org.openscience.cdk.io.MDLReader Maven / Gradle / Ivy
/* Copyright (C) 1997-2007 Christoph Steinbeck
*
* 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.Iterator;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import javax.vecmath.Point2d;
import javax.vecmath.Point3d;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.config.Isotopes;
import org.openscience.cdk.config.IsotopeFactory;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomContainerSet;
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.IIsotope;
import org.openscience.cdk.interfaces.IPseudoAtom;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.MDLFormat;
import org.openscience.cdk.io.setting.BooleanIOSetting;
import org.openscience.cdk.io.setting.IOSetting;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* Reads a molecule from the original MDL MOL or SDF file {@cdk.cite DAL92}. An SD files
* is read into a {@link IChemSequence} of {@link IChemModel}'s. Each ChemModel will contain one
* Molecule. If the MDL molfile contains a property block, the {@link MDLV2000Reader} should be
* used.
*
* If all z coordinates are 0.0, then the xy coordinates are taken as
* 2D, otherwise the coordinates are read as 3D.
*
*
The title of the MOL file is read and can be retrieved with:
*
* molecule.getProperty(CDKConstants.TITLE);
*
*
* @cdk.module io
* @cdk.githash
* @cdk.iooptions
*
* @author steinbeck
* @author Egon Willighagen
* @cdk.created 2000-10-02
* @cdk.keyword file format, MDL molfile
* @cdk.keyword file format, SDF
*
* @see org.openscience.cdk.io.MDLV2000Reader
* @deprecated This reader is only for molfiles without a version tag, typically the most
* common molfile now encountered is V2000 and the {@link MDLV2000Reader} should be used
* instead. The V2000 reader can actually read files missing the version tag when
* in relaxed mode.
*/
@Deprecated
public class MDLReader extends DefaultChemObjectReader {
BufferedReader input = null;
private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(MDLReader.class);
private BooleanIOSetting forceReadAs3DCoords;
private static final Pattern TRAILING_SPACE = Pattern.compile("\\s+$");
public MDLReader() {
this(new StringReader(""));
}
/**
* Constructs a new MDLReader that can read Molecule from a given InputStream.
*
*@param in The InputStream to read from
*/
public MDLReader(InputStream in) {
this(in, Mode.RELAXED);
}
public MDLReader(InputStream in, Mode mode) {
this(new InputStreamReader(in));
super.mode = mode;
}
/**
* Constructs a new MDLReader that can read Molecule from a given Reader.
*
* @param in The Reader to read from
*/
public MDLReader(Reader in) {
this(in, Mode.RELAXED);
}
public MDLReader(Reader in, Mode mode) {
super.mode = mode;
input = new BufferedReader(in);
initIOSettings();
}
@Override
public IResourceFormat getFormat() {
return MDLFormat.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;
if (IChemModel.class.equals(classObject)) return true;
if (IAtomContainer.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;
if (IChemModel.class.equals(interfaces[i])) return true;
if (IAtomContainer.class.equals(interfaces[i])) return true;
}
Class superClass = classObject.getSuperclass();
if (superClass != null) return this.accepts(superClass);
return false;
}
/**
* Takes an object which subclasses IChemObject, e.g. Molecule, and will read
* this (from file, database, internet etc). If the specific implementation
* does not support a specific IChemObject it will throw an Exception.
*
*@param object The object that subclasses
* IChemObject
*@return The IChemObject read
*@exception CDKException
*/
@Override
public T read(T object) throws CDKException {
if (object instanceof IChemFile) {
return (T) readChemFile((IChemFile) object);
} else if (object instanceof IChemModel) {
return (T) readChemModel((IChemModel) object);
} else if (object instanceof IAtomContainer) {
return (T) readMolecule((IAtomContainer) object);
} else {
throw new CDKException("Only supported are ChemFile and Molecule.");
}
}
private IChemModel readChemModel(IChemModel chemModel) throws CDKException {
IAtomContainerSet setOfMolecules = chemModel.getMoleculeSet();
if (setOfMolecules == null) {
setOfMolecules = chemModel.getBuilder().newInstance(IAtomContainerSet.class);
}
IAtomContainer m = readMolecule(chemModel.getBuilder().newInstance(IAtomContainer.class));
if (m != null) {
setOfMolecules.addAtomContainer(m);
}
chemModel.setMoleculeSet(setOfMolecules);
return chemModel;
}
/**
* Read a ChemFile from a file in MDL SDF format.
