org.xmlcml.cml.tools.FragmentConverter Maven / Gradle / Ivy
/**
* Copyright 2011 Peter Murray-Rust et. al.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
package org.xmlcml.cml.tools;
import java.io.BufferedOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.OutputStream;
import java.util.ArrayList;
import java.util.List;
import nu.xom.Attribute;
import nu.xom.Document;
import nu.xom.Node;
import nu.xom.Serializer;
import org.xmlcml.cml.attribute.IdAttribute;
import org.xmlcml.cml.base.AbstractTool;
import org.xmlcml.cml.base.CMLBuilder;
import org.xmlcml.cml.base.CMLConstants;
import org.xmlcml.cml.base.CMLElement;
import org.xmlcml.cml.base.CMLElements;
import org.xmlcml.cml.base.CMLUtil;
import org.xmlcml.cml.element.CMLAngle;
import org.xmlcml.cml.element.CMLArg;
import org.xmlcml.cml.element.CMLAtom;
import org.xmlcml.cml.element.CMLBond;
import org.xmlcml.cml.element.CMLFragment;
import org.xmlcml.cml.element.CMLFragmentList;
import org.xmlcml.cml.element.CMLLength;
import org.xmlcml.cml.element.CMLMolecule;
import org.xmlcml.cml.element.CMLMoleculeList;
import org.xmlcml.cml.element.CMLTorsion;
import org.xmlcml.euclid.EuclidConstants;
import org.xmlcml.euclid.Util;
/** processes conventional molecule into fragment.
*
* @author pm286
*
*/
public class FragmentConverter extends AbstractTool {
private CMLMolecule molecule;
private String molId;
/**
* constructor
* @param molecule
*/
public FragmentConverter(CMLMolecule molecule) {
this.molecule = molecule;
}
/** processes conventional molecule into fragment.
* @return fragment
*/
public CMLFragment convertToFragment() {
//
//
// acet_{$idx}
molId = molecule.getId();
if (molId == null) {
throw new RuntimeException("molecule must have id");
}
molecule.addAttribute(new Attribute("role", "fragment"));
CMLArg arg = new CMLArg();
arg.setParameterName(FragmentTool.IDX);
molecule.appendChild(arg);
arg = new CMLArg();
arg.setParentAttribute("id");
arg.appendChild(molId + CMLConstants.S_UNDER + CMLConstants.S_LCURLY + CMLConstants.S_DOLLAR + FragmentTool.IDX + CMLConstants.S_RCURLY);
molecule.appendChild(arg);
createAtomArguments();
createBondArguments();
createLengthArguments();
createAngleArguments();
createTorsionArguments();
// deal with R
List rGroups = CMLUtil.getQueryNodes(molecule,
".//"+CMLAtom.NS+"[@elementType='R']", CMLConstants.CML_XPATH);
for (Node node : rGroups) {
try {
AtomTool.getOrCreateTool((CMLAtom) node).translateToCovalentRadius();
} catch (RuntimeException e) {
// no coordinates, not an error
}
}
CMLFragment fragment = new CMLFragment();
fragment.setId(molecule.getId());
FragmentTool.getOrCreateTool(fragment).setMolecule(molecule);
molecule.removeAttribute(IdAttribute.NAME);
return fragment;
}
private void createAtomArguments() {
//
//
// acet_{$idx}_a1
//
List atoms = molecule.getAtoms();
for (CMLAtom atom : atoms) {
String atomId = atom.getId();
CMLArg arg = new CMLArg();
arg.setParentAttribute("id");
arg.appendChild(createMolIdArg() + atomId);
atom.appendChild(arg);
}
}
private void createBondArguments() {
// ...
