/*
* 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/
*
* Author: Daniel Asarnow
* Date: 2012-7-23
*/
package org.biojava.nbio.structure.cath;
/**
* @author Daniel Asarnow
*/
import java.io.IOException;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import org.biojava.nbio.structure.ResidueRange;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.biojava.nbio.structure.StructureIdentifier;
import org.biojava.nbio.structure.SubstructureIdentifier;
import org.biojava.nbio.structure.align.util.AtomCache;
/**
* A class which represents a single CATH domain.
*/
public class CathDomain implements Serializable, StructureIdentifier {
public static final long serialVersionUID = 1L;
/**
* The CATH domain code. Always 7 characters in length, combining the PDB and chain letter with the number of the domain within CATH.
* Example: 1aoiA00
* If the chain letter '0', domain refers to an entire PDB entry.
*/
String domainName; // 7 characters 1oaiA00
/**
* The class number of this domain.
*/
Integer classId; // C
/**
* The architecture number of this domain.
*/
Integer architectureId; // A
/**
* The topology number of this domain.
*/
Integer topologyId; // T
/**
* The homologous superfamily number of this domain.
*/
Integer homologyId; // H
/**
* The sequence family (35% identity) number of this domain.
*/
Integer sequenceFamilyId; // S
/**
* The "orthologous" sequence family (60% identity) number of this domain.
*/
Integer orthologousSequenceFamilyId; // O
/**
* The "Like" sequence family (95% identity) number of this domain.
*/
Integer likeSequenceFamilyId; // L
/**
* The identical sequence family (100% identity) number of this domain.
*/
Integer identicalSequenceFamilyId; // I
/**
* The count of this domain among the identical sequence family members.
*/
Integer domainCounter; // D
/**
* The domain length..
*/
Integer length;
/**
* The resolution of the domain structure. Nominally in Angstroms,
* the values 999.000 and 1000.000 signify NMR structures and obsolete structures, respectively.
*/
Double resolution;
/**
* The format and version of the CathDomainDescriptionFile.
*/
String format;
/**
* The CATH version.
*/
String version;
Date date;
/**
* The so-called name field holds a potentially long description of the domain.
*/
String name;
/**
* Complete source organism listing.
*/
String source;
/**
* FASTA header.
*/
String sequenceHeader;
/**
* FASTA sequence.
*/
String sequence;
/**
* List of all sub-domain segments.
*/
List<CathSegment> segments;
/**
* A (potentially long) comment. Usually empty.
*/
String comment;
public String getDomainName() {
return domainName;
}
public void setDomainName(String domainName) {
this.domainName = domainName;
}
/**
* Returns a string of the form {@code PDBID.CHAIN}.
* For example: {@code 1hiv.A}.
* @deprecated This method is poorly named; use {@link #getThePdbId()} or {@link #getPdbIdAndChain()} instead
*/
@Deprecated
public String getPdbId() {
return getPdbIdAndChain();
}
/**
* Returns the PDB ID.
*/
public String getThePdbId() {
return domainName.substring(0, 4);
}
/**
* Returns a string of the form {@code PDBID.CHAIN}.
* For example: {@code 1hiv.A}.
*/
public String getPdbIdAndChain() {
return domainName.substring(0, 4) +
(!domainName.substring(4, 5).equals("0") ? "." + domainName.substring(4, 5) : "");
}
public Integer getDomainId() {
return Integer.parseInt(domainName.substring(5));
}
public Integer getClassId() {
return classId;
}
public void setClassId(Integer classId) {
this.classId = classId;
}
public Integer getArchitectureId() {
return architectureId;
}
public void setArchitectureId(Integer architectureId) {
this.architectureId = architectureId;
}
public Integer getTopologyId() {
return topologyId;
}
public void setTopologyId(Integer topologyId) {
this.topologyId = topologyId;
}
public Integer getHomologyId() {
return homologyId;
}
public void setHomologyId(Integer homologyId) {
this.homologyId = homologyId;
}
public Integer getSequenceFamilyId() {
return sequenceFamilyId;
}
public void setSequenceFamilyId(Integer sequenceFamilyId) {
this.sequenceFamilyId = sequenceFamilyId;
}
public Integer getOrthologousSequenceFamilyId() {
return orthologousSequenceFamilyId;
}
public void setOrthologousSequenceFamilyId(Integer orthologousSequenceFamilyId) {
this.orthologousSequenceFamilyId = orthologousSequenceFamilyId;
}
public Integer getLikeSequenceFamilyId() {
return likeSequenceFamilyId;
}
public void setLikeSequenceFamilyId(Integer likeSequenceFamilyId) {
this.likeSequenceFamilyId = likeSequenceFamilyId;
}
public Integer getIdenticalSequenceFamilyId() {
return identicalSequenceFamilyId;
}
public void setIdenticalSequenceFamilyId(Integer identicalSequenceFamilyId) {
this.identicalSequenceFamilyId = identicalSequenceFamilyId;
}
public Integer getDomainCounter() {
return domainCounter;
