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/* $Revision: 9050 $ $Author: egonw $ $Date: 2007-10-14 20:23:40 +0200 (Sun, 14 Oct 2007) $
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* Copyright (C) 2002-2007 Christoph Steinbeck <steinbeck@users.sf.net>
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* Contact: cdk-devel@lists.sourceforge.net
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* This program is free software; you can redistribute it and/or
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* modify it under the terms of the GNU Lesser General Public License
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* as published by the Free Software Foundation; either version 2.1
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* of the License, or (at your option) any later version.
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* All I ask is that proper credit is given for my work, which includes
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* - but is not limited to - adding the above copyright notice to the beginning
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* of your source code files, and to any copyright notice that you may distribute
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* with programs based on this work.
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU Lesser General Public License for more details.
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* You should have received a copy of the GNU Lesser General Public License
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* along with this program; if not, write to the Free Software
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* Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
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package org.openscience.cdk.smiles;
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import java.util.Enumeration;
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import java.util.Stack;
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import java.util.StringTokenizer;
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import org.openscience.cdk.CDKConstants;
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import org.openscience.cdk.DefaultChemObjectBuilder;
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import org.openscience.cdk.aromaticity.HueckelAromaticityDetector;
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import org.openscience.cdk.exception.CDKException;
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import org.openscience.cdk.exception.InvalidSmilesException;
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import org.openscience.cdk.graph.ConnectivityChecker;
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import org.openscience.cdk.interfaces.IAtom;
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import org.openscience.cdk.interfaces.IAtomContainer;
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import org.openscience.cdk.interfaces.IBond;
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import org.openscience.cdk.interfaces.IChemObjectBuilder;
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import org.openscience.cdk.interfaces.IMolecule;
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import org.openscience.cdk.interfaces.IMoleculeSet;
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import org.openscience.cdk.interfaces.IReaction;
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import org.openscience.cdk.tools.HydrogenAdder;
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import org.openscience.cdk.tools.LoggingTool;
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import org.openscience.cdk.tools.ValencyHybridChecker;
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* Parses a SMILES {@cdk.cite SMILESTUT} string and an AtomContainer. The full
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* SSMILES subset {@cdk.cite SSMILESTUT} and the '%' tag for more than 10 rings
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* at a time are supported. An example:
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* SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
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* IMolecule m = sp.parseSmiles("c1ccccc1");
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* } catch (InvalidSmilesException ise) {
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* <p>This parser does not parse stereochemical information, but the following
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* features are supported: reaction smiles, partitioned structures, charged
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* atoms, implicit hydrogen count, '*' and isotope information.
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* <p>See {@cdk.cite WEI88} for further information.
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* @author Christoph Steinbeck
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* @author Egon Willighagen
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* @cdk.created 2002-04-29
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* @cdk.keyword SMILES, parser
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* @see org.openscience.cdk.smiles.InterruptableSmilesParser
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public class SmilesParser {
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private LoggingTool logger;
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private HydrogenAdder hAdder;
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// private SmilesValencyChecker valencyChecker;
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private ValencyHybridChecker valencyChecker;
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private int status = 0;
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protected IChemObjectBuilder builder;
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* Constructor for the SmilesParser object.
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* @deprecated Use SmilesParser(IChemObjectBuilder instead)
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this(DefaultChemObjectBuilder.getInstance());
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* Constructor for the SmilesParser object.
