org.biojava.nbio.structure.io.PDBFileReader Maven / Gradle / Ivy
Show all versions of biojava-structure Show documentation
/*
* 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/
*
* Created on 16.03.2004
* @author Andreas Prlic
*
*
*/
package org.biojava.nbio.structure.io;
import org.biojava.nbio.structure.Chain;
import org.biojava.nbio.structure.EntityInfo;
import org.biojava.nbio.structure.Group;
import org.biojava.nbio.structure.Structure;
import org.biojava.nbio.structure.align.util.UserConfiguration;
import java.io.IOException;
import java.io.InputStream;
import java.util.List;
/**
*
* The wrapper class for parsing a PDB file.
*
*
*
*
* Several flags can be set for this class
*
*
* - {@link #setAutoFetch(boolean)} - if the PDB file can not be found locally, should it be fetched
* from the PDB ftp servers? (default:false)
* - Other parameters can be set using the {@link #setFileParsingParameters(FileParsingParameters)}
*
*
*
*
*
*Example
*
* Q: How can I get a Structure object from a PDB file?
*
*
* A:
*
* public {@link Structure} loadStructure(String pathToPDBFile){
* {@link PDBFileReader} pdbreader = new {@link PDBFileReader}();
*
* {@link Structure} structure = null;
* try{
* structure = pdbreader.getStructure(pathToPDBFile);
* System.out.println(structure);
* } catch (IOException e) {
* e.printStackTrace();
* }
* return structure;
* }
*
*
* Access PDB files from a directory, take care of compressed PDB files
*
* public {@link Structure} loadStructureById() {
* String path = "/path/to/PDB/directory/";
*
* {@link PDBFileReader} pdbreader = new {@link PDBFileReader}();
* pdbreader.setPath(path);
* {@link Structure} structure = null;
* try {
* structure = pdbreader.getStructureById("5pti");
* } catch (IOException e){
* e.printStackTrace();
* }
* return structure;
*
* }
*
*
*
* @author Andreas Prlic
*
*/
public class PDBFileReader extends LocalPDBDirectory {
//private static final Logger logger = LoggerFactory.getLogger(PDBFileReader.class);
// a list of big pdb files for testing
// "1htq",
// "1c2w",
// "1ffk",
// "1giy",
// "1j5a",
// "1jj2",
// "1jzx",
// "1jzy",
// "1jzz",
// "1k01",
// "1k73",
// "1k8a",
// "1k9m",
// "1kc8",
// "1kd1",
// "1kqs",
// "1m1k",
// "1m90",
// "1mkz",
// "1ml5",
// "1n8r",
public static final String[] PDB_SPLIT_DIR = new String[]{"data","structures","divided" ,"pdb"};
public static final String[] PDB_OBSOLETE_DIR = new String[]{"data","structures","obsolete","pdb"};
public static void main(String[] args){
PDBFileReader pdbreader = new PDBFileReader();
// set the path to cache files
String property = "java.io.tmpdir";
String tempdir = System.getProperty(property);
// tempdir = "/path/to/local/PDB/installation/";
pdbreader.setPath(tempdir);
FileParsingParameters params = new FileParsingParameters();
pdbreader.setFileParsingParameters(params);
try{
Structure struc = pdbreader.getStructureById("193D");
System.out.println(struc);
List compounds = struc.getEntityInfos();
for (EntityInfo comp : compounds ){
List chains = comp.getChains();
System.out.print(">Chains :" );
for (Chain c : chains){
System.out.print(c.getChainID() + " " );
}
System.out.println();
if ( chains.size() > 0) {
System.out.println(chains.get(0).getAtomSequence());
System.out.println(chains.get(0).getSeqResSequence());
System.out.print(" Atom Ligands: ");
for ( Group g: chains.get(0).getAtomLigands()){
System.out.print( g.getPDBName() + " ");
}
System.out.println(" ");
}
}
/*
GroupIterator gi = new GroupIterator(struc);
while (gi.hasNext()){
Group g = (Group) gi.next();
Chain c = g.getParent();
if ( g instanceof AminoAcid ){
AminoAcid aa = (AminoAcid)g;
Map sec = aa.getSecStruc();
//System.out.println(c.getName() + " " + g + " " + sec);
ChemComp cc = g.getChemComp();
System.out.println(c.getName() + " " + g.getPDBCode() + " " + g.getPDBName() + " " + cc + " " +sec);
}
}
*/
} catch (IOException e) {
e.printStackTrace();
}
}
/**
* Constructs a new PDBFileReader, initializing the extensions member variable.
