org.openscience.cdk.io.PCCompoundASNReader Maven / Gradle / Ivy
/* Copyright (C) 2006-2007 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.HashMap;
import java.util.Map;
import org.openscience.cdk.CDKConstants;
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.io.formats.IResourceFormat;
import org.openscience.cdk.io.formats.PubChemASNFormat;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
/**
* Reads an object from ASN formated input for PubChem Compound entries. The following
* bits are supported: atoms.aid, atoms.element, bonds.aid1, bonds.aid2. Additionally,
* it extracts the InChI and canonical SMILES properties.
*
* @cdk.module io
* @cdk.githash
* @cdk.iooptions
*
* @cdk.keyword file format, PubChem Compound ASN
*/
public class PCCompoundASNReader extends DefaultChemObjectReader {
private BufferedReader input;
private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(PCCompoundASNReader.class);
IAtomContainer molecule = null;
Map atomIDs = null;
/**
* Construct a new reader from a Reader type object.
*
* @param input reader from which input is read
*/
public PCCompoundASNReader(Reader input) {
this.input = new BufferedReader(input);
}
public PCCompoundASNReader(InputStream input) {
this(new InputStreamReader(input));
}
public PCCompoundASNReader() {
this(new StringReader(""));
}
@Override
public IResourceFormat getFormat() {
return PubChemASNFormat.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;
}
@Override
public T read(T object) throws CDKException {
if (object instanceof IChemFile) {
try {
return (T) readChemFile((IChemFile) object);
} catch (IOException e) {
throw new CDKException("An IO Exception occured while reading the file.", e);
} catch (CDKException e) {
throw e;
} catch (Exception e) {
throw new CDKException("An error occured.", e);
}
} else {
throw new CDKException("Only supported is reading of ChemFile objects.");
}
}
@Override
public void close() throws IOException {
input.close();
}
// private procedures
private IChemFile readChemFile(IChemFile file) throws Exception {
IChemSequence chemSequence = file.getBuilder().newInstance(IChemSequence.class);
IChemModel chemModel = file.getBuilder().newInstance(IChemModel.class);
IAtomContainerSet moleculeSet = file.getBuilder().newInstance(IAtomContainerSet.class);
molecule = file.getBuilder().newInstance(IAtomContainer.class);
atomIDs = new HashMap();
String line = input.readLine();
while (input.ready() && line != null) {
if (line.indexOf('{') != -1) {
processBlock(line);
} else {
logger.warn("Skipping non-block: " + line);
}
line = input.readLine();
}
moleculeSet.addAtomContainer(molecule);
chemModel.setMoleculeSet(moleculeSet);
chemSequence.addChemModel(chemModel);
file.addChemSequence(chemSequence);
return file;
}
private void processBlock(String line) throws Exception {
String command = getCommand(line);
if (command.equals("atoms")) {
// parse frame by frame
logger.debug("ASN atoms found");
processAtomBlock();
} else if (command.equals("bonds")) {
// ok, that fine
logger.debug("ASN bonds found");
processBondBlock();
} else if (command.equals("props")) {
// ok, that fine
logger.debug("ASN props found");
processPropsBlock();
} else if (command.equals("PC-Compound ::=")) {
// ok, that fine
logger.debug("ASN PC-Compound found");
} else {
logger.warn("Skipping block: " + command);
skipBlock();
}
}
private void processPropsBlock() throws Exception {
String line = input.readLine();
while (input.ready() && line != null) {
if (line.indexOf('{') != -1) {
processPropsBlockBlock();
} else if (line.indexOf('}') != -1) {
return;
} else {
logger.warn("Skipping non-block: " + line);
}
line = input.readLine();
}
}
private void processPropsBlockBlock() throws Exception {
String line = input.readLine();
URN urn = null;
while (input.ready() && line != null) {
if (line.indexOf("urn") != -1) {
urn = extractURN();
} else if (line.indexOf("value") != -1) {
logger.debug("Found a prop value line: " + line);
if (line.indexOf(" sval") != -1) {
logger.debug("Label: " + urn.label);
logger.debug("Name: " + urn.name);
if ("InChI".equals(urn.label)) {
String value = getQuotedValue(line.substring(line.indexOf("value sval") + 10));
molecule.setProperty(CDKConstants.INCHI, value);
} else if ("SMILES".equals(urn.label) && "Canonical".equals(urn.name)) {
String value = getQuotedValue(line.substring(line.indexOf("value sval") + 10));
molecule.setProperty(CDKConstants.SMILES, value);
}
}
} else if (line.indexOf('}') != -1) {
return;
} else {
logger.warn("Skipping non-block: " + line);
}
line = input.readLine();
}
}
private URN extractURN() throws Exception {
URN urn = new URN();
String line = input.readLine();
while (input.ready() && line != null) {
if (line.indexOf("name") != -1) {
urn.name = getQuotedValue(line.substring(line.indexOf("name") + 4));
} else if (line.indexOf("label") != -1) {
urn.label = getQuotedValue(line.substring(line.indexOf("label") + 4));
} else if (line.indexOf('}') != -1 && line.indexOf('\"') == -1) {
// ok, don't return if it also has a "
return urn;
} else {
logger.warn("Ignoring URN statement: " + line);
}
line = input.readLine();
}
return urn;
}
private void processAtomBlock() throws Exception {
String line = input.readLine();