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* @param builder IChemObjectBuilder used to create the IMolecules from
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public SmilesParser(IChemObjectBuilder builder)
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logger = new LoggingTool(this);
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this.builder = builder;
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valencyChecker = new ValencyHybridChecker();
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hAdder = new HydrogenAdder(valencyChecker);
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} catch (Exception exception)
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logger.error("Could not instantiate valencyChecker or hydrogenAdder: ",
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exception.getMessage());
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logger.debug(exception);
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int nodeCounter = -1;
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String smiles = null;
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double bondStatus = -1;
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double bondStatusForRingClosure = 1;
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boolean bondIsAromatic = false;
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IAtom[] rings = null;
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double[] ringbonds = null;
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IMolecule molecule = null;
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String currentSymbol = null;
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public IReaction parseReactionSmiles(String smiles) throws InvalidSmilesException
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StringTokenizer tokenizer = new StringTokenizer(smiles, ">");
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String reactantSmiles = tokenizer.nextToken();
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String agentSmiles = "";
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String productSmiles = tokenizer.nextToken();
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if (tokenizer.hasMoreTokens())
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agentSmiles = productSmiles;
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productSmiles = tokenizer.nextToken();
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IReaction reaction = builder.newReaction();
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IMolecule reactantContainer = parseSmiles(reactantSmiles);
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IMoleculeSet reactantSet = ConnectivityChecker.partitionIntoMolecules(reactantContainer);
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for (int i = 0; i < reactantSet.getAtomContainerCount(); i++)
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reaction.addReactant(reactantSet.getMolecule(i));
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if (agentSmiles.length() > 0)
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IMolecule agentContainer = parseSmiles(agentSmiles);
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IMoleculeSet agentSet = ConnectivityChecker.partitionIntoMolecules(agentContainer);
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for (int i = 0; i < agentSet.getAtomContainerCount(); i++)
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reaction.addAgent(agentSet.getMolecule(i));
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IMolecule productContainer = parseSmiles(productSmiles);
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IMoleculeSet productSet = ConnectivityChecker.partitionIntoMolecules(productContainer);
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for (int i = 0; i < productSet.getAtomContainerCount(); i++)
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reaction.addProduct(productSet.getMolecule(i));
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* Parses a SMILES string and returns a Molecule object.
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*@param smiles A SMILES string
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*@return A Molecule representing the constitution
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* given in the SMILES string
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*@exception InvalidSmilesException Exception thrown when the SMILES string
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public IMolecule parseSmiles(String smiles) throws InvalidSmilesException {
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setInterrupted(false);
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DeduceBondSystemTool dbst=new DeduceBondSystemTool();
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IMolecule m2=this.parseString(smiles);
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m=(IMolecule)m2.clone();
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} catch (java.lang.CloneNotSupportedException exception) {
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logger.debug(exception);
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// add implicit hydrogens
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this.addImplicitHydrogens(m);
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// setup missing bond orders
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this.setupMissingBondOrders(m);
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// conceive aromatic perception
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this.conceiveAromaticPerception(m);
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boolean HaveSP2=false;
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for (int j=0;j<=m.getAtomCount()-1;j++) {
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if (m.getAtom(j).getHybridization()==2) {
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if (HaveSP2) { // have lower case (aromatic) element symbols that may need to be fixed
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dbst.setInterrupted(isInterrupted());
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if (!(dbst.isOK(m))) {
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m = (IMolecule) dbst.fixAromaticBondOrders(m2);
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if (!(m instanceof IMolecule)) {
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throw new InvalidSmilesException("Could not deduce aromatic bond orders.");
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// doesnt need to fix aromatic bond orders
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} catch (CDKException ex) {
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throw new InvalidSmilesException(ex.getMessage(), ex);
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* This routine parses the smiles string into a molecule but does not add hydrogens, saturate, or perceive aromaticity
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* @throws InvalidSmilesException
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private IMolecule parseString(String smiles) throws InvalidSmilesException
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logger.debug("parseSmiles()...");
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bondIsAromatic = false;
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boolean bondExists = true;
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currentSymbol = null;
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molecule = builder.newMolecule();
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// we don't want more than 1024 rings
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rings = new IAtom[1024];
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ringbonds = new double[1024];
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for (int f = 0; f < 1024; f++)