* The path is initialized in the same way as {@link UserConfiguration},
* i.e. to system property/environment variable {@link UserConfiguration#PDB_DIR}.
* Both autoFetch and splitDir are initialized to false
*/
public PDBFileReader() {
this(null);
}
/**
* Constructs a new PDBFileReader, initializing the extensions member variable.
* The path is initialized to the given path, both autoFetch and splitDir are initialized to false.
*
* If path is null, initialize using the system property/environment variable
* {@link UserConfiguration#PDB_DIR}.
* @param path Path to the PDB file directory
*/
public PDBFileReader(String path) {
super(path);
addExtension(".ent");
addExtension(".pdb");
addExtension(".ent.gz");
addExtension(".pdb.gz");
addExtension(".ent.Z");
addExtension(".pdb.Z");
}
@Deprecated
public void downloadPDB(String pdbId) throws IOException {
downloadStructure(pdbId);
}
/**
* N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true.
* @param fetchFileEvenIfObsolete the fetchFileEvenIfObsolete to set
* @deprecated Use {@link FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)}
*/
@Deprecated
public void setFetchFileEvenIfObsolete(boolean fetchFileEvenIfObsolete) {
if(fetchFileEvenIfObsolete) {
setObsoleteBehavior(ObsoleteBehavior.FETCH_OBSOLETE);
} else {
if(getObsoleteBehavior() == ObsoleteBehavior.FETCH_OBSOLETE) {
setObsoleteBehavior(ObsoleteBehavior.DEFAULT);
}
}
}
/**forces the reader to fetch the file if its status is OBSOLETE.
* This feature has a higher priority than {@link #setFetchCurrent(boolean)}.
* N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true.
* @return the fetchFileEvenIfObsolete
* @author Amr AL-Hossary
* @see #fetchCurrent
* @since 3.0.2
* @deprecated Use {@link FileParsingParameters#getObsoleteBehavior()}
*/
@Deprecated
public boolean isFetchFileEvenIfObsolete() {
return getObsoleteBehavior() == ObsoleteBehavior.FETCH_OBSOLETE;
}
/**if enabled, the reader searches for the newest possible PDB ID, if not present in he local installation.
* The {@link #setFetchFileEvenIfObsolete(boolean)} function has a higher priority than this function.
* N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true.
* @param fetchCurrent the fetchCurrent to set
* @author Amr AL-Hossary
* @see #setFetchFileEvenIfObsolete(boolean)
* @since 3.0.2
* @deprecated Use {@link FileParsingParameters#setObsoleteBehavior(ObsoleteBehavior)}
*/
@Deprecated
public void setFetchCurrent(boolean fetchNewestCurrent) {
if(fetchNewestCurrent) {
setObsoleteBehavior(ObsoleteBehavior.FETCH_CURRENT);
} else {
if(getObsoleteBehavior() == ObsoleteBehavior.FETCH_CURRENT) {
setObsoleteBehavior(ObsoleteBehavior.DEFAULT);
}
}
}
/**
* N.B. This feature won't work unless the structure wasn't found & autoFetch is set to true.
* @return the fetchCurrent
* @deprecated Use {@link FileParsingParameters#getObsoleteBehavior()}
*/
@Deprecated
public boolean isFetchCurrent() {
return getObsoleteBehavior() == ObsoleteBehavior.FETCH_CURRENT;
}
@Override
protected String getFilename(String pdbId) {
return "pdb"+pdbId.toLowerCase()+".ent.gz";
}
@Override
public Structure getStructure(InputStream inStream) throws IOException {
PDBFileParser pdbpars = new PDBFileParser();
pdbpars.setFileParsingParameters(getFileParsingParameters());
Structure struc = pdbpars.parsePDBFile(inStream) ;
return struc ;
}
@Override
protected String[] getSplitDirPath() {
return PDB_SPLIT_DIR;
}
@Override
protected String[] getObsoleteDirPath() {
return PDB_OBSOLETE_DIR;
}
}