org.openscience.cdk.io.PMPReader Maven / Gradle / Ivy
/* Copyright (C) 2004-2008 Egon Willighagen
*
* Contact: [email protected]
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU Lesser General Public License
* as published by the Free Software Foundation; either version 2.1
* of the License, or (at your option) any later version.
* All we ask is that proper credit is given for our work, which includes
* - but is not limited to - adding the above copyright notice to the beginning
* of your source code files, and to any copyright notice that you may distribute
* with programs based on this work.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
*
*/
package org.openscience.cdk.io;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.StringReader;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.Map;
import java.util.StringTokenizer;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.vecmath.Point3d;
import javax.vecmath.Vector3d;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.graph.rebond.RebondTool;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemFile;
import org.openscience.cdk.interfaces.IChemModel;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.interfaces.IChemSequence;
import org.openscience.cdk.interfaces.ICrystal;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.PMPFormat;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* Reads an frames from a PMP formated input.
* Both compilation and use of this class requires Java 1.4.
*
* @cdk.module io
* @cdk.githash
* @cdk.iooptions
*
* @cdk.keyword file format, Polymorph Predictor (tm)
*
* @author E.L. Willighagen
* @cdk.require java1.4+
*/
public class PMPReader extends DefaultChemObjectReader {
private static final String PMP_ZORDER = "ZOrder";
private static final String PMP_ID = "Id";
private BufferedReader input;
private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(PMPReader.class);
/* Keep a copy of the PMP model */
private IAtomContainer modelStructure;
private IChemObject chemObject;
/* Keep an index of PMP id -> AtomCountainer id */
private Map atomids = new Hashtable();
private Map atomGivenIds = new Hashtable();
private Map atomZOrders = new Hashtable();
private Map bondids = new Hashtable();
private Map bondAtomOnes = new Hashtable();
private Map bondAtomTwos = new Hashtable();
private Map bondOrders = new Hashtable();
/* Often used patterns */
Pattern objHeader;
Pattern objCommand;
Pattern atomTypePattern;
int lineNumber = 0;
int bondCounter = 0;
private RebondTool rebonder;
/*
* construct a new reader from a Reader type object
* @param input reader from which input is read
*/
public PMPReader(Reader input) {
this.input = new BufferedReader(input);
this.lineNumber = 0;
/* compile patterns */
objHeader = Pattern.compile(".*\\((\\d+)\\s(\\w+)$");
objCommand = Pattern.compile(".*\\(A\\s(C|F|D|I|O)\\s(\\w+)\\s+\"?(.*?)\"?\\)$");
atomTypePattern = Pattern.compile("^(\\d+)\\s+(\\w+)$");
rebonder = new RebondTool(2.0, 0.5, 0.5);
}
public PMPReader(InputStream input) {
this(new InputStreamReader(input));
}
public PMPReader() {
this(new StringReader(""));
}
@Override
public IResourceFormat getFormat() {
return PMPFormat.getInstance();
}
@Override
public void setReader(Reader input) throws CDKException {
if (input instanceof BufferedReader) {
this.input = (BufferedReader) input;
} else {
this.input = new BufferedReader(input);
}
}
@Override
public void setReader(InputStream input) throws CDKException {
setReader(new InputStreamReader(input));
}
@Override
public boolean accepts(Class classObject) {
if (IChemFile.class.equals(classObject)) return true;
Class[] interfaces = classObject.getInterfaces();
for (int i = 0; i < interfaces.length; i++) {
if (IChemFile.class.equals(interfaces[i])) return true;
}
Class superClass = classObject.getSuperclass();
if (superClass != null) return this.accepts(superClass);
return false;
}
/**
* reads the content from a PMP input. It can only return a
* IChemObject of type ChemFile
*
* @param object class must be of type ChemFile
*
* @see IChemFile
*/
@Override
public T read(T object) throws CDKException {
if (object instanceof IChemFile) {
return (T) readChemFile((IChemFile) object);
} else {
throw new CDKException("Only supported is reading of ChemFile objects.");
}
}
// private procedures
private String readLine() throws IOException {
String line = input.readLine();
lineNumber = lineNumber + 1;
logger.debug("LINE (" + lineNumber + "): ", line);
return line;
}
/**
* Private method that actually parses the input to read a ChemFile
* object.