//
// acet_{$idx}_r1
//
//
//
// acet_{$idx}_a1_acet_{$idx}_a2 acet_{$idx}_a1 acet_{$idx}_a2
// acet_{$idx}_a4_acet_{$idx}_r1 acet_{$idx}_a4 acet_{$idx}_r1
//
// acet_{$idx} bonds = molecule.getBonds();
for (CMLBond bond : bonds) {
// String bondId = bond.getId();
String[] atomRefs2 = bond.getAtomRefs2();
CMLArg arg = new CMLArg();
arg.setParentAttribute("id");
arg.appendChild(
createMolIdArg()+atomRefs2[0]+EuclidConstants.S_UNDER+
createMolIdArg()+atomRefs2[1]
);
bond.appendChild(arg);
arg = new CMLArg();
arg.setParentAttribute("atomRefs2");
arg.appendChild(
createMolIdArg()+atomRefs2[0]+EuclidConstants.S_SPACE+
createMolIdArg()+atomRefs2[1]
);
bond.appendChild(arg);
}
}
private void createLengthArguments() {
//
// gly_{$idx}_a1 gly_{$idx}_a2
// {$psi}
//
MoleculeTool moleculeTool = MoleculeTool.getOrCreateTool(molecule);
List lengths = moleculeTool.getLengthElements();
for (CMLLength length : lengths) {
// id
String lengthId = length.getId();
CMLArg arg = new CMLArg();
arg.setParentAttribute("id");
arg.appendChild(createMolIdArg() + lengthId);
length.appendChild(arg);
// atomRefs4
String[] atomRefs2 = length.getAtomRefs2();
arg = new CMLArg();
arg.setParentAttribute("atomRefs2");
arg.appendChild(
createMolIdArg() + atomRefs2[0] +EuclidConstants.S_SPACE+
createMolIdArg() + atomRefs2[1]
);
length.appendChild(arg);
addArg(length, lengthId);
}
}
private void createTorsionArguments() {
//
// gly_{$idx}_a1 gly_{$idx}_a2 gly_{$idx}_a3 gly_{$idx}_r2
// {$psi}
//
MoleculeTool moleculeTool = MoleculeTool.getOrCreateTool(molecule);
List torsions = moleculeTool.getTorsionElements();
for (CMLTorsion torsion : torsions) {
// id
String torsionId = torsion.getId();
CMLArg arg = new CMLArg();
arg.setParentAttribute("id");
arg.appendChild(createMolIdArg() + torsionId);
torsion.appendChild(arg);
// atomRefs4
String[] atomRefs4 = torsion.getAtomRefs4();
arg = new CMLArg();
arg.setParentAttribute("atomRefs4");
arg.appendChild(
createMolIdArg() + atomRefs4[0] +EuclidConstants.S_SPACE+
createMolIdArg() + atomRefs4[1] +EuclidConstants.S_SPACE+
createMolIdArg() + atomRefs4[2] +EuclidConstants.S_SPACE+
createMolIdArg() + atomRefs4[3]
);
torsion.appendChild(arg);
addArg(torsion, torsionId);
}
}
private void createAngleArguments() {
//
// gly_{$idx}_a1 gly_{$idx}_a2 gly_{$idx}_a3 gly_{$idx}_r2
// {$psi}
//
MoleculeTool moleculeTool = MoleculeTool.getOrCreateTool(molecule);
List angles = moleculeTool.getAngleElements();
for (CMLAngle angle : angles) {
// id
String angleId = angle.getId();
CMLArg arg = new CMLArg();
arg.setParentAttribute("id");
arg.appendChild(createMolIdArg() + angleId);
angle.appendChild(arg);
// atomRefs4
String[] atomRefs3 = angle.getAtomRefs3();
arg = new CMLArg();
arg.setParentAttribute("atomRefs3");
arg.appendChild(
createMolIdArg() + atomRefs3[0] +EuclidConstants.S_SPACE+
createMolIdArg() + atomRefs3[1] +EuclidConstants.S_SPACE+
createMolIdArg() + atomRefs3[2]
);
angle.appendChild(arg);
addArg(angle, angleId);
}
}
private void addArg(CMLElement element, String id) {
// substitute
CMLArg arg = new CMLArg();
arg.setSubstitute(EuclidConstants.S_PERIOD);
arg.appendChild(createIdArg(id));
element.appendChild(arg);
// append args to molecule
arg = new CMLArg();
arg.setParameterName(id);
molecule.appendChild(arg);
}
// at present gly_{$idx}_
private String createMolIdArg() {
return molId +
S_UNDER + createIdArg(FragmentTool.IDX) + CMLConstants.S_UNDER;
}
// at present {$id}
private static String createIdArg(String id) {
return CMLConstants.S_LCURLY + CMLConstants.S_DOLLAR + id + CMLConstants.S_RCURLY;
}
/** convenience method.
