/*
* 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.nbio.structure.secstruc;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import org.biojava.nbio.structure.Group;
import org.biojava.nbio.structure.ResidueNumber;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.StructureException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Class to parse a DSSP file (output of the DSSP program),
* that contains the secondary structure assignment of a structure.
* <p>
* This class has been ported from the OWL Java library for
* Structural Bioinformatics (https://github.com/eppic-team/owl).
* <p>
* As of September 2015, the DSSP source code and executables can
* be downloaded from http://swift.cmbi.ru.nl/gv/dssp/.
*
* @author Aleix Lafita
* @since 4.1.1
*
*/
public class DSSPParser {
private static final Logger logger =
LoggerFactory.getLogger(DSSPParser.class);
/**
* Parse a DSSP output file and return the secondary structure
* annotation as a List of {@link SecStrucState} objects.
*
* @param dsspPath path to the DSSP file to parse
* @param structure Structure object associated to the dssp
* @param assign assigns the SS to the structure if true
* @return a List of SS annotation objects
* @throws StructureException
* @throws IOException
*/
public static List<SecStrucState> parseFile(String dsspPath,
Structure structure, boolean assign)
throws IOException, StructureException {
File file = new File(dsspPath);
Reader read = new FileReader(file);
BufferedReader reader = new BufferedReader(read);
return generalParse(reader, structure, assign);
}
/**
* Fetch and parse the DSSP file of the specified pdb code
* from the PDB web server and return the secondary structure
* annotation as a List of {@link SecStrucState} objects.
*
* @param pdb path to the DSSP file to parse
* @param structure Structure object associated to the dssp
* @param assign assigns the SS to the structure if true
* @return a List of SS annotation objects
* @throws StructureException
* @throws IOException
*/
public static List<SecStrucState> fetch(String pdb,
Structure structure, boolean assign)
throws IOException, StructureException {
InputStream in = new URL("http://www.rcsb.org/pdb/files/"+
pdb+".dssp").openStream();
Reader read = new InputStreamReader(in);
BufferedReader reader = new BufferedReader(read);
return generalParse(reader, structure, assign);
}
/**
* Parse a DSSP format String and return the secondary structure
* annotation as a List of {@link SecStrucState} objects.
*
* @param dsspOut String with the DSSP output to parse
* @param structure Structure object associated to the dssp
* @param assign assigns the SS to the structure if true
* @return a List of SS annotation objects
* @throws StructureException
* @throws IOException
*/
public static List<SecStrucState> parseString(String dsspOut,
Structure structure, boolean assign)
throws IOException, StructureException {
Reader read = new StringReader(dsspOut);
BufferedReader reader = new BufferedReader(read);
return generalParse(reader, structure, assign);
}
private static List<SecStrucState> generalParse(BufferedReader reader,
Structure structure, boolean assign)
throws IOException, StructureException {
String startLine = " # RESIDUE AA STRUCTURE BP1 BP2 ACC";
String line;
List<SecStrucState> secstruc = new ArrayList<SecStrucState>();
//Find the first line of the DSSP output
while((line = reader.readLine()) != null) {
if(line.startsWith(startLine)) break;
}
while((line = reader.readLine()) != null) {
String indexStr = line.substring(0,5).trim();
String resNumStr = line.substring(5,10).trim();
//Only happens if dssp inserts a line indicating a chain break
if(!resNumStr.equals("")) {
int index = Integer.parseInt(indexStr);
//Get the group of the structure corresponding to the residue
int resNum = Integer.parseInt(resNumStr);
char insCode = line.charAt(10);
String chainId = line.substring(11,13).trim();
ResidueNumber r = new ResidueNumber(chainId, resNum, insCode);
Group parent = structure.getPolyChainByPDB(chainId)
.getGroupByPDB(r);
SecStrucType ssType =
SecStrucType.fromCharacter(line.charAt(16));
SecStrucState ss = new SecStrucState(parent,
SecStrucInfo.DSSP_ASSIGNMENT, ssType);
//Parse the Bridge partners - TODO parallel or antiparallel?
String bp = line.substring(25,29).trim();
if (bp != "") {
BetaBridge bb = new BetaBridge(
index, Integer.valueOf(bp), BridgeType.parallel);
ss.addBridge(bb);
} else logger.warn("Unable to parse beta Bridge for resn "+index);
bp = line.substring(29,33).trim();
if (bp != "") {
BetaBridge bb = new BetaBridge(
index, Integer.valueOf(bp), BridgeType.parallel);
ss.addBridge(bb);
} else logger.warn("Unable to parse beta Bridge for resn "+index);
//Parse the energy terms of donor and acceptor
for (int i=0; i<4; i++){
int a = 42 + i*11;
int b = a + 8;
String val = line.substring(a,b).trim();
if (val == "") {
logger.warn("Unable to parse energy for resn "+index);
continue;
}
String[] p = val.split(",");
int partner = Integer.parseInt(p[0]);
if (partner != 0) partner += index;
double energy = Double.valueOf(p[1]) * 1000.0;
switch(i){
case 0:
ss.getAccept1().setPartner(partner);
ss.getAccept1().setEnergy(energy);
break;
case 1:
ss.getDonor1().setPartner(partner);
ss.getDonor1().setEnergy(energy);
break;
case 2:
ss.getAccept2().setPartner(partner);
ss.getAccept2().setEnergy(energy);
break;
case 3:
ss.getDonor2().setPartner(partner);
ss.getDonor1().setEnergy(energy);
break;
}
}
//Angle properties
String val = line.substring(91,97).trim();
if (val != "") ss.setKappa(Float.valueOf(val));
else logger.warn("Unable to parse kappa for resn "+index);
val = line.substring(103,109).trim();
if (val != "") ss.setPhi(Float.valueOf(val));
else logger.warn("Unable to parse phi for resn "+index);
val = line.substring(109,116).trim();
if (val != "") ss.setPsi(Float.valueOf(val));
else logger.warn("Unable to parse psi for resn "+index);
if (assign) parent.setProperty(Group.SEC_STRUC, ss);
secstruc.add(ss);
}
}
reader.close();
return secstruc;
}
}