org.biojava.bio.program.sax.PdbSAXParser Maven / Gradle / Ivy
/*
* 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/
*
*/
package org.biojava.bio.program.sax;
import java.io.BufferedReader;
import java.io.IOException;
import java.util.ArrayList;
import org.xml.sax.Attributes;
import org.xml.sax.InputSource;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.AttributesImpl;
/**
* A SAX2 parser for dealing with native PDB files. That is,
* this class allows native PDB format files to be processed
* as if they were in PdbXML format, but without an interconversion
* step. That is, events are generated that call methods
* on an XML document handler.
*
* Note this code is experimental, and may change without notice.
*
*
*
*
* Copyright © 2000 - 2002 Cambridge Antibody Technology.
*
*
* Primary author -
* - Simon Brocklehurst (CAT)
*
* Other authors -
* - Neil Benn (CAT)
*
- Derek Crockford (CAT)
*
- Tim Dilks (CAT)
*
- Colin Hardman (CAT)
*
- Stuart Johnston (CAT)
*
*
*
* @author Cambridge Antibody Technology (CAT)
* @author Greg Cox
* @version 0.8
*
*/
public class PdbSAXParser extends AbstractNativeAppSAXParser {
private ArrayList oRecordList = new ArrayList();
private String oRecord;
private int iPos;
private int iModelStart;
private int iModelStop;
private AttributesImpl oAtts = new AttributesImpl();
private QName oAttQName = new QName(this);
/**
* Sets namespace prefix to "biojava"
*/
public PdbSAXParser() {
this.setNamespacePrefix("biojava");
}
public void parse (String poURI) throws IOException,SAXException {
this.parse(new InputSource(poURI));
}
/**
* Describe 'parse' method here.
*
* @param poSource -
*/
public void parse(InputSource poSource )
throws IOException,SAXException {
BufferedReader oContents;
String oLine = null;
//Use method form superclass
oContents = this.getContentStream(poSource);
try {
// loop over file
oLine = oContents.readLine();
while (oLine != null) {
String oPadLine = this.padLine(oLine);
// put padded line into ArrayList
oRecordList.add(oPadLine);
//System.out.println(oLine);
oLine = oContents.readLine();
} // end while
//-----------------------
//At this point, have the entire raw file in core memory.
//Now parse it and fire of relevant events
//First preprocess file
//Rule
//If there are no model records, then insert records
//for a single model. MODEL record before first ATOM,
//ENDMDL and before, CONECT, MASTER, END
boolean tIsModel = false;
for (int i = 0; i < oRecordList.size(); i++) {
oRecord = (String)oRecordList.get(i);
if (oRecord.startsWith("MODEL")) {
tIsModel = true;
break;
}
}
boolean tFoundFirstAtom = false;
if (!tIsModel) {
//System.out.println("No MODEL records");
for (int i = 0; i < oRecordList.size(); i++) {
oRecord = (String)oRecordList.get(i);
if ( ((oRecord.startsWith("ATOM ")) ||
(oRecord.startsWith("HETATM"))) &&
(!tFoundFirstAtom)) {
tFoundFirstAtom = true;
//System.out.println("Found first atom>"+i+"<");
oRecordList.add(i,"MODEL 1");
break;
}
}
boolean tFoundLastAtom = false;
for (int i = oRecordList.size() - 1; i > 0; i--) {
oRecord = (String)oRecordList.get(i);
if ( ((oRecord.startsWith("ATOM ")) ||
(oRecord.startsWith("HETATM")) ||
(oRecord.startsWith("TER") )) &&
(!tFoundLastAtom)) {
tFoundLastAtom = true;
//System.out.println("Found last atom>"+i+"<");
oRecordList.add(i+1,"ENDMDL");
break;
}
}
} //end if tIsModel == false
//End preprocess file
//At this point, the PDB records should be
//in a suitable state for parsing...
oAtts.clear();
this.startElement(new QName(this,
this.prefix("MolecularStructureList")),
(Attributes)oAtts);
//Start at beginning of RecordList and progress
//through to end using global iPos variable
//to keep track of position
iPos = 0;
//keep track of start pos of model -
//need this for multiple passes through
//to get protein, dna, solvent etc.
iModelStart = 0;
iModelStop = 0;
String oModelId;
String oStructureId;
while (iPos < oRecordList.size()) {
//System.out.println("Line: "+iPos);
oRecord = (String)oRecordList.get(iPos);
if (oRecord.startsWith("HEADER")) {
oStructureId = oRecord.substring(62,66).trim();
System.out.println(oStructureId);
oAtts.clear();
oAttQName.setQName("id");
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"CDATA",oStructureId);
//TODO EMPTY ELEMENT
this.startElement(new QName(this,this.prefix("PdbCode")),
(Attributes)oAtts);
this.endElement(new QName(this,this.prefix("PdbCode")));
}
if (oRecord.startsWith("MODEL")) {
iModelStart = iPos;
oModelId = oRecord.substring(10,14).trim();
oAtts.clear();
oAttQName.setQName("modelId");
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"CDATA",oModelId);
this.startElement(new QName(this,this.prefix("MolecularStructure")),
(Attributes)oAtts);
}
if (oRecord.startsWith("ENDMDL")) {
//keep position of the end of this model
iModelStop = iPos;
//at this point have start and end positions
//of current model
//do multiple passes for each type of molecule
//parse protein for this model...
oAtts.clear();
this.startElement(new QName(this,this.prefix("Protein")),
(Attributes)oAtts);
oAtts.clear();
this.startElement(new QName(this,
this.prefix("ProteinChainList")),
(Attributes)oAtts);
this.parseProtein(iModelStart,iModelStop);
//close final Atom Residue and ProteinChain
this.endElement(new QName(this,this.prefix("Atom")));
this.endElement(
new QName(this,this.prefix("AminoAcidResidue")));
this.endElement(new QName(this,
this.prefix("ProteinChain")));
this.endElement(new QName(this,
this.prefix("ProteinChainList")));
//todo parse solvent, dna etc.