while (input.ready() && line != null) {
if (line.indexOf('{') != -1) {
processAtomBlockBlock(line);
} else if (line.indexOf('}') != -1) {
return;
} else {
logger.warn("Skipping non-block: " + line);
}
line = input.readLine();
}
}
private void processBondBlock() throws Exception {
String line = input.readLine();
while (input.ready() && line != null) {
if (line.indexOf('{') != -1) {
processBondBlockBlock(line);
} else if (line.indexOf('}') != -1) {
return;
} else {
logger.warn("Skipping non-block: " + line);
}
line = input.readLine();
}
}
private IAtom getAtom(int i) {
if (molecule.getAtomCount() <= i) {
molecule.addAtom(molecule.getBuilder().newInstance(IAtom.class));
}
return molecule.getAtom(i);
}
private IBond getBond(int i) {
if (molecule.getBondCount() <= i) {
molecule.addBond(molecule.getBuilder().newInstance(IBond.class));
}
return molecule.getBond(i);
}
private void processAtomBlockBlock(String line) throws Exception {
String command = getCommand(line);
if (command.equals("aid")) {
// assume this is the first block in the atom block
logger.debug("ASN atoms aid found");
processAtomAIDs();
} else if (command.equals("element")) {
// assume this is the first block in the atom block
logger.debug("ASN atoms element found");
processAtomElements();
} else {
logger.warn("Skipping atom block block: " + command);
skipBlock();
}
}
private void processBondBlockBlock(String line) throws Exception {
String command = getCommand(line);
if (command.equals("aid1")) {
// assume this is the first block in the atom block
logger.debug("ASN bonds aid1 found");
processBondAtomIDs(0);
} else if (command.equals("aid2")) {
// assume this is the first block in the atom block
logger.debug("ASN bonds aid2 found");
processBondAtomIDs(1);
} else {
logger.warn("Skipping atom block block: " + command);
skipBlock();
}
}
private void processAtomAIDs() throws Exception {
String line = input.readLine();
int atomIndex = 0;
while (input.ready() && line != null) {
if (line.indexOf('}') != -1) {
// done
return;
} else {
// logger.debug("Found an atom ID: " + line);
// logger.debug(" index: " + atomIndex);
IAtom atom = getAtom(atomIndex);
String id = getValue(line);
atom.setID(id);
atomIDs.put(id, atom);
atomIndex++;
}
line = input.readLine();
}
}
private void processBondAtomIDs(int pos) throws Exception {
String line = input.readLine();
int bondIndex = 0;
while (input.ready() && line != null) {
if (line.indexOf('}') != -1) {
// done
return;
} else {
// logger.debug("Found an atom ID: " + line);
// logger.debug(" index: " + atomIndex);
IBond bond = getBond(bondIndex);
String id = getValue(line);
IAtom atom = (IAtom) atomIDs.get(id);
if (atom == null) {
throw new CDKException("File is corrupt: atom ID does not exist " + id);
}
bond.setAtom(atom, pos);
bondIndex++;
}
line = input.readLine();
}
}
private void processAtomElements() throws Exception {
String line = input.readLine();
int atomIndex = 0;
while (input.ready() && line != null) {
if (line.indexOf('}') != -1) {
// done
return;
} else {
// logger.debug("Found symbol: " + toSymbol(getValue(line)));
// logger.debug(" index: " + atomIndex);
IAtom atom = getAtom(atomIndex);
atom.setSymbol(toSymbol(getValue(line)));
atomIndex++;
}
line = input.readLine();
}
}
private String toSymbol(String value) {
if (value.length() == 1) return value.toUpperCase();
return value.substring(0, 1).toUpperCase() + value.substring(1);
}
private void skipBlock() throws IOException {
String line = input.readLine();
int openBrackets = 0;
while (line != null) {
// logger.debug("SkipBlock: line=" + line);
if (line.indexOf('{') != -1) {
openBrackets++;
}
// logger.debug(" #open brackets: " + openBrackets);
if (line.indexOf('}') != -1) {
if (openBrackets == 0) return;
openBrackets--;
}
line = input.readLine();
}
}
private String getCommand(String line) {
StringBuffer buffer = new StringBuffer();
int i = 0;
boolean foundBracket = false;
while (i < line.length() && !foundBracket) {
char currentChar = line.charAt(i);
if (currentChar == '{') {
foundBracket = true;
} else {
buffer.append(currentChar);
}
i++;
}
return foundBracket ? buffer.toString().trim() : null;
}
private String getValue(String line) {
StringBuffer buffer = new StringBuffer();
int i = 0;
boolean foundComma = false;
boolean preWS = true;
while (i < line.length() && !foundComma) {
char currentChar = line.charAt(i);
if (Character.isWhitespace(currentChar)) {
if (!preWS) buffer.append(currentChar);
} else if (currentChar == ',') {
foundComma = true;
} else {
buffer.append(currentChar);
preWS = false;
}
i++;
}
return buffer.toString();
}
private String getQuotedValue(String line) throws Exception {
StringBuffer buffer = new StringBuffer();
int i = 0;
// logger.debug("QV line: " + line);
boolean startQuoteFound = false;
while (line != null) {
while (i < line.length()) {
char currentChar = line.charAt(i);
if (currentChar == '"') {
if (startQuoteFound) {
return buffer.toString();
} else {
startQuoteFound = true;
}
} else if (startQuoteFound) {
buffer.append(currentChar);
}
i++;
}
line = input.readLine();
i = 0;
}
return null;
}
class URN {
String name = null;
String label = null;
}
}
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