*
* @return The ChemFile that was read from the MDL file.
*/
private IChemFile readChemFile(IChemFile chemFile) throws CDKException {
IChemSequence chemSequence = chemFile.getBuilder().newInstance(IChemSequence.class);
IChemModel chemModel = chemFile.getBuilder().newInstance(IChemModel.class);
IAtomContainerSet setOfMolecules = chemFile.getBuilder().newInstance(IAtomContainerSet.class);
IAtomContainer m = readMolecule(chemFile.getBuilder().newInstance(IAtomContainer.class));
if (m != null) {
setOfMolecules.addAtomContainer(m);
}
chemModel.setMoleculeSet(setOfMolecules);
chemSequence.addChemModel(chemModel);
setOfMolecules = chemFile.getBuilder().newInstance(IAtomContainerSet.class);
chemModel = chemFile.getBuilder().newInstance(IChemModel.class);
String str;
try {
String line;
while ((line = input.readLine()) != null) {
logger.debug("line: ", line);
// apparently, this is a SDF file, continue with
// reading mol files
str = line;
if (line.equals("M END"))
continue;
if (str.equals("$$$$")) {
m = readMolecule(chemFile.getBuilder().newInstance(IAtomContainer.class));
if (m != null) {
setOfMolecules.addAtomContainer(m);
chemModel.setMoleculeSet(setOfMolecules);
chemSequence.addChemModel(chemModel);
setOfMolecules = chemFile.getBuilder().newInstance(IAtomContainerSet.class);
chemModel = chemFile.getBuilder().newInstance(IChemModel.class);
}
} else {
// here the stuff between 'M END' and '$$$$'
if (m != null) {
// ok, the first lines should start with '>'
String fieldName = null;
if (str.startsWith("> ")) {
// ok, should extract the field name
str.substring(2); // String content =
int index = str.indexOf('<');
if (index != -1) {
int index2 = str.substring(index).indexOf('>');
if (index2 != -1) {
fieldName = str.substring(index + 1, index + index2);
}
}
// end skip all other lines
while ((line = input.readLine()) != null && line.startsWith(">")) {
logger.debug("data header line: ", line);
}
}
if (line == null) {
throw new CDKException("Expecting data line here, but found null!");
}
String data = line;
while ((line = input.readLine()) != null && line.trim().length() > 0) {
if (line.equals("$$$$")) {
logger.error("Expecting data line here, but found end of molecule: ", line);
break;
}
logger.debug("data line: ", line);
data += line;
// preserve newlines, unless the line is exactly 80 chars; in that case it
// is assumed to continue on the next line. See MDL documentation.
if (line.length() < 80) data += System.getProperty("line.separator");
}
if (fieldName != null) {
logger.info("fieldName, data: ", fieldName, ", ", data);
m.setProperty(fieldName, data);
}
}
}
}
} catch (CDKException cdkexc) {
throw cdkexc;
} catch (IOException | IllegalArgumentException exception) {
String error = "Error while parsing SDF";
logger.error(error);
logger.debug(exception);
throw new CDKException(error, exception);
}
try {
input.close();
} catch (Exception exc) {
String error = "Error while closing file: " + exc.getMessage();
logger.error(error);
throw new CDKException(error, exc);
}
chemFile.addChemSequence(chemSequence);
return chemFile;
}
/**
* Read a Molecule from a file in MDL sd format
*
*@return The Molecule that was read from the MDL file.