//having parsed all content, end model
this.endElement(new QName(this,this.prefix("MolecularStructure")));
}
iPos++;
}
this.endElement(new QName(this,
this.prefix("MolecularStructureList")));
//System.out.println("Finished parsing");
} catch (java.io.IOException x) {
System.out.println(x.getMessage());
System.out.println("File read interupted");
} // end try/catch
}
//==================================================================
//private methods
//==================================================================
/**
* Parse protein content of pdb output
*
* @param nil -
*/
private void parseProtein(int piStart, int piStop)
throws SAXException {
String oChainId;
String oAtomId;
String oAtomType;
String oResidueId;
String oResidueType;
String oX;
String oY;
String oZ;
String oOccupancy;
String oTemperatureFactor;
String oElement;
String oCurrentChainId;
String oCurrentResidueId;
boolean tFirstChain = true;
boolean tFirstResidue = true;
oCurrentChainId="XXX"; //set as an impossible initial value
oCurrentResidueId="A*ZZ**"; //set as an impossible initial value
for (int i = piStart; i < piStop; i++) {
oRecord = (String)oRecordList.get(i);
//System.out.println("parsing protein>" + oRecord);
if ( (oRecord.startsWith("ATOM ")) ||
(oRecord.startsWith("HETATM")) ) {
//System.out.println(">"+oRecord.substring(17,20)+"<");
oAtomId = oRecord.substring(6,11).trim();
oAtomType = oRecord.substring(12,16).trim();
oResidueType = oRecord.substring(17,20).trim();
//go straight to next atom if this one not protein
if (!checkIfProtein(oResidueType)) continue;
//assign varables from ATOM record
oChainId = oRecord.substring(21,23).trim();
oResidueId = oRecord.substring(23,27).trim();
oX = oRecord.substring(30,38).trim();
oY = oRecord.substring(38,46).trim();
oZ = oRecord.substring(46,54).trim();
oOccupancy = oRecord.substring(54,60).trim();
oTemperatureFactor = oRecord.substring(60,66).trim();
oElement = oRecord.substring(76,78).trim();
//check new residue event
if (!oResidueId.equals(oCurrentResidueId)) {
if (!tFirstResidue) {
this.endElement(new QName(this,
this.prefix("AminoAcidResidue")));
}
if (!oChainId.equals(oCurrentChainId)) {
if (!tFirstChain) {
this.endElement(new QName(this,
this.prefix("ProteinChain")));
}
//check new chain event
oAtts.clear();
oAttQName.setQName("chainId");
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"CDATA",oChainId);
this.startElement(new QName(this,
this.prefix("ProteinChain")),
(Attributes)oAtts);
tFirstChain = false; //a bit ugly to set all the time.
oCurrentChainId = oChainId;
}
oAtts.clear();
oAttQName.setQName("residueId");
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"CDATA",oResidueId);
oAttQName.setQName("residueType");
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"CDATA",oResidueType);
this.startElement(
new QName(this,this.prefix("AminoAcidResidue")),
(Attributes)oAtts);
tFirstResidue = false; //a bit ugly to set all the time.
oCurrentResidueId = oResidueId;
}
//finally fire new atom-related events
oAtts.clear();
oAttQName.setQName("atomId");
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"CDATA",oAtomId);
oAttQName.setQName("atomType");
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"CDATA",oAtomType);
if ( ! oElement.equals("") ) {
oAttQName.setQName("element");
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"CDATA", oElement);
}
oAttQName.setQName("occupancy");
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"CDATA",oOccupancy);
oAttQName.setQName("temperatureFactor");
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"CDATA", oTemperatureFactor);
this.startElement(new QName(this,this.prefix("Atom")),
(Attributes)oAtts);
oAtts.clear();
oAttQName.setQName("x");
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"CDATA",oX);
oAttQName.setQName("y");
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"CDATA",oY);
oAttQName.setQName("z");
oAtts.addAttribute(oAttQName.getURI(),
oAttQName.getLocalName(),
oAttQName.getQName(),
"CDATA",oZ);
this.startElement(new QName(this,this.prefix("Coordinates")),
(Attributes)oAtts);
this.endElement(new QName(this,this.prefix("Coordinates")));
this.endElement(new QName(this,this.prefix("Atom")));
}
}
}
/**
* Checks to see if a given residue type is part of a protein.
* NB at the moment, this doesn't work - just returns true.
* FIX THIS
*
* @param poResType Three-letter residue code
* @return boolean Returns true if a protein, false if not.
*/
private boolean checkIfProtein(String poResType) {
return true;
}
/**
* Takes a a line. If shorted that 80 characters
* returns a new version of the line, with spaces
* appended so that it is 80 characers.
*
* @param poLine a String value
* @return a String value
*/
private String padLine(String poLine) {
int iLength = poLine.length();
int iDesiredLength = 80;
char cPadChar = ' ';
//do nothing if line length more than or equals to 80
if (iLength >= 80) {
return poLine;
}
//else pad with spaces
//System.out.println("Length: " + poLine.length());
StringBuffer oBuff = new StringBuffer(poLine);
int iInsertLength = iDesiredLength - iLength;
char[] aoInsert = new char[iInsertLength];
// System.out.println("Insert Length: " + iInsertLength);
for (int i = 0; i < iInsertLength; i++) {
aoInsert[i] = cPadChar;
}
oBuff.append(aoInsert);
return oBuff.substring(0);
}
}