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char[] chars = new char[1];
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IAtom lastNode = null;
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Stack atomStack = new Stack();
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Stack bondStack = new Stack();
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mychar = smiles.charAt(position);
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logger.debug("Processing: " + mychar);
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if (lastNode != null)
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logger.debug("Lastnode: ", lastNode.hashCode());
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if ((mychar >= 'A' && mychar <= 'Z') || (mychar >= 'a' && mychar <= 'z') ||
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logger.debug("Found a must-be 'organic subset' element");
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// only 'organic subset' elements allowed
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atom = builder.newPseudoAtom("*");
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currentSymbol = getSymbolForOrganicSubsetElement(smiles, position);
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if (currentSymbol != null)
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if (currentSymbol.length() == 1)
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if (!(currentSymbol.toUpperCase()).equals(currentSymbol))
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currentSymbol = currentSymbol.toUpperCase();
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atom = builder.newAtom(currentSymbol);
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atom.setHybridization(CDKConstants.HYBRIDIZATION_SP2);
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atom = builder.newAtom(currentSymbol);
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atom = builder.newAtom(currentSymbol);
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logger.debug("Made atom: ", atom);
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throw new InvalidSmilesException(
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"Found element which is not a 'organic subset' element. You must " +
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"use [" + mychar + "].");
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molecule.addAtom(atom);
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logger.debug("Adding atom ", atom.hashCode());
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if ((lastNode != null) && bondExists)
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logger.debug("Creating bond between ", atom.getSymbol(), " and ", lastNode.getSymbol());
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bond = builder.newBond(atom, lastNode, bondStatus);
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if (bondIsAromatic) {
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bond.setFlag(CDKConstants.ISAROMATIC, true);
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molecule.addBond(bond);
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bondStatus = CDKConstants.BONDORDER_SINGLE;
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position = position + currentSymbol.length();
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bondIsAromatic = false;
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} else if (mychar == '=')
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if (status == 2 || !((smiles.charAt(position) >= '0' && smiles.charAt(position) <= '9') || smiles.charAt(position) == '%'))
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bondStatus = CDKConstants.BONDORDER_DOUBLE;
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bondStatusForRingClosure = CDKConstants.BONDORDER_DOUBLE;
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} else if (mychar == '#')
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if (status == 2 || !((smiles.charAt(position) >= '0' && smiles.charAt(position) <= '9') || smiles.charAt(position) == '%'))
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bondStatus = CDKConstants.BONDORDER_TRIPLE;
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bondStatusForRingClosure = CDKConstants.BONDORDER_TRIPLE;
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} else if (mychar == '(')
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atomStack.push(lastNode);
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logger.debug("Stack:");
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Enumeration ses = atomStack.elements();
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while (ses.hasMoreElements())
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IAtom a = (IAtom) ses.nextElement();
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logger.debug("", a.hashCode());
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logger.debug("------");
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bondStack.push(new Double(bondStatus));
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} else if (mychar == ')')
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lastNode = (IAtom) atomStack.pop();
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logger.debug("Stack:");
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Enumeration ses = atomStack.elements();
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while (ses.hasMoreElements())
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IAtom a = (IAtom) ses.nextElement();
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logger.debug("", a.hashCode());
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logger.debug("------");
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bondStatus = ((Double) bondStack.pop()).doubleValue();
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} else if (mychar >= '0' && mychar <= '9')
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currentSymbol = new String(chars);
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thisRing = (new Integer(currentSymbol)).intValue();
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handleRing(lastNode);
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} else if (mychar == '%')
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currentSymbol = getRingNumber(smiles, position);
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thisRing = (new Integer(currentSymbol)).intValue();
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handleRing(lastNode);
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position += currentSymbol.length() + 1;
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} else if (mychar == '[')
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currentSymbol = getAtomString(smiles, position);
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atom = assembleAtom(currentSymbol);
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molecule.addAtom(atom);
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logger.debug("Added atom: ", atom);
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if (lastNode != null && bondExists)
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bond = builder.newBond(atom, lastNode, bondStatus);
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if (bondIsAromatic) {
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bond.setFlag(CDKConstants.ISAROMATIC, true);
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molecule.addBond(bond);
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logger.debug("Added bond: ", bond);
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bondStatus = CDKConstants.BONDORDER_SINGLE;
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bondIsAromatic = false;
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position = position + currentSymbol.length() + 2;
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// plus two for [ and ]
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} else if (mychar == '.')
