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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/
*
*/
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 currentChainIDs = new ArrayList();
private Matrix currentMatrix = null;
private double[] shift = null;
private Map transformationMap = new HashMap();
private int modelNumber = 1;
private int currentMmSize;
private List 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());
} 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
currentMmSize = getMmSize(line);
} 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 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);
if (currentMmSize==0) {
logger.warn("No macromolecular size could be parsed for biological assembly {}",currentBioMolecule);
}
bioAssembly.setMacromolecularSize(currentMmSize);
bioAssembly.setTransforms(transformations);
transformationMap.put(currentBioMolecule,bioAssembly);
}
}
private int getMmSize(String line) {
int index = line.indexOf(':');
String mmString = line.substring(index+1,line.length()-1).trim().toLowerCase();
return getSizefromString(mmString);
}
private static int getSizefromString(String oligomer){
int size=0;
oligomer = oligomer.toLowerCase();
if (oligomer.equals("monomeric")) {
size = 1;
} else if (oligomer.equals("dimeric")) {
size = 2;
} else if (oligomer.equals("trimeric")) {
size = 3;
} else if (oligomer.equals("tetrameric")) {
size = 4;
} else if (oligomer.equals("pentameric")) {
size = 5;
} else if (oligomer.equals("hexameric")) {
size = 6;
} else if (oligomer.equals("heptameric")) {
size = 7;
} else if (oligomer.equals("octameric")) {
size = 8;
} else if (oligomer.equals("nonameric")) {
size = 9;
} else if (oligomer.equals("decameric")) {
size = 10;
} else if (oligomer.equals("undecameric")) {
size = 11;
} else if (oligomer.equals("dodecameric")) {
size = 12;
} else if (oligomer.equals("tridecameric")) {
size = 13;
} else if (oligomer.equals("tetradecameric")) {
size = 14;
} else if (oligomer.equals("pentadecameric")) {
size = 15;
} else if (oligomer.equals("hexadecameric")) {
size = 16;
} else if (oligomer.equals("heptadecameric")) {
size = 17;
} else if (oligomer.equals("octadecameric")) {
size = 18;
} else if (oligomer.equals("nonadecameric")) {
size = 19;
} else if (oligomer.equals("eicosameric")) {
size = 20;
} else if( oligomer.matches("(\\d+).*")) {
size = Integer.parseInt((oligomer.replaceAll("(\\d+).*", "$1")));
}
return size;
}
/**
* 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();
currentMatrix = Matrix.identity(3,3);
currentBioMolecule = null;
shift = new double[3];
modelNumber = 1;
currentMmSize = 0;
}
}
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