*
* @param moleculeList list to convert
* @return list for fragments
*/
public static List convertMolecules(List moleculeList) {
List fragmentList = new ArrayList();
for (CMLMolecule molecule : moleculeList) {
FragmentConverter fragmentConverter = new FragmentConverter(molecule);
CMLFragment fragment =fragmentConverter.convertToFragment();
fragmentList.add(fragment);
}
return fragmentList;
}
/** convenience method.
*
* @param moleculeList list to convert
* @return list for fragments
*/
public static CMLFragmentList convertMolecules(CMLMoleculeList moleculeList) {
CMLFragmentList fragmentList = new CMLFragmentList();
FragmentListTool fragmentListTool = FragmentListTool.getOrCreateTool(fragmentList);
CMLElements molecules = moleculeList.getMoleculeElements();
for (CMLMolecule molecule : molecules) {
FragmentConverter fragmentConverter = new FragmentConverter(molecule);
CMLFragment fragment =fragmentConverter.convertToFragment();
fragmentListTool.addFragment(fragment);
}
return fragmentListTool.getFragmentList();
}
/**Call with to set up polinfo fragments:
* -indir src/test/java/org/xmlcml/cml/tools/examples/molecules/polyinfomol -outdir src/test/java/org/xmlcml/cml/tools/examples/molecules/polyinfo/
* @param args
*/
public static void main(String[] args) {
CommandlineFragmentConverter converter = new CommandlineFragmentConverter(args);
if (converter.indir != null) {
File[] files = new File(converter.indir).listFiles();
for (File file : files) {
try {
CMLMolecule molecule = (CMLMolecule) new CMLBuilder().build(new FileInputStream(file)).getRootElement();
FragmentConverter fragmentConverter = new FragmentConverter(molecule);
CMLFragment fragment = fragmentConverter.convertToFragment();
if(converter.outdir!=null){converter.setOutputFile(converter.outdir+"/"+file.getName());}
else{System.err.println("indir but no outdir");
System.exit(-1);
}
converter.writeFragment(fragment);
} catch (Exception e) {
System.err.println("Cannot find/parse file: "+file.getAbsolutePath());
}
}
}
else if(converter.infile !=null){
File file = new File(converter.infile);
try {
CMLMolecule molecule = (CMLMolecule) new CMLBuilder().build(new FileInputStream(file)).getRootElement();
FragmentConverter fragmentConverter = new FragmentConverter(molecule);
CMLFragment fragment = fragmentConverter.convertToFragment();
if(converter.outfile!=null){converter.setOutputFile(converter.outfile);}
else{System.err.println("infile but no outfile");
System.exit(-1);
}
converter.writeFragment(fragment);
} catch (Exception e) {
System.err.println("Cannot find/parse file: "+file.getAbsolutePath());
}
}
}
private static class CommandlineFragmentConverter {
String infile = null;
String outfile = null;
String indir = null;
String outdir = null;
File output=null;
/**
* @param args
*/
public CommandlineFragmentConverter(String[] args){
if (args.length==0 || args.length%2==1){
usage();
System.exit(-1);
}
for(int i=0;i");
Util.println(" -in (filename) //Input File");
Util.println(" -out (filename) //Output File");
Util.println(" -indir (dirname) //Whole directory to be input");
Util.println(" -outdir (dirname) //Whole directory to be output");
}
private void setOutputFile(String file){
output = new File(file);
}
private void writeFragment(CMLFragment fragment){
OutputStream out=null;
Document doc = new Document(fragment);
try{
out = new BufferedOutputStream(new FileOutputStream(output));
Serializer serializer = new Serializer(out, "ISO-8859-1");
serializer.setIndent(4);
serializer.write(doc);
}
catch (IOException ex){
System.err.println("Failed outputting "+ex);
}
finally{
if (out != null) {
Util.println("Writing fragment "+output.getAbsolutePath());
try {
out.close();
} catch (IOException e) {
System.err.println("Error while closing outputstrem");
e.printStackTrace();
}
}
}
}
}
}
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