*
* Each PMP frame is stored as a Crystal in a ChemModel. The PMP
* file is stored as a ChemSequence of ChemModels.
*
* @return A ChemFile containing the data parsed from input.
*/
private IChemFile readChemFile(IChemFile chemFile) {
IChemSequence chemSequence = chemFile.getBuilder().newInstance(IChemSequence.class);
IChemModel chemModel = chemFile.getBuilder().newInstance(IChemModel.class);
ICrystal crystal = chemFile.getBuilder().newInstance(ICrystal.class);
try {
String line = readLine();
while (input.ready() && line != null) {
if (line.startsWith("%%Header Start")) {
// parse Header section
while (input.ready() && line != null && !(line.startsWith("%%Header End"))) {
if (line.startsWith("%%Version Number")) {
String version = readLine().trim();
if (!version.equals("3.00")) {
logger.error("The PMPReader only supports PMP files with version 3.00");
return null;
}
}
line = readLine();
}
} else if (line.startsWith("%%Model Start")) {
// parse Model section
modelStructure = chemFile.getBuilder().newInstance(IAtomContainer.class);
while (input.ready() && line != null && !(line.startsWith("%%Model End"))) {
Matcher objHeaderMatcher = objHeader.matcher(line);
if (objHeaderMatcher.matches()) {
String object = objHeaderMatcher.group(2);
constructObject(chemFile.getBuilder(), object);
int id = Integer.parseInt(objHeaderMatcher.group(1));
// logger.debug(object + " id: " + id);
line = readLine();
while (input.ready() && line != null && !(line.trim().equals(")"))) {
// parse object command (or new object header)
Matcher objCommandMatcher = objCommand.matcher(line);
objHeaderMatcher = objHeader.matcher(line);
if (objHeaderMatcher.matches()) {
// ok, forget about nesting and hope for the best
object = objHeaderMatcher.group(2);
id = Integer.parseInt(objHeaderMatcher.group(1));
constructObject(chemFile.getBuilder(), object);
} else if (objCommandMatcher.matches()) {
String format = objCommandMatcher.group(1);
String command = objCommandMatcher.group(2);
String field = objCommandMatcher.group(3);
processModelCommand(object, command, format, field);
} else {
logger.warn("Skipping line: " + line);
}
line = readLine();
}
if (chemObject instanceof IAtom) {
atomids.put(Integer.valueOf(id), Integer.valueOf(modelStructure.getAtomCount()));
atomZOrders.put(Integer.valueOf((String) chemObject.getProperty(PMP_ZORDER)),
Integer.valueOf(id));
atomGivenIds.put(Integer.valueOf((String) chemObject.getProperty(PMP_ID)),
Integer.valueOf(id));
modelStructure.addAtom((IAtom) chemObject);
// } else if (chemObject instanceof IBond) {
// bondids.put(new Integer(id), new Integer(molecule.getAtomCount()));
// molecule.addBond((IBond)chemObject);
} else {
logger.error("chemObject is not initialized or of bad class type");
}
// logger.debug(molecule.toString());
}
line = readLine();
}
if (line.startsWith("%%Model End")) {
// during the Model Start, all bonds are cached as PMP files might
// define bonds *before* the involved atoms :(
// the next lines dump the cache into the atom container
// bondids.put(new Integer(id), new Integer(molecule.getAtomCount()));
// molecule.addBond((IBond)chemObject);
int bondsFound = bondids.size();
logger.debug("Found #bonds: ", bondsFound);
logger.debug("#atom ones: ", bondAtomOnes.size());
logger.debug("#atom twos: ", bondAtomTwos.size());
logger.debug("#orders: ", bondOrders.size());
Iterator bonds = bondids.keySet().iterator();
while (bonds.hasNext()) {
Integer index = bonds.next();
double order = (bondOrders.get(index) != null ? ((Double) bondOrders.get(index))
.doubleValue() : 1.0);
logger.debug("index: ", index);