*/
private IAtomContainer readMolecule(IAtomContainer molecule) throws CDKException {
logger.debug("Reading new molecule");
int linecount = 0;
int atoms = 0;
int bonds = 0;
int atom1 = 0;
int atom2 = 0;
int order = 0;
IBond.Stereo stereo = (IBond.Stereo) CDKConstants.UNSET;
int RGroupCounter = 1;
int Rnumber = 0;
String[] rGroup = null;
double x = 0.0;
double y = 0.0;
double z = 0.0;
double totalX = 0.0;
double totalY = 0.0;
double totalZ = 0.0;
//int[][] conMat = new int[0][0];
//String help;
IAtom atom;
String line = "";
try {
IsotopeFactory isotopeFactory = Isotopes.getInstance();
logger.info("Reading header");
line = input.readLine();
linecount++;
if (line == null) {
return null;
}
logger.debug("Line " + linecount + ": " + line);
if (line.startsWith("$$$$")) {
logger.debug("File is empty, returning empty molecule");
return molecule;
}
if (line.length() > 0) {
molecule.setProperty(CDKConstants.TITLE, line);
}
line = input.readLine();
linecount++;
logger.debug("Line " + linecount + ": " + line);
line = input.readLine();
linecount++;
logger.debug("Line " + linecount + ": " + line);
if (line.length() > 0) {
molecule.setProperty(CDKConstants.REMARK, line);
}
logger.info("Reading rest of file");
line = input.readLine();
linecount++;
logger.debug("Line " + linecount + ": " + line);
if (mode == Mode.STRICT) {
if (line.contains("V2000") || line.contains("v2000")) {
throw new CDKException("This file must be read with the MDLV2000Reader.");
}
if (line.contains("V3000") || line.contains("v3000")) {
throw new CDKException("This file must be read with the MDLV3000Reader.");
}
}
atoms = Integer.valueOf(line.substring(0, 3).trim()).intValue();
logger.debug("Atomcount: " + atoms);
bonds = Integer.valueOf(line.substring(3, 6).trim()).intValue();
logger.debug("Bondcount: " + bonds);
// read ATOM block
logger.info("Reading atom block");
for (int f = 0; f < atoms; f++) {
line = input.readLine();
linecount++;
Matcher trailingSpaceMatcher = TRAILING_SPACE.matcher(line);
if (trailingSpaceMatcher.find()) {
handleError("Trailing space found", linecount, trailingSpaceMatcher.start(),
trailingSpaceMatcher.end());
line = trailingSpaceMatcher.replaceAll("");
}
x = new Double(line.substring(0, 10).trim()).doubleValue();
y = new Double(line.substring(10, 20).trim()).doubleValue();
z = new Double(line.substring(20, 30).trim()).doubleValue();
// *all* values should be zero, not just the sum
totalX += Math.abs(x);
totalY += Math.abs(y);
totalZ += Math.abs(z);
logger.debug("Coordinates: " + x + "; " + y + "; " + z);
String element = line.substring(31, Math.min(34, line.length())).trim();
if (line.length() < 34) {
handleError("Element atom type does not follow V2000 format type should of length three"
+ " and padded with space if required", linecount, 31, 34);
}
logger.debug("Atom type: ", element);
if (isotopeFactory.isElement(element)) {
atom = isotopeFactory.configure(molecule.getBuilder().newInstance(IAtom.class, element));
} else if ("A".equals(element)) {
atom = molecule.getBuilder().newInstance(IPseudoAtom.class, element);
} else if ("Q".equals(element)) {
