/*
* 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.xtal;
import org.biojava.nbio.structure.xtal.io.SpaceGroupMapRoot;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import javax.xml.bind.JAXBException;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.util.HashMap;
import java.util.TreeMap;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
/**
* A class containing static methods to parse the symop.lib file from the
* CCP4 package. The file contains the transformations belonging to all
* protein crystallography space groups.
*
* See http://structure.usc.edu/ccp4/symlib.html for documentation
*
* @author duarte_j
*
*/
public class SymoplibParser {
private static final Logger logger = LoggerFactory.getLogger(SymoplibParser.class);
private static final String newline = System.getProperty("line.separator");
private static final String SPACE_GROUPS_FILE = "org/biojava/nbio/structure/xtal/spacegroups.xml";
private static final Pattern namePat = Pattern.compile(".*\\s([A-Z]+)(\\s'.+')?\\s+'(.+)'.*");
private static TreeMap<Integer, SpaceGroup> sgs = parseSpaceGroupsXML();
private static HashMap<String, SpaceGroup> name2sgs; // map for lookups based on short names
/**
* Gets the space group for the given standard identifier.
* See for example http://en.wikipedia.org/wiki/Space_group
* @param id
* @return
*/
public static SpaceGroup getSpaceGroup(int id) {
return sgs.get(id);
}
/**
* Load all SpaceGroup information from the file spacegroups.xml
*
* @return a map providing information for all spacegroups
*/
private static TreeMap<Integer, SpaceGroup> parseSpaceGroupsXML() {
// NOTE: if the space group file is requested by some part of the code (i.e. this method is called) and
// there is a problem in reading it, then that's truly a FATAL problem, since this is not a user file
// but a file that's part of the distribution: it MUST be there and MUST have the right format. A failure
// to read it is more of a "compilation" error than a runtime error. That's the reason that System.exit
// is called (which otherwise usually is not a good idea).
//
// The rest of the application will simply not work: there are 3 options to handle it
// a) returning null and then a NullPointer will happen down the line and thus a not very clear
// error message will be printed
// b) throw the exception forward and catch it in the final main but that would also be bad because
// this is a file that the user didn't input but that should be part of the distribution
// c) call System.exit(1) and "crash" the application with a human-understandable error message
InputStream spaceGroupIS = SymoplibParser.class.getClassLoader().getResourceAsStream(SPACE_GROUPS_FILE);
if ( spaceGroupIS == null) {
logger.error("Fatal error! Could not find resource: " + SPACE_GROUPS_FILE + ". This probably means that your biojava jar file is corrupt or incorrectly built.");
System.exit(1);
}
TreeMap<Integer, SpaceGroup> map = new TreeMap<Integer, SpaceGroup>();
try {
map = parseSpaceGroupsXML(spaceGroupIS);
} catch (IOException e) {
logger.error("Fatal error! Could not parse resource: "+SPACE_GROUPS_FILE+". Error: "+e.getMessage());
System.exit(1);
} catch (JAXBException e) {
logger.error("Fatal error! Could not parse resource: "+SPACE_GROUPS_FILE+". Problem in xml formatting: "+e.getMessage());
System.exit(1);
}
name2sgs = new HashMap<String, SpaceGroup>();
for (SpaceGroup sg:map.values()) {
sg.initializeCellTranslations();
name2sgs.put(sg.getShortSymbol(), sg);
if (sg.getAltShortSymbol()!=null) {
// we add also alternative name to map so we can look it up
name2sgs.put(sg.getAltShortSymbol(), sg);
}
}
return map;
}
/**
* Load all SpaceGroup information from the file spacegroups.xml
*
* @return a map providing information for all spacegroups
*/
public static TreeMap<Integer, SpaceGroup> parseSpaceGroupsXML(
InputStream spaceGroupIS) throws IOException, JAXBException {