logger.debug("ones: ", bondAtomOnes.get(index));
IAtom atom1 = modelStructure.getAtom(((Integer) atomids.get((Integer) bondAtomOnes
.get(index))).intValue());
IAtom atom2 = modelStructure.getAtom(((Integer) atomids.get((Integer) bondAtomTwos
.get(index))).intValue());
IBond bond = modelStructure.getBuilder().newInstance(IBond.class, atom1, atom2);
if (order == 1.0) {
bond.setOrder(IBond.Order.SINGLE);
} else if (order == 2.0) {
bond.setOrder(IBond.Order.DOUBLE);
} else if (order == 3.0) {
bond.setOrder(IBond.Order.TRIPLE);
} else if (order == 4.0) {
bond.setOrder(IBond.Order.QUADRUPLE);
}
modelStructure.addBond(bond);
}
}
} else if (line.startsWith("%%Traj Start")) {
chemSequence = chemFile.getBuilder().newInstance(IChemSequence.class);
double energyFragment = 0.0;
double energyTotal = 0.0;
int Z = 1;
while (input.ready() && line != null && !(line.startsWith("%%Traj End"))) {
if (line.startsWith("%%Start Frame")) {
chemModel = chemFile.getBuilder().newInstance(IChemModel.class);
crystal = chemFile.getBuilder().newInstance(ICrystal.class);
while (input.ready() && line != null && !(line.startsWith("%%End Frame"))) {
// process frame data
if (line.startsWith("%%Atom Coords")) {
// calculate Z: as it is not explicitely given, try to derive it from the
// energy per fragment and the total energy
if (energyFragment != 0.0 && energyTotal != 0.0) {
Z = (int) Math.round(energyTotal / energyFragment);
logger.debug("Z derived from energies: ", Z);
}
// add atomC as atoms to crystal
int expatoms = modelStructure.getAtomCount();
for (int molCount = 1; molCount <= Z; molCount++) {
IAtomContainer clone = modelStructure.getBuilder().newInstance(
IAtomContainer.class);
for (int i = 0; i < expatoms; i++) {
line = readLine();
IAtom a = clone.getBuilder().newInstance(IAtom.class);
StringTokenizer st = new StringTokenizer(line, " ");
a.setPoint3d(new Point3d(Double.parseDouble(st.nextToken()), Double
.parseDouble(st.nextToken()), Double.parseDouble(st.nextToken())));
a.setCovalentRadius(0.6);
IAtom modelAtom = modelStructure.getAtom(atomids.get(atomGivenIds
.get(Integer.valueOf(i + 1))));
a.setSymbol(modelAtom.getSymbol());
clone.addAtom(a);
}
rebonder.rebond(clone);
crystal.add(clone);
}
} else if (line.startsWith("%%E/Frag")) {
line = readLine().trim();
energyFragment = Double.parseDouble(line);
} else if (line.startsWith("%%Tot E")) {
line = readLine().trim();
energyTotal = Double.parseDouble(line);
} else if (line.startsWith("%%Lat Vects")) {
StringTokenizer st;
line = readLine();
st = new StringTokenizer(line, " ");
crystal.setA(new Vector3d(Double.parseDouble(st.nextToken()), Double.parseDouble(st
.nextToken()), Double.parseDouble(st.nextToken())));
line = readLine();
st = new StringTokenizer(line, " ");
crystal.setB(new Vector3d(Double.parseDouble(st.nextToken()), Double.parseDouble(st
.nextToken()), Double.parseDouble(st.nextToken())));
line = readLine();
st = new StringTokenizer(line, " ");
crystal.setC(new Vector3d(Double.parseDouble(st.nextToken()), Double.parseDouble(st
.nextToken()), Double.parseDouble(st.nextToken())));
} else if (line.startsWith("%%Space Group")) {
line = readLine().trim();
/*
* standardize space group name. See
* Crystal.setSpaceGroup()
*/
if ("P 21 21 21 (1)".equals(line)) {
crystal.setSpaceGroup("P 2_1 2_1 2_1");
} else {
crystal.setSpaceGroup("P1");
}
} else {
}
line = readLine();
}
chemModel.setCrystal(crystal);
chemSequence.addChemModel(chemModel);
}
line = readLine();
}
chemFile.addChemSequence(chemSequence);
} else {
// disregard line
}
// read next line
line = readLine();