}
public void setDomainCounter(Integer domainCounter) {
this.domainCounter = domainCounter;
}
public Integer getLength() {
return length;
}
public void setLength(Integer length) {
this.length = length;
}
public Double getResolution() {
return resolution;
}
public void setResolution(Double resolution) {
this.resolution = resolution;
}
public void setCATH(String cathCode) {
String[] token = cathCode.split("[.]");
setClassId(Integer.parseInt(token[0]));
setArchitectureId(Integer.parseInt(token[1]));
setTopologyId(Integer.parseInt(token[2]));
setHomologyId(Integer.parseInt(token[3]));
}
public String getCATH() {
return Integer.toString(getClassId()) + "." +
Integer.toString(getArchitectureId()) + "." +
Integer.toString(getTopologyId()) + "." +
Integer.toString(getHomologyId());
}
public void setSOLID(String cathCode) {
String[] token = cathCode.split("[.]");
setSequenceFamilyId(Integer.parseInt(token[0]));
setOrthologousSequenceFamilyId(Integer.parseInt(token[1]));
setLikeSequenceFamilyId(Integer.parseInt(token[2]));
setIdenticalSequenceFamilyId(Integer.parseInt(token[3]));
setDomainCounter(Integer.parseInt(token[4]));
}
public String getSOILD() {
return Integer.toString(getSequenceFamilyId()) + "." +
Integer.toString(getOrthologousSequenceFamilyId()) + "." +
Integer.toString(getLikeSequenceFamilyId()) + "." +
Integer.toString(getIdenticalSequenceFamilyId()) + "." +
Integer.toString(getDomainCounter());
}
public Integer getClassificationId(CathCategory cathCategory) {
switch (cathCategory) {
case Class:
return getClassId();
case Architecture:
return getArchitectureId();
case Topolgy:
return getTopologyId();
case Homology:
return getHomologyId();
case SequenceFamily:
return getSequenceFamilyId();
case OrthologousSequenceFamily:
return getOrthologousSequenceFamilyId();
case LikeSequenceFamily:
return getLikeSequenceFamilyId();
case IdenticalSequenceFamily:
return getIdenticalSequenceFamilyId();
case DomainCounter:
return getDomainCounter();
default:
return null;
}
}
public String getFormat() {
return format;
}
public void setFormat(String format) {
this.format = format;
}
public String getVersion() {
return version;
}
public void setVersion(String version) {
this.version = version;
}
public Date getDate() {
return date;
}
public void setDate(Date date) {
this.date = date;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public String getSource() {
return source;
}
public void setSource(String source) {
this.source = source;
}
public String getSequenceHeader() {
return sequenceHeader;
}
public void setSequenceHeader(String sequenceHeader) {
this.sequenceHeader = sequenceHeader;
}
public String getSequence() {
return sequence;
}
public void setSequence(String sequence) {
this.sequence = sequence;
}
public List<CathSegment> getSegments() {
return segments;
}
public void setSegments(List<CathSegment> segments) {
this.segments = segments;
}
public String getComment() {
return comment;
}
public void setComment(String comment) {
this.comment = comment;
}
@Override
public String toString() {
return "CathDomain [domainName=" + domainName + ", classId=" + classId
+ ", architectureId=" + architectureId + ", topologyId="
+ topologyId + ", homologyId=" + homologyId
+ ", sequenceFamilyId=" + sequenceFamilyId
+ ", orthologousSequenceFamilyId="
+ orthologousSequenceFamilyId + ", likeSequenceFamilyId="
+ likeSequenceFamilyId + ", identicalSequenceFamilyId="
+ identicalSequenceFamilyId + ", domainCounter="
+ domainCounter + ", length=" + length + ", resolution="
+ resolution + ", format=" + format + ", version=" + version
+ ", date=" + date + ", name=" + name + ", source=" + source
+ ", sequenceHeader=" + sequenceHeader + ", sequence="
+ sequence + ", segments=" + segments + ", comment=" + comment
+ "]";
}
/**
* Returns the chains this domain is defined over; contains more than 1 element only if this domains is a multi-chain domain.
*/
public Set<String> getChains() {
Set<String> chains = new HashSet<String>();
List<ResidueRange> rrs = toCanonical().getResidueRanges();
for (ResidueRange rr : rrs) chains.add(rr.getChainName());
return chains;
}
@Override
public String getIdentifier() {
return getCATH();
}
@Override
public SubstructureIdentifier toCanonical() {
List<ResidueRange> ranges = new ArrayList<ResidueRange>();
String chain = String.valueOf(getDomainName().charAt(getDomainName().length() - 3));
for (CathSegment segment : this.getSegments()) {
ranges.add(new ResidueRange(chain, segment.getStart(), segment.getStop()));
}
return new SubstructureIdentifier(getThePdbId(), ranges);
}
@Override
public Structure reduce(Structure input) throws StructureException {
return toCanonical().reduce(input);
}
@Override
public Structure loadStructure(AtomCache cache) throws StructureException,
IOException {
return cache.getStructure(getThePdbId());
}
}