/
SmilesParser.java
1037 lines (985 loc) · 34.9 KB
/
SmilesParser.java
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/* $Revision$ $Author$ $Date$
*
* Copyright (C) 2002-2007 Christoph Steinbeck <steinbeck@users.sf.net>
* 200?-2007 Egon Willighagen <egonw@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 I ask is that proper credit is given for my 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.smiles;
import java.util.Enumeration;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;
import java.util.Stack;
import java.util.StringTokenizer;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.aromaticity.CDKHueckelAromaticityDetector;
import org.openscience.cdk.atomtype.CDKAtomTypeMatcher;
import org.openscience.cdk.exception.InvalidSmilesException;
import org.openscience.cdk.exception.NoSuchAtomTypeException;
import org.openscience.cdk.graph.ConnectivityChecker;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IAtomType.Hybridization;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IBond.Order;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IPseudoAtom;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.ITetrahedralChirality;
import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo;
import org.openscience.cdk.stereo.TetrahedralChirality;
import org.openscience.cdk.tools.CDKHydrogenAdder;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
import org.openscience.cdk.tools.manipulator.AtomTypeManipulator;
import org.openscience.cdk.tools.manipulator.BondManipulator;
import org.openscience.cdk.tools.periodictable.PeriodicTable;
/**
* Parses a SMILES {@cdk.cite SMILESTUT} string and an AtomContainer. The full
* SSMILES subset {@cdk.cite SSMILESTUT} and the '%' tag for more than 10 rings
* at a time are supported. An example:
* <pre>
* try {
* SmilesParser sp = new SmilesParser(NewDefaultChemObjectBuilder.getInstance());
* IMolecule m = sp.parseSmiles("c1ccccc1");
* } catch (InvalidSmilesException ise) {
* }
* </pre>
*
* <p>This parser does not parse stereochemical information, but the following
* features are supported: reaction smiles, partitioned structures, charged
* atoms, implicit hydrogen count, '*' and isotope information.
*
* <p>See {@cdk.cite WEI88} for further information.
*
* @author Christoph Steinbeck
* @author Egon Willighagen
* @cdk.module smiles
* @cdk.githash
* @cdk.created 2002-04-29
* @cdk.keyword SMILES, parser
* @cdk.bug 1579230
* @cdk.bug 1579235
* @cdk.bug 1579244
*/
@TestClass("org.openscience.cdk.smiles.SmilesParserTest")
public class SmilesParser {
private final static String HAS_HARDCODED_HYDROGEN_COUNT = "SmilesParser.HasHardcodedHydrogenCount";
private static ILoggingTool logger =
LoggingToolFactory.createLoggingTool(SmilesParser.class);
private CDKHydrogenAdder hAdder;
private int status = 0;
protected IChemObjectBuilder builder;
private enum Chirality {
ANTI_CLOCKWISE, // aka @
CLOCKWISE // aka @@
}
/*
* Boolean to preserve aromaticity as provided in the Smiles itself (through lowecase letters (c1cccc1) or colons).
* Setting this to true means that CDK will not do aromaticity detection, nor atom typing (as this may conflict
* with the preserved aromaticity).
*/
private boolean preservingAromaticity=false;
/**
* Constructor for the SmilesParser object.
*
* @param builder IChemObjectBuilder used to create the IMolecules from
*/
public SmilesParser(IChemObjectBuilder builder)
{
this.builder = builder;
try {
hAdder = CDKHydrogenAdder.getInstance(builder);
} catch (Exception exception) {
logger.error("Could not instantiate hydrogenAdder: ",
exception.getMessage());
logger.debug(exception);
}
}
int position = -1;
int nodeCounter = -1;
String smiles = null;
IBond.Order bondStatus = null;
IBond.Order bondStatusForRingClosure = IBond.Order.SINGLE;
boolean bondIsAromatic = false;
// array of atoms that initiated a ring closure
IAtom[] rings = null;
// array of atoms that complete a ring closure
IAtom[] ringOtherAtoms = null;
IBond.Order[] ringbonds = null;
int thisRing = -1;
IMolecule molecule = null;
String currentSymbol = null;
Map<IAtom,TemporaryChiralityStorage> chiralityInfo = null;
/**
* Internal storage for temporary stereochemistry info. In particular, the atoms
* involved are generally not known until the full SMILES is processed.
*/
class TemporaryChiralityStorage {
Chirality chiralityValue;
IAtom[] atoms;
int counter;
public TemporaryChiralityStorage() {
chiralityValue = null;
atoms = new IAtom[4];
counter = 0;
}
public TemporaryChiralityStorage(IAtom atom) {
chiralityValue = null;
atoms = new IAtom[4];
atoms[0] = atom;
counter = 1;
}
public void addAtom(IAtom atom) {
atoms[counter] = atom;
counter++;
}
}
/**
* Parse a reaction SMILES.
*
* @param smiles The SMILES string to parse
* @return An instance of {@link org.openscience.cdk.interfaces.IReaction}
* @see #parseSmiles(String)
* @throws InvalidSmilesException if the string cannot be parsed
*/
@TestMethod("testReaction,testReactionWithAgents")
public IReaction parseReactionSmiles(String smiles) throws InvalidSmilesException
{
StringTokenizer tokenizer = new StringTokenizer(smiles, ">");
String reactantSmiles = tokenizer.nextToken();
String agentSmiles = "";
String productSmiles = tokenizer.nextToken();
if (tokenizer.hasMoreTokens())
{
agentSmiles = productSmiles;
productSmiles = tokenizer.nextToken();
}
IReaction reaction = builder.newInstance(IReaction.class