org.openscience.cdk.io.RGroupQueryWriter Maven / Gradle / Ivy
/*
* Copyright (C) 2010 Mark Rijnbeek
*
* 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.BufferedWriter;
import java.io.IOException;
import java.io.OutputStream;
import java.io.OutputStreamWriter;
import java.io.StringWriter;
import java.io.Writer;
import java.text.SimpleDateFormat;
import java.util.List;
import java.util.Map;
import org.openscience.cdk.exception.CDKException;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObject;
import org.openscience.cdk.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.RGroupQueryFormat;
import org.openscience.cdk.isomorphism.matchers.IRGroupQuery;
import org.openscience.cdk.isomorphism.matchers.RGroup;
import org.openscience.cdk.isomorphism.matchers.RGroupList;
/**
* A writer for Symyx' Rgroup files (RGFiles).
* An RGfile describes a single molecular query with Rgroups.
* Each RGfile is a combination of Ctabs defining the root molecule and each
* member of each Rgroup in the query.
*
* This class relies on the {@link org.openscience.cdk.io.MDLV2000Writer} to
* create CTAB data blocks.
*
* @cdk.module io
* @cdk.githash
* @cdk.iooptions
* @cdk.keyword Rgroup
* @cdk.keyword R group
* @cdk.keyword R-group
* @author Mark Rijnbeek
*/
public class RGroupQueryWriter extends DefaultChemObjectWriter {
private BufferedWriter writer;
private static String LSEP = System.getProperty("line.separator");
/**
* Constructs a new writer that can write an {@link IRGroupQuery}
* to the Symx RGFile format.
*
* @param out The Writer to write to
*/
public RGroupQueryWriter(Writer out) {
if (out instanceof BufferedWriter) {
writer = (BufferedWriter) out;
} else {
writer = new BufferedWriter(out);
}
}
/**
* Zero argument constructor.
*/
public RGroupQueryWriter() {
this(new StringWriter());
}
/**
* Returns true for accepted input types.
*/
@SuppressWarnings("unchecked")
@Override
public boolean accepts(Class classObject) {
Class[] interfaces = classObject.getInterfaces();
for (Class anInterface : interfaces) {
if (IRGroupQuery.class.equals(anInterface)) return true;
}
Class superClass = classObject.getSuperclass();
if (superClass != null) return this.accepts(superClass);
return false;
}
/**
* Flushes the output and closes this object.
*/
@Override
public void close() throws IOException {
writer.close();
}
/**
* Produces a CTAB block for an atomContainer, without the header lines.
* @param atomContainer
* @return CTAB block
* @throws CDKException
*/
private String getCTAB(IAtomContainer atomContainer) throws CDKException {
StringWriter strWriter = new StringWriter();
MDLV2000Writer mdlWriter = new MDLV2000Writer(strWriter);
mdlWriter.write(atomContainer);
try {
mdlWriter.close();
} catch (IOException exception) {
// FIXME
}
String ctab = strWriter.toString();
//strip of the individual header, as we have one super header instead.
for (int line = 1; line <= 3; line++) {
ctab = ctab.substring(ctab.indexOf(LSEP) + (LSEP.length()));
}
return ctab;
}
/**
* Returns output format.
*/
@Override
public IResourceFormat getFormat() {
return RGroupQueryFormat.getInstance();
}
/**
* Sets the writer to given output stream.
*/
@Override
public void setWriter(OutputStream output) throws CDKException {
setWriter(new OutputStreamWriter(output));
}
/**
* Sets the writer.
*/
@Override
public void setWriter(Writer out) throws CDKException {
if (out instanceof BufferedWriter) {
writer = (BufferedWriter) out;
} else {
writer = new BufferedWriter(out);
}
}
/**
* The actual writing of the output.
* @throws CDKException
* @throws IOException
*/
@Override
public void write(IChemObject object) throws CDKException {
if (!(object instanceof IRGroupQuery)) {
throw new CDKException("Only IRGroupQuery input is accepted.");
}
try {
IRGroupQuery rGroupQuery = (IRGroupQuery) object;
String now = new SimpleDateFormat("MMddyyHHmm").format(System.currentTimeMillis());
IAtomContainer rootAtc = rGroupQuery.getRootStructure();
//Construct header
StringBuffer rootBlock = new StringBuffer();
String header = "$MDL REV 1 " + now + LSEP + "$MOL" + LSEP + "$HDR" + LSEP
+ " Rgroup query file (RGFile)" + LSEP + " CDK " + now + "2D" + LSEP + LSEP + "$END HDR"
+ LSEP + "$CTAB";
rootBlock.append(header).append(LSEP);
//Construct the root structure, the scaffold
String rootCTAB = getCTAB(rootAtc);
rootCTAB = rootCTAB.replaceAll(LSEP + "M END" + LSEP, "");
rootBlock.append(rootCTAB).append(LSEP);
//Write the root's LOG lines
for (Integer rgrpNum : rGroupQuery.getRGroupDefinitions().keySet()) {
RGroupList rgList = rGroupQuery.getRGroupDefinitions().get(rgrpNum);
int restH = rgList.isRestH() ? 1 : 0;
String logLine = "M LOG" + MDLV2000Writer.formatMDLInt(1, 3) + MDLV2000Writer.formatMDLInt(rgrpNum, 4)
+ MDLV2000Writer.formatMDLInt(rgList.getRequiredRGroupNumber(), 4)
+ MDLV2000Writer.formatMDLInt(restH, 4) + " " + rgList.getOccurrence();
rootBlock.append(logLine).append(LSEP);
}
//AAL lines are optional, they are needed for R-atoms with multiple bonds to the root
//for which the order of the attachment points can not be implicitly derived
//from the order in the atom block. See CT spec for more on that.