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} else if (mychar == '-')
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// a simple single bond
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} else if (mychar == ':') {
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bondIsAromatic = true;
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} else if (mychar == '/' || mychar == '\\')
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logger.warn("Ignoring stereo information for double bond");
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} else if (mychar == '@')
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if (position < smiles.length() - 1 && smiles.charAt(position + 1) == '@')
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logger.warn("Ignoring stereo information for atom");
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throw new InvalidSmilesException("Unexpected character found: " + mychar);
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} catch (InvalidSmilesException exc)
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logger.error("InvalidSmilesException while parsing char (in parseSmiles()): " + mychar);
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} catch (Exception exception)
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logger.error("Error while parsing char: " + mychar);
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logger.debug(exception);
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throw new InvalidSmilesException("Error while parsing char: " + mychar, exception);
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logger.debug("Parsing next char");
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} while (position < smiles.length());
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private String getAtomString(String smiles, int pos) throws InvalidSmilesException
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logger.debug("getAtomString()");
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StringBuffer atomString = new StringBuffer();
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for (int f = pos + 1; f < smiles.length(); f++)
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char character = smiles.charAt(f);
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if (character == ']')
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atomString.append(character);
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} catch (Exception exception)
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String message = "Problem parsing Atom specification given in brackets.\n";
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message += "Invalid SMILES string was: " + smiles;
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logger.error(message);
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logger.debug(exception);
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throw new InvalidSmilesException(message, exception);
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return atomString.toString();
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private int getCharge(String chargeString, int position)
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logger.debug("getCharge(): Parsing charge from: ", chargeString.substring(position));
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if (chargeString.charAt(position) == '+')
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} else if (chargeString.charAt(position) == '-')
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StringBuffer multiplier = new StringBuffer();
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while (position < chargeString.length() && Character.isDigit(chargeString.charAt(position)))
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multiplier.append(chargeString.charAt(position));
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if (multiplier.length() > 0)
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logger.debug("Found multiplier: ", multiplier);
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charge = charge * Integer.parseInt(multiplier.toString());
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} catch (Exception exception)
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logger.error("Could not parse positive atomic charge!");
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logger.debug(exception);
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logger.debug("Found charge: ", charge);
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private int getImplicitHydrogenCount(String s, int position)
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logger.debug("getImplicitHydrogenCount(): Parsing implicit hydrogens from: " + s);
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if (s.charAt(position) == 'H')
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StringBuffer multiplier = new StringBuffer();
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while (position < (s.length() - 1) && Character.isDigit(s.charAt(position + 1)))
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multiplier.append(position + 1);
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if (multiplier.length() > 0)
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count = count + Integer.parseInt(multiplier.toString());
560
} catch (Exception exception)
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logger.error("Could not parse number of implicit hydrogens!");
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logger.debug(exception);
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private String getElementSymbol(String s, int pos)
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logger.debug("getElementSymbol(): Parsing element symbol (pos=" + pos + ") from: " + s);
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// try to match elements not in the organic subset.
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// first, the two char elements
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if (pos < s.length() - 1)
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String possibleSymbol = s.substring(pos, pos + 2);
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logger.debug("possibleSymbol: ", possibleSymbol);
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if (("HeLiBeNeNaMgAlSiClArCaScTiCrMnFeCoNiCuZnGaGeAsSe".indexOf(possibleSymbol) >= 0) ||
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("BrKrRbSrZrNbMoTcRuRhPdAgCdInSnSbTeXeCsBaLuHfTaRe".indexOf(possibleSymbol) >= 0) ||
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("OsIrPtAuHgTlPbBiPoAtRnFrRaLrRfDbSgBhHsMtDs".indexOf(possibleSymbol) >= 0))
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return possibleSymbol;
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// if that fails, the one char elements
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String possibleSymbol = s.substring(pos, pos + 1);
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logger.debug("possibleSymbol: ", possibleSymbol);
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if (("HKUVY".indexOf(possibleSymbol) >= 0))
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return possibleSymbol;
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// if that failed too, then possibly a organic subset element
594
return getSymbolForOrganicSubsetElement(s, pos);
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* Gets the ElementSymbol for an element in the 'organic subset' for which
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* brackets may be omited. <p>
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* See: <a href="http://www.daylight.com/dayhtml/smiles/smiles-atoms.html">
603
* http://www.daylight.com/dayhtml/smiles/smiles-atoms.html</a> .
