/*
* 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.io;
import org.biojava.nbio.structure.jama.Matrix;
import org.biojava.nbio.structure.quaternary.BioAssemblyInfo;
import org.biojava.nbio.structure.quaternary.BiologicalAssemblyTransformation;
//import org.slf4j.Logger;
//import org.slf4j.LoggerFactory;
import java.util.*;
/**
* Parses REMARK 350 records in a PDB file and creates transformations to
* construct the quaternary structure of a protein from an asymmetric unit
*
* @author Peter Rose
* @author Andreas Prlic
*
*/
public class PDBBioAssemblyParser {
//private static final Logger logger = LoggerFactory.getLogger(PDBBioAssemblyParser.class);
private Integer currentBioMolecule = null;
private List<String> currentChainIDs = new ArrayList<String>();
private Matrix currentMatrix = null;
private double[] shift = null;
private Map<Integer,BioAssemblyInfo> transformationMap = new HashMap<Integer, BioAssemblyInfo>();
private int modelNumber = 1;
private List<BiologicalAssemblyTransformation> transformations;
/**
* Parses REMARK 350 line. See format description:
* http://www.wwpdb.org/documentation/format33/remarks2.html
*
* @param line
*/
public void pdb_REMARK_350_Handler(String line) {
if (line.startsWith("REMARK 350 BIOMOLECULE:")) {
initialize();
currentBioMolecule = Integer.parseInt(line.substring(24).trim());
}
// not parsing anymore the size (from biojava 5.0), thus this is not needed anymore
// eventually if needed this could be used to
// infer if bioassembly is author or software determined
//else if ( line.matches("REMARK 350 \\w+ DETERMINED BIOLOGICAL UNIT:.*" ) ||
// line.matches("REMARK 350 \\w+ DETERMINED QUATERNARY STRUCTURE:.*" )) {
// text can be :
// author determined biological unit
// software determined quaternary structure
//}
else if ( line.startsWith("REMARK 350 APPLY THE FOLLOWING TO CHAINS:")) {
currentChainIDs.clear();
addToCurrentChainList(line);
} else if ( line.startsWith("REMARK 350 IN ADDITION APPLY THE FOLLOWING TO CHAINS:")) {
currentChainIDs.clear();
addToCurrentChainList(line);
} else if ( line.startsWith("REMARK 350") && line.contains("AND CHAINS:")) {
addToCurrentChainList(line);
} else if ( line.startsWith("REMARK 350 BIOMT")) {
if (readMatrix(line)) {
saveMatrix();
modelNumber++;
}
}
}
/**
* Returns a map of bioassembly transformations
* @return
*/
public Map<Integer, BioAssemblyInfo> getTransformationMap() {
return transformationMap;
}
/**
* Parses a row of a BIOMT matrix in a REMARK 350 record.
* Example: REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000
* @param line
* @return true if 3rd line of matrix has been parsed (matrix is complete)
*/
private boolean readMatrix(String line) {
// split by one or more spaces
String[] items = line.split("[ ]+");
// parse BIOMTx, where x is the position in the matrix
String pos = items[2].substring(5);
int row = Integer.parseInt(pos);
if (row == 1) {
currentMatrix = Matrix.identity(3,3);
shift = new double[3];
}
currentMatrix.set((row-1), 0,Float.parseFloat(items[4]));
currentMatrix.set((row-1), 1,Float.parseFloat(items[5]));
currentMatrix.set((row-1), 2,Float.parseFloat(items[6]));
shift[row-1] = Float.parseFloat(items[7]);
// return true if 3rd row of matrix has been processed
return row == 3;
}
/**
* Saves transformation matrix for the list of current chains
*/
private void saveMatrix() {
for (String chainId : currentChainIDs) {
BiologicalAssemblyTransformation transformation = new BiologicalAssemblyTransformation();
transformation.setRotationMatrix(currentMatrix.getArray());
transformation.setTranslation(shift);
transformation.setId(String.valueOf(modelNumber));
transformation.setChainId(chainId);
transformations.add(transformation);
}
if (!transformationMap.containsKey(currentBioMolecule)) {
BioAssemblyInfo bioAssembly = new BioAssemblyInfo();
bioAssembly.setId(currentBioMolecule);
bioAssembly.setTransforms(transformations);
transformationMap.put(currentBioMolecule,bioAssembly);
}
}
/**
* Parses list of chain ids (A, B, C, etc.)
*/
private void addToCurrentChainList(String line) {
int index = line.indexOf(":");
String chainList = line.substring(index+1).trim();
// split by spaces or commas
String[] chainIds = chainList.split("[ ,]+");
currentChainIDs.addAll(Arrays.asList(chainIds));
}
private void initialize() {
transformations = new ArrayList<BiologicalAssemblyTransformation>();
currentMatrix = Matrix.identity(3,3);
currentBioMolecule = null;
shift = new double[3];
modelNumber = 1;
}
/**
* Set the macromolecularSize fields of the parsed bioassemblies.
* This can only be called after the full PDB file has been read so that
* all the info for all bioassemblies has been gathered.
* Note that an explicit method to set the field is necessary here because
* in PDB files the transformations contain only the author chain ids, corresponding
* to polymeric chains, whilst in mmCIF files the transformations
* contain all asym ids of both polymers and non-polymers.
*/
public void setMacromolecularSizes() {
for (BioAssemblyInfo bioAssembly : transformationMap.values()) {
bioAssembly.setMacromolecularSize(bioAssembly.getTransforms().size());
}
}
}