in this case the entry priority that is an AminoAcid / comes first...
// a good example of same residue number for 2 residues is 3th3, chain T, residue 201 (a LYS and a sugar BGC covalently attached to it) - JD 2016-03-09
if ( pdbResnumMap.containsKey(pdbResnum)) {
logger.warn("Adding residue {}({}) to chain {} but a residue with same residue number is already present: {}({}). Will add only the aminoacid residue (if any) to the lookup, lookups for that residue number won't work properly.",
pdbResnum, group.getPDBName(), getChainID(), groups.get(pdbResnumMap.get(pdbResnum)).getResidueNumber(), groups.get(pdbResnumMap.get(pdbResnum)).getPDBName());
if ( group instanceof AminoAcid)
pdbResnumMap.put(pdbResnum,pos);
} else
pdbResnumMap.put(pdbResnum,pos);
}
}
/**
* {@inheritDoc}
*/
@Override
public Group getAtomGroup(int position) {
return groups.get(position);
}
/**
* {@inheritDoc}
*/
@Override
public List getAtomGroups(GroupType type){
List tmp = new ArrayList() ;
for (Group g : groups) {
if (g.getType().equals(type)) {
tmp.add(g);
}
}
return tmp ;
}
/** {@inheritDoc}
*
*/
@Override
public List getAtomGroups(){
return groups ;
}
/** {@inheritDoc}
*
*/
@Override
public void setAtomGroups(List groups){
for (Group g:groups){
g.setChain(this);
}
this.groups = groups;
}
@Override
@Deprecated // TODO dmyersturnbull: why is this deprecated if it's declared in Chain?
public Group[] getGroupsByPDB(ResidueNumber start, ResidueNumber end, boolean ignoreMissing)
throws StructureException {
if (! ignoreMissing )
return getGroupsByPDB(start, end);
List retlst = new ArrayList();
String pdbresnumStart = start.toString();
String pdbresnumEnd = end.toString();
int startPos = Integer.MIN_VALUE;
int endPos = Integer.MAX_VALUE;
startPos = start.getSeqNum();
endPos = end.getSeqNum();
boolean adding = false;
boolean foundStart = false;
for (Group g: groups){
if ( g.getResidueNumber().toString().equals(pdbresnumStart)) {
adding = true;
foundStart = true;
}
if ( ! (foundStart && adding) ) {
int pos = g.getResidueNumber().getSeqNum();
if ( pos >= startPos) {
foundStart = true;
adding = true;
}
}
if ( adding)
retlst.add(g);
if ( g.getResidueNumber().toString().equals(pdbresnumEnd)) {
if ( ! adding)
throw new StructureException("did not find start PDB residue number " + pdbresnumStart + " in chain " + chainID);
adding = false;
break;
}
if (adding){
int pos = g.getResidueNumber().getSeqNum();
if (pos >= endPos) {
adding = false;
break;
}
}
}
if ( ! foundStart){
throw new StructureException("did not find start PDB residue number " + pdbresnumStart + " in chain " + chainID);
}
//not checking if the end has been found in this case...
return retlst.toArray(new Group[retlst.size()] );
}
/**
* {@inheritDoc}
*
*/
@Override
public Group getGroupByPDB(ResidueNumber resNum) throws StructureException {
String pdbresnum = resNum.toString();
if ( pdbResnumMap.containsKey(pdbresnum)) {
Integer pos = pdbResnumMap.get(pdbresnum);
return groups.get(pos);
} else {
throw new StructureException("unknown PDB residue number " + pdbresnum + " in chain " + chainID);
}
}
/**
* {@inheritDoc}
*
*/
@Override
public Group[] getGroupsByPDB(ResidueNumber start, ResidueNumber end)
throws StructureException {
String pdbresnumStart = start.toString();
String pdbresnumEnd = end.toString();
List retlst = new ArrayList();
Iterator iter = groups.iterator();
boolean adding = false;
boolean foundStart = false;
while ( iter.hasNext()){
Group g = iter.next();
if ( g.getResidueNumber().toString().equals(pdbresnumStart)) {
adding = true;
foundStart = true;
}
if ( adding)
retlst.add(g);
if ( g.getResidueNumber().toString().equals(pdbresnumEnd)) {
if ( ! adding)
throw new StructureException("did not find start PDB residue number " + pdbresnumStart + " in chain " + chainID);
adding = false;
break;
}
}
if ( ! foundStart){
throw new StructureException("did not find start PDB residue number " + pdbresnumStart + " in chain " + chainID);
}
if ( adding) {
throw new StructureException("did not find end PDB residue number " + pdbresnumEnd + " in chain " + chainID);
}
return retlst.toArray(new Group[retlst.size()] );
}
/**
* {@inheritDoc}
*/
@Override
public int getSeqResLength() {
//new method returns the length of the sequence defined in the SEQRES records
return seqResGroups.size();
}
/**
* {@inheritDoc}
*/
@Override
public void setChainID(String nam) { chainID = nam; }
/**
* {@inheritDoc}
*/
@Override
public String getChainID() { return chainID; }
/** String representation.