atom = molecule.getBuilder().newInstance(IPseudoAtom.class, element);
} else if ("*".equals(element)) {
atom = molecule.getBuilder().newInstance(IPseudoAtom.class, element);
} else if ("LP".equals(element)) {
atom = molecule.getBuilder().newInstance(IPseudoAtom.class, element);
} else if ("L".equals(element)) {
atom = molecule.getBuilder().newInstance(IPseudoAtom.class, element);
} else if (element.length() > 0 && element.charAt(0) == 'R') {
logger.debug("Atom ", element, " is not an regular element. Creating a PseudoAtom.");
//check if the element is R
rGroup = element.split("^R");
if (rGroup.length > 1) {
try {
Rnumber = Integer.parseInt(rGroup[(rGroup.length - 1)]);
RGroupCounter = Rnumber;
} catch (Exception ex) {
Rnumber = RGroupCounter;
RGroupCounter++;
}
element = "R" + Rnumber;
}
atom = molecule.getBuilder().newInstance(IPseudoAtom.class, element);
} else {
if (mode == ISimpleChemObjectReader.Mode.STRICT) {
throw new CDKException(
"Invalid element type. Must be an existing element, or one in: A, Q, L, LP, *.");
}
atom = molecule.getBuilder().newInstance(IPseudoAtom.class, element);
}
// store as 3D for now, convert to 2D (if totalZ == 0.0) later
atom.setPoint3d(new Point3d(x, y, z));
// parse further fields
if (line.length() >= 36) {
String massDiffString = line.substring(34, 36).trim();
logger.debug("Mass difference: ", massDiffString);
if (!(atom instanceof IPseudoAtom)) {
try {
int massDiff = Integer.parseInt(massDiffString);
if (massDiff != 0) {
IIsotope major = Isotopes.getInstance().getMajorIsotope(element);
atom.setAtomicNumber(major.getAtomicNumber() + massDiff);
}
} catch (NumberFormatException | IOException exception) {
logger.error("Could not parse mass difference field");
}
} else {
logger.error("Cannot set mass difference for a non-element!");
}
} else {
handleError("Mass difference is missing", linecount, 34, 36);
}
if (line.length() >= 39) {
String chargeCodeString = line.substring(36, 39).trim();
logger.debug("Atom charge code: ", chargeCodeString);
int chargeCode = Integer.parseInt(chargeCodeString);
if (chargeCode == 0) {
// uncharged species
} else if (chargeCode == 1) {
atom.setFormalCharge(+3);
} else if (chargeCode == 2) {
atom.setFormalCharge(+2);
} else if (chargeCode == 3) {
atom.setFormalCharge(+1);
} else if (chargeCode == 4) {
} else if (chargeCode == 5) {
atom.setFormalCharge(-1);
} else if (chargeCode == 6) {
atom.setFormalCharge(-2);
} else if (chargeCode == 7) {
atom.setFormalCharge(-3);
}
} else {
handleError("Atom charge count is empty", linecount, 35, 39);
}
try {
// read the mmm field as position 61-63
String reactionAtomIDString = line.substring(60, 63).trim();
logger.debug("Parsing mapping id: ", reactionAtomIDString);
try {
int reactionAtomID = Integer.parseInt(reactionAtomIDString);
if (reactionAtomID != 0) {
atom.setProperty(CDKConstants.ATOM_ATOM_MAPPING, reactionAtomID);
}
} catch (Exception exception) {
logger.error("Mapping number ", reactionAtomIDString, " is not an integer.");
logger.debug(exception);
}
} catch (Exception exception) {
// older mol files don't have all these fields...
