/*
* Copyright (C) 2010 Mark Rijnbeek <mark_rynbeek@users.sf.net>
*
* Contact: cdk-devel@lists.sourceforge.net
*
* 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.annotations.TestMethod;
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).<br>
* 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.
* <br>
* This class relies on the {@link org.openscience.cdk.io.MDLWriter} to
* create CTAB data blocks.
*
* @cdk.module io
* @cdk.githash
* @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")
@TestMethod("testAccepts")
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.
*/
@TestMethod("testClose")
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();
MDLWriter mdlWriter = new MDLWriter(strWriter);
mdlWriter.write(atomContainer);
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)+1);
}
return ctab;
}
/**
* Returns output format.
*/
@TestMethod("testGetFormat")
public IResourceFormat getFormat() {
return RGroupQueryFormat.getInstance();
}
/**
* Sets the writer to given output stream.
*/
public void setWriter(OutputStream output) throws CDKException {
setWriter(new OutputStreamWriter(output));
}
/**
* Sets the writer.
*/
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
*/
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\n" +
"$HDR\n" +
" Rgroup query file (RGFile)\n"+
" CDK "+now+"2D\n\n"+
"$END HDR\n"+
"$CTAB";
rootBlock.append(header).append(LSEP);
//Construct the root structure, the scaffold
String rootCTAB = getCTAB(rootAtc);
rootCTAB = rootCTAB.replaceAll("\nM END\n","");
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"+
MDLWriter.formatMDLInt(1, 3)+
MDLWriter.formatMDLInt(rgrpNum, 4)+
MDLWriter.formatMDLInt(rgList.getRequiredRGroupNumber(), 4)+
MDLWriter.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<Integer, IBond> 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(MDLWriter.formatMDLInt((atIdx+1), 4));
aalLine.append(MDLWriter.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(MDLWriter.formatMDLInt(a+1, 4));
aalLine.append(MDLWriter.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<RGroup> rgrpList = rGroupQuery.getRGroupDefinitions().get(rgrpNum).getRGroups();
if(rgrpList!=null && rgrpList.size()!=0) {
rgpBlock.append("$RGP").append(LSEP);;
rgpBlock.append(MDLWriter.formatMDLInt(rgrpNum, 4)).append(LSEP);
for (RGroup rgroup : rgrpList) {
//CTAB block
rgpBlock.append("$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(MDLWriter.formatMDLInt((atIdx+1), 3));
apoCount++;
if (secondAttachmentPoint!=null &&
secondAttachmentPoint.equals(firstAttachmentPoint)) {
apoLine.append(MDLWriter.formatMDLInt(3, 3));
}
else {
apoLine.append(MDLWriter.formatMDLInt(1, 3));
}
}
}
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(MDLWriter.formatMDLInt((atIdx+1), 3));
apoLine.append(MDLWriter.formatMDLInt(2, 3));
}
}
}
if (apoCount>0) {
apoLine.insert(0, "M APO"+MDLWriter.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 excpetion when writing RGFile.\n"+e.getMessage());
}
}
}