}
} catch (IOException e) {
logger.error("An IOException happened: ", e.getMessage());
logger.debug(e);
chemFile = null;
} catch (CDKException e) {
logger.error("An CDKException happened: ", e.getMessage());
logger.debug(e);
chemFile = null;
}
return chemFile;
}
private void processModelCommand(String object, String command, String format, String field) {
logger.debug(object + "->" + command + " (" + format + "): " + field);
if ("Model".equals(object)) {
logger.warn("Unkown PMP Model command: " + command);
} else if ("Atom".equals(object)) {
if ("ACL".equals(command)) {
Matcher atomTypeMatcher = atomTypePattern.matcher(field);
if (atomTypeMatcher.matches()) {
int atomicnum = Integer.parseInt(atomTypeMatcher.group(1));
String type = atomTypeMatcher.group(2);
((IAtom) chemObject).setAtomicNumber(atomicnum);
((IAtom) chemObject).setSymbol(type);
} else {
logger.error("Incorrectly formated field value: " + field + ".");
}
} else if ("Charge".equals(command)) {
try {
double charge = Double.parseDouble(field);
((IAtom) chemObject).setCharge(charge);
} catch (NumberFormatException e) {
logger.error("Incorrectly formated float field: " + field + ".");
}
} else if ("CMAPPINGS".equals(command)) {
} else if ("FFType".equals(command)) {
} else if ("Id".equals(command)) {
// ok, should take this into account too
chemObject.setProperty(PMP_ID, field);
} else if ("Mass".equals(command)) {
} else if ("XYZ".equals(command)) {
} else if ("ZOrder".equals(command)) {
// ok, should take this into account too
chemObject.setProperty(PMP_ZORDER, field);
} else {
logger.warn("Unkown PMP Atom command: " + command);
}
} else if ("Bond".equals(object)) {
if ("Atom1".equals(command)) {
int atomid = Integer.parseInt(field);
// this assumes that the atoms involved in this bond are
// already added, which seems the case in the PMP files
bondAtomOnes.put(Integer.valueOf(bondCounter), Integer.valueOf(atomid));
// IAtom a = molecule.getAtom(realatomid);
// ((IBond)chemObject).setAtomAt(a, 0);
} else if ("Atom2".equals(command)) {
int atomid = Integer.parseInt(field);
// this assumes that the atoms involved in this bond are
// already added, which seems the case in the PMP files
logger.debug("atomids: " + atomids);
logger.debug("atomid: " + atomid);
bondAtomTwos.put(Integer.valueOf(bondCounter), Integer.valueOf(atomid));
// IAtom a = molecule.getAtom(realatomid);
// ((IBond)chemObject).setAtomAt(a, 1);
} else if ("Order".equals(command)) {
double order = Double.parseDouble(field);
bondOrders.put(Integer.valueOf(bondCounter), order);
// ((IBond)chemObject).setOrder(order);
} else if ("Id".equals(command)) {
int bondid = Integer.parseInt(field);
bondids.put(Integer.valueOf(bondCounter), Integer.valueOf(bondid));
} else if ("Label".equals(command)) {
} else if ("3DGridOrigin".equals(command)) {
} else if ("3DGridMatrix".equals(command)) {
} else if ("3DGridDivision".equals(command)) {
} else {
logger.warn("Unkown PMP Bond command: " + command);
}
} else {
logger.warn("Unkown PMP object: " + object);
}
}
private void constructObject(IChemObjectBuilder builder, String object) {
if ("Atom".equals(object)) {
chemObject = builder.newInstance(IAtom.class, "C");
} else if ("Bond".equals(object)) {
bondCounter++;
chemObject = builder.newInstance(IBond.class);
} else if ("Model".equals(object)) {
modelStructure = builder.newInstance(IAtomContainer.class);
} else {
logger.error("Cannot construct PMP object type: " + object);
}
};
@Override
public void close() throws IOException {
input.close();
}
}
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