String xml = convertStreamToString(spaceGroupIS);
SpaceGroupMapRoot spaceGroups = SpaceGroupMapRoot.fromXML(xml);
return spaceGroups.getMapProperty();
}
private static String convertStreamToString(InputStream stream) throws IOException {
BufferedReader reader = new BufferedReader(new InputStreamReader(stream));
StringBuilder sb = new StringBuilder();
String line = null;
while ((line = reader.readLine()) != null) {
sb.append(line).append(newline);
}
return sb.toString();
}
/**
* Get the space group for the given international short name, using
* the PDB format, e.g. 'P 21 21 21' or 'C 1 c 1'
* @param shortName
* @return the SpaceGroup or null if the shortName is not valid
*/
public static SpaceGroup getSpaceGroup(String shortName) {
if (shortName==null || shortName.length()<=2) return null;
// PDB uses group "P 1-" for 13 racemic mixture entries (as of Sep2011), e.g. 3e7r
// they call the space group "P 1-" unusually (symop.lib and everyone else call it "P -1")
if (shortName.equals("P 1-")) shortName="P -1";
// enantiomorphic space groups contain sometime letters indicating glide planes which should always be lower case
// in some PDB entries like 4gwv they are in upper case, we fix that here: convert any non-first letter to lower case
shortName = shortName.substring(0, 1)+shortName.substring(1).toLowerCase();
return name2sgs.get(shortName);
}
public static TreeMap<Integer,SpaceGroup> getAllSpaceGroups() {
return sgs;
}
/**
* A parser for the symop.lib file provided by CCP4. Note: this file is not getting re-distributed by BioJava.
* It can be downloaded from:
*
* http://www.ccp4.ac.uk/cvs/viewvc.cgi/libccp4/data/symop.lib?revision=1.10&view=markup
*
* Note: this file is not needed by BioJava. BioJava loads equivalent information from the file spacegroups.xml
*
* @param symoplibIS
* @return
*/
public static TreeMap<Integer,SpaceGroup> parseSymopLib(InputStream symoplibIS) {
TreeMap<Integer, SpaceGroup> map = new TreeMap<Integer, SpaceGroup>();
name2sgs = new HashMap<String, SpaceGroup>();
try {
BufferedReader br = new BufferedReader(new InputStreamReader(symoplibIS));
String line;
SpaceGroup currentSG = null;
while ((line=br.readLine())!=null) {
if (!line.startsWith(" ")) {
if (currentSG!=null) {
map.put(currentSG.getId(),currentSG);
name2sgs.put(currentSG.getShortSymbol(), currentSG);
if (currentSG.getAltShortSymbol()!=null) {
// we add also alternative name to map so we can look it up
name2sgs.put(currentSG.getAltShortSymbol(), currentSG);
}
}
int idxFirstSpace = line.indexOf(' ');
int idxSecondSpace = line.indexOf(' ',idxFirstSpace+1);
int idxThirdSpace = line.indexOf(' ',idxSecondSpace+1);
int id = Integer.parseInt(line.substring(0, idxFirstSpace));
int multiplicity = Integer.parseInt(line.substring(idxFirstSpace+1, idxSecondSpace));
int primitiveMultiplicity = Integer.parseInt(line.substring(idxSecondSpace+1, idxThirdSpace));
Matcher m = namePat.matcher(line);
String shortSymbol = null;
String altShortSymbol = null;
String brav = null;
if (m.matches()) {
brav = m.group(1);
altShortSymbol = m.group(2); // null if there is no match
if (altShortSymbol!=null) altShortSymbol = altShortSymbol.trim().replaceAll("'", "");
shortSymbol = m.group(3);
}
currentSG = new SpaceGroup(id, multiplicity, primitiveMultiplicity, shortSymbol, altShortSymbol, BravaisLattice.getByName(brav));
} else {
currentSG.addTransformation(line.trim());
}
}
br.close();
// and we add the last SG
map.put(currentSG.getId(), currentSG);
name2sgs.put(currentSG.getShortSymbol(), currentSG);
if (currentSG.getAltShortSymbol()!=null) {
// we add also alternative name to map so we can look it up
name2sgs.put(currentSG.getAltShortSymbol(), currentSG);
}
} catch (IOException e) {
logger.error("Fatal error! Can't read symop.lib file. Error: "+e.getMessage()+". ");
System.exit(1);
}
for (SpaceGroup sg:map.values()) {
sg.initializeCellTranslations();
}
return map;
}
}