logger.warn("A few fields are missing. Older MDL MOL file?");
}
//shk3: This reads shifts from after the molecule. I don't think this is an official format, but I saw it frequently 80=>78 for alk
if (line.length() >= 78) {
double shift = Double.parseDouble(line.substring(69, 80).trim());
atom.setProperty("first shift", new Double(shift));
}
if (line.length() >= 87) {
double shift = Double.parseDouble(line.substring(79, 87).trim());
atom.setProperty("second shift", new Double(shift));
}
molecule.addAtom(atom);
}
// convert to 2D, if totalZ == 0
if (totalX == 0.0 && totalY == 0.0 && totalZ == 0.0) {
logger.info("All coordinates are 0.0");
for (IAtom atomToUpdate : molecule.atoms()) {
atomToUpdate.setPoint3d(null);
}
} else if (totalZ == 0.0 && !forceReadAs3DCoords.isSet()) {
logger.info("Total 3D Z is 0.0, interpreting it as a 2D structure");
Iterator atomsToUpdate = molecule.atoms().iterator();
while (atomsToUpdate.hasNext()) {
IAtom atomToUpdate = (IAtom) atomsToUpdate.next();
Point3d p3d = atomToUpdate.getPoint3d();
atomToUpdate.setPoint2d(new Point2d(p3d.x, p3d.y));
atomToUpdate.setPoint3d(null);
}
}
// read BOND block
logger.info("Reading bond block");
for (int f = 0; f < bonds; f++) {
line = input.readLine();
linecount++;
atom1 = java.lang.Integer.valueOf(line.substring(0, 3).trim()).intValue();
atom2 = java.lang.Integer.valueOf(line.substring(3, 6).trim()).intValue();
order = java.lang.Integer.valueOf(line.substring(6, 9).trim()).intValue();
if (line.length() > 12) {
int mdlStereo = Integer.valueOf(line.substring(9, 12).trim());
if (mdlStereo == 1) {
// MDL up bond
stereo = IBond.Stereo.UP;
} else if (mdlStereo == 6) {
// MDL down bond
stereo = IBond.Stereo.DOWN;
} else if (mdlStereo == 0) {
// bond has no stereochemistry
stereo = IBond.Stereo.NONE;
} else if (mdlStereo == 4) {
//MDL up or down bond
stereo = IBond.Stereo.UP_OR_DOWN;
} else if (mdlStereo == 3) {
//MDL e or z undefined
stereo = IBond.Stereo.E_OR_Z;
}
} else {
logger.warn("Missing expected stereo field at line: " + line);
}
if (logger.isDebugEnabled()) {
logger.debug("Bond: " + atom1 + " - " + atom2 + "; order " + order);
}
// interpret CTfile's special bond orders
IAtom a1 = molecule.getAtom(atom1 - 1);
IAtom a2 = molecule.getAtom(atom2 - 1);
IBond newBond = null;
if (order >= 1 && order <= 3) {
IBond.Order cdkOrder = IBond.Order.SINGLE;
if (order == 2) cdkOrder = IBond.Order.DOUBLE;
if (order == 3) cdkOrder = IBond.Order.TRIPLE;
if (stereo != null) {
newBond = molecule.getBuilder().newInstance(IBond.class, a1, a2, cdkOrder, stereo);
} else {
newBond = molecule.getBuilder().newInstance(IBond.class, a1, a2, cdkOrder);
}
} else if (order == 4) {
// aromatic bond
if (stereo != null) {
newBond = molecule.getBuilder().newInstance(IBond.class, a1, a2, IBond.Order.SINGLE, stereo);
} else {
newBond = molecule.getBuilder().newInstance(IBond.class, a1, a2, IBond.Order.SINGLE);
}
// mark both atoms and the bond as aromatic
newBond.setFlag(CDKConstants.ISAROMATIC, true);
a1.setFlag(CDKConstants.ISAROMATIC, true);
a2.setFlag(CDKConstants.ISAROMATIC, true);
}
molecule.addBond(newBond);
}
} catch (IOException | CDKException | IllegalArgumentException exception) {
exception.printStackTrace();
String error = "Error while parsing line " + linecount + ": " + line + " -> " + exception.getMessage();
logger.error(error);
logger.debug(exception);
throw new CDKException(error, exception);
}
return molecule;
}
@Override
public void close() throws IOException {
input.close();
}
private void initIOSettings() {
forceReadAs3DCoords = addSetting(new BooleanIOSetting("ForceReadAs3DCoordinates", IOSetting.Importance.LOW,
"Should coordinates always be read as 3D?", "false"));
}
public void customizeJob() {
fireIOSettingQuestion(forceReadAs3DCoords);
}
}
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