* @return String representation of the Chain
*/
@Override
public String toString(){
String newline = System.getProperty("line.separator");
StringBuilder str = new StringBuilder();
str.append("Chain >").append(getChainID()).append("<").append(newline);
if ( mol != null ){
if ( mol.getDescription() != null){
str.append(mol.getDescription()).append(newline);
}
}
str.append("total SEQRES length: ").append(getSeqResGroups().size()).append(" total ATOM length:")
.append(getAtomLength()).append(" residues ").append(newline);
return str.toString() ;
}
/**
* {@inheritDoc}
*/
@Override
public Sequence getBJSequence() {
String seq = getSeqResSequence();
Sequence s = null;
try {
s = new ProteinSequence(seq);
} catch (CompoundNotFoundException e) {
logger.error("Could not create sequence object from seqres sequence. Some unknown compound: {}",e.getMessage());
}
//TODO: return a DNA sequence if the content is DNA...
return s;
}
/**
* {@inheritDoc}
*/
@Override
public String getAtomSequence(){
List groups = getAtomGroups();
StringBuilder sequence = new StringBuilder() ;
for ( Group g: groups){
ChemComp cc = g.getChemComp();
if ( PolymerType.PROTEIN_ONLY.contains(cc.getPolymerType()) ||
PolymerType.POLYNUCLEOTIDE_ONLY.contains(cc.getPolymerType())){
// an amino acid residue.. use for alignment
String oneLetter= ChemCompGroupFactory.getOneLetterCode(cc);
if ( oneLetter == null)
oneLetter = Character.toString(StructureTools.UNKNOWN_GROUP_LABEL);
sequence.append(oneLetter);
}
}
return sequence.toString();
}
/**
* {@inheritDoc}
*/
@Override
public String getSeqResSequence(){
StringBuilder str = new StringBuilder();
for (Group g : seqResGroups) {
ChemComp cc = g.getChemComp();
if ( cc == null) {
logger.warn("Could not load ChemComp for group: ", g);
str.append(StructureTools.UNKNOWN_GROUP_LABEL);
} else if ( PolymerType.PROTEIN_ONLY.contains(cc.getPolymerType()) ||
PolymerType.POLYNUCLEOTIDE_ONLY.contains(cc.getPolymerType())){
// an amino acid residue.. use for alignment
String oneLetter= ChemCompGroupFactory.getOneLetterCode(cc);
if ( oneLetter == null || oneLetter.isEmpty() || oneLetter.equals("?"))
oneLetter = Character.toString(StructureTools.UNKNOWN_GROUP_LABEL);
str.append(oneLetter);
} else {
str.append(StructureTools.UNKNOWN_GROUP_LABEL);
}
}
return str.toString();
}
/**
* {@inheritDoc}
*/
@Override
public Group getSeqResGroup(int position) {
return seqResGroups.get(position);
}
/**
* {@inheritDoc}
*/
@Override
public List getSeqResGroups(GroupType type) {
List tmp = new ArrayList() ;
for (Group g : seqResGroups) {
if (g.getType().equals(type)) {
tmp.add(g);
}
}
return tmp ;
}
/** {@inheritDoc}
*
*/
@Override
public List getSeqResGroups() {
return seqResGroups;
}
/** {@inheritDoc}
*
*/
@Override
public void setSeqResGroups(List groups){
for (Group g: groups){
g.setChain(this);
}
this.seqResGroups = groups;
}
protected void addSeqResGroup(Group g){
seqResGroups.add(g);
}
/** {@inheritDoc}
*
*/
@Override
public int getAtomLength() {
return groups.size();
}
/** {@inheritDoc}
*
*/
@Override
public List getAtomLigands(){
List ligands = new ArrayList();
for (Group g : groups)
if (!seqResGroups.contains(g) && !g.isWater())
ligands.add(g);
return ligands;
}
@Override
public String getInternalChainID() {
return internalChainID;
}
@Override
public void setInternalChainID(String internalChainID) {
this.internalChainID = internalChainID;
}
@Override
public String toPDB() {
return FileConvert.toPDB(this);
}
@Override
public String toMMCIF() {
return FileConvert.toMMCIF(this, true);
}
@Override
public void setSeqMisMatches(List seqMisMatches) {
this.seqMisMatches = seqMisMatches;
}
@Override
public List getSeqMisMatches() {
return seqMisMatches;
}
}
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