for (IAtom rgroupAtom : rGroupQuery.getRootAttachmentPoints().keySet()) {
Map rApo = rGroupQuery.getRootAttachmentPoints().get(rgroupAtom);
if (rApo.size() > 1) {
int prevPos = -1;
int apoIdx = 1;
boolean implicitlyOrdered = true;
while (rApo.get(apoIdx) != null && implicitlyOrdered) {
IAtom partner = rApo.get(apoIdx).getConnectedAtom(rgroupAtom);
for (int atIdx = 0; atIdx < rootAtc.getAtomCount(); atIdx++) {
if (rootAtc.getAtom(atIdx).equals(partner)) {
if (atIdx < prevPos) implicitlyOrdered = false;
prevPos = atIdx;
break;
}
}
apoIdx++;
}
if (!implicitlyOrdered) {
StringBuffer aalLine = new StringBuffer("M AAL");
for (int atIdx = 0; atIdx < rootAtc.getAtomCount(); atIdx++) {
if (rootAtc.getAtom(atIdx).equals(rgroupAtom)) {
aalLine.append(MDLV2000Writer.formatMDLInt((atIdx + 1), 4));
aalLine.append(MDLV2000Writer.formatMDLInt(rApo.size(), 3));
apoIdx = 1;
while (rApo.get(apoIdx) != null) {
IAtom partner = rApo.get(apoIdx).getConnectedAtom(rgroupAtom);
for (int a = 0; a < rootAtc.getAtomCount(); a++) {
if (rootAtc.getAtom(a).equals(partner)) {
aalLine.append(MDLV2000Writer.formatMDLInt(a + 1, 4));
aalLine.append(MDLV2000Writer.formatMDLInt(apoIdx, 4));
}
}
apoIdx++;
}
}
}
rootBlock.append(aalLine.toString()).append(LSEP);
}
}
}
rootBlock.append("M END").append(LSEP).append("$END CTAB").append(LSEP);
//Construct each R-group block
StringBuffer rgpBlock = new StringBuffer();
for (Integer rgrpNum : rGroupQuery.getRGroupDefinitions().keySet()) {
List rgrpList = rGroupQuery.getRGroupDefinitions().get(rgrpNum).getRGroups();
if (rgrpList != null && rgrpList.size() != 0) {
rgpBlock.append("$RGP").append(LSEP);;
rgpBlock.append(MDLV2000Writer.formatMDLInt(rgrpNum, 4)).append(LSEP);
for (RGroup rgroup : rgrpList) {
//CTAB block
rgpBlock.append("$CTAB").append(LSEP);
String ctab = getCTAB(rgroup.getGroup());
ctab = ctab.replaceAll(LSEP + "M END" + LSEP, "");
rgpBlock.append(ctab).append(LSEP);
//The APO line
IAtom firstAttachmentPoint = rgroup.getFirstAttachmentPoint();
IAtom secondAttachmentPoint = rgroup.getSecondAttachmentPoint();
int apoCount = 0;
if (firstAttachmentPoint != null) {
StringBuffer apoLine = new StringBuffer();
for (int atIdx = 0; atIdx < rgroup.getGroup().getAtomCount(); atIdx++) {
if (rgroup.getGroup().getAtom(atIdx).equals(firstAttachmentPoint)) {
apoLine.append(MDLV2000Writer.formatMDLInt((atIdx + 1), 4));
apoCount++;
if (secondAttachmentPoint != null
&& secondAttachmentPoint.equals(firstAttachmentPoint)) {
apoLine.append(MDLV2000Writer.formatMDLInt(3, 4));
} else {
apoLine.append(MDLV2000Writer.formatMDLInt(1, 4));
}
}
}
if (secondAttachmentPoint != null && !secondAttachmentPoint.equals(firstAttachmentPoint)) {
for (int atIdx = 0; atIdx < rgroup.getGroup().getAtomCount(); atIdx++) {
if (rgroup.getGroup().getAtom(atIdx).equals(secondAttachmentPoint)) {
apoCount++;
apoLine.append(MDLV2000Writer.formatMDLInt((atIdx + 1), 4));
apoLine.append(MDLV2000Writer.formatMDLInt(2, 4));
}
}
}
if (apoCount > 0) {
apoLine.insert(0, "M APO" + MDLV2000Writer.formatMDLInt(apoCount, 3));
rgpBlock.append(apoLine).append(LSEP);
}
}
rgpBlock.append("M END").append(LSEP);
rgpBlock.append("$END CTAB").append(LSEP);
}
rgpBlock.append("$END RGP").append(LSEP);
}
}
rgpBlock.append("$END MOL").append(LSEP);
writer.write(rootBlock.toString());
writer.write(rgpBlock.toString());
writer.flush();
} catch (IOException e) {
e.printStackTrace();
throw new CDKException("Unexpected exception when writing RGFile" + LSEP + e.getMessage());
}
}
}
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