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private String getSymbolForOrganicSubsetElement(String s, int pos)
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logger.debug("getSymbolForOrganicSubsetElement(): Parsing organic subset element from: ", s);
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if (pos < s.length() - 1)
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String possibleSymbol = s.substring(pos, pos + 2);
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if (("ClBr".indexOf(possibleSymbol) >= 0))
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return possibleSymbol;
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if ("BCcNnOoFPSsI".indexOf((s.charAt(pos))) >= 0)
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return s.substring(pos, pos + 1);
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if ("fpi".indexOf((s.charAt(pos))) >= 0)
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logger.warn("Element ", s, " is normally not sp2 hybridisized!");
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return s.substring(pos, pos + 1);
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logger.warn("Subset element not found!");
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* Gets the RingNumber attribute of the SmilesParser object
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private String getRingNumber(String s, int pos) throws InvalidSmilesException {
634
logger.debug("getRingNumber()");
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// Two digits impossible due to end of string
638
if (pos >= s.length() - 1)
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throw new InvalidSmilesException("Percent sign ring closure numbers must be two-digit.");
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String retString = s.substring(pos, pos + 2);
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if (retString.charAt(0) < '0' || retString.charAt(0) > '9' ||
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retString.charAt(1) < '0' || retString.charAt(1) > '9')
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throw new InvalidSmilesException("Percent sign ring closure numbers must be two-digit.");
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private IAtom assembleAtom(String s) throws InvalidSmilesException
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logger.debug("assembleAtom(): Assembling atom from: ", s);
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String currentSymbol = null;
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StringBuffer isotopicNumber = new StringBuffer();
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logger.debug("Parse everythings before and including element symbol");
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mychar = s.charAt(position);
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logger.debug("Parsing char: " + mychar);
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if ((mychar >= 'A' && mychar <= 'Z') || (mychar >= 'a' && mychar <= 'z'))
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currentSymbol = getElementSymbol(s, position);
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if (currentSymbol == null)
670
throw new InvalidSmilesException(
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"Expected element symbol, found null!"
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logger.debug("Found element symbol: ", currentSymbol);
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position = position + currentSymbol.length();
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if (currentSymbol.length() == 1)
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if (!(currentSymbol.toUpperCase()).equals(currentSymbol))
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currentSymbol = currentSymbol.toUpperCase();
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atom = builder.newAtom(currentSymbol);
683
atom.setHybridization(CDKConstants.HYBRIDIZATION_SP2);
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if (atom.getHydrogenCount() > 0)
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atom.setHydrogenCount(atom.getHydrogenCount() - 1);
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atom = builder.newAtom(currentSymbol);
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atom = builder.newAtom(currentSymbol);
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logger.debug("Made atom: ", atom);
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} else if (mychar >= '0' && mychar <= '9')
701
isotopicNumber.append(mychar);
703
} else if (mychar == '*')
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atom = builder.newPseudoAtom(currentSymbol);
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logger.debug("Made atom: ", atom);
712
throw new InvalidSmilesException("Found unexpected char: " + mychar);
714
} catch (InvalidSmilesException exc)
716
logger.error("InvalidSmilesException while parsing atom string: " + s);
719
} catch (Exception exception)
721
logger.error("Could not parse atom string: ", s);
722
logger.debug(exception);
723
throw new InvalidSmilesException("Could not parse atom string: " + s, exception);
725
} while (position < s.length());
726
if (isotopicNumber.toString().length() > 0)
730
atom.setMassNumber(Integer.parseInt(isotopicNumber.toString()));
731
} catch (Exception exception)
733
logger.error("Could not set atom's atom number.");
734
logger.debug(exception);
737
logger.debug("Parsing part after element symbol (like charge): ", s.substring(position));
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int implicitHydrogens = 0;
740
while (position < s.length())
744
mychar = s.charAt(position);
745
logger.debug("Parsing char: " + mychar);
748
// count implicit hydrogens
749
implicitHydrogens = getImplicitHydrogenCount(s, position);
751
if (implicitHydrogens > 1)
755
atom.setHydrogenCount(implicitHydrogens);
756
} else if (mychar == '+' || mychar == '-')
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charge = getCharge(s, position);
760
if (charge < -1 || charge > 1)
764
atom.setFormalCharge(charge);
765
} else if (mychar == '@')
767
if (position < s.length() - 1 && s.charAt(position + 1) == '@')
771
logger.warn("Ignoring stereo information for atom");
775
throw new InvalidSmilesException("Found unexpected char: " + mychar);
777
} catch (InvalidSmilesException exc)
779
logger.error("InvalidSmilesException while parsing atom string: ", s);
782
} catch (Exception exception)
784
logger.error("Could not parse atom string: ", s);
785
logger.debug(exception);
786
throw new InvalidSmilesException("Could not parse atom string: " + s, exception);
794
* We call this method when a ring (depicted by a number) has been found.
796
private void handleRing(IAtom atom)
798
logger.debug("handleRing():");
799
double bondStat = bondStatusForRingClosure;
800
if (ringbonds[thisRing] > bondStat)
801
bondStat = ringbonds[thisRing];
803
IAtom partner = null;
804
IAtom thisNode = rings[thisRing];
806
if (thisNode != null)
809
bond = builder.newBond(atom, partner, bondStat);
810
if (bondIsAromatic) {
812
bond.setFlag(CDKConstants.ISAROMATIC, true);
814
molecule.addBond(bond);
815
bondIsAromatic = false;
816
rings[thisRing] = null;
817
ringbonds[thisRing] = -1;
822
* First occurence of this ring:
823
* - add current atom to list
825
rings[thisRing] = atom;
826
ringbonds[thisRing] = bondStatusForRingClosure;
828
bondStatusForRingClosure = 1;
831
private void addImplicitHydrogens(IMolecule m) {
833
logger.debug("before H-adding: ", m);
834
hAdder.addImplicitHydrogensToSatisfyValency(m);
835
logger.debug("after H-adding: ", m);
836
} catch (Exception exception) {
837
logger.error("Error while calculation Hcount for SMILES atom: ", exception.getMessage());
841
private void setupMissingBondOrders(IMolecule m) {
843
valencyChecker.saturate(m);
844
logger.debug("after adding missing bond orders: ", m);
845
} catch (Exception exception) {
846
logger.error("Error while calculation Hcount for SMILES atom: ", exception.getMessage());
850
private void conceiveAromaticPerception(IMolecule m) {
851
IMoleculeSet moleculeSet = ConnectivityChecker.partitionIntoMolecules(m);
852
logger.debug("#mols ", moleculeSet.getAtomContainerCount());
853
for (int i = 0; i < moleculeSet.getAtomContainerCount(); i++) {
854
IAtomContainer molecule = moleculeSet.getAtomContainer(i);
855
logger.debug("mol: ", molecule);
857
valencyChecker.saturate(molecule);
858
logger.debug(" after saturation: ", molecule);
859
if (HueckelAromaticityDetector
860
.detectAromaticity(molecule)) {
861
logger.debug("Structure is aromatic...");
863
} catch (Exception exception) {
864
logger.error("Could not perceive aromaticity: ", exception
866
logger.debug(exception);
871
public boolean isInterrupted() {
872
return valencyChecker.isInterrupted();
875
public void setInterrupted(boolean interrupted) {
876
valencyChecker.setInterrupted(interrupted);
added
removed
src/org/openscience/cdk/smiles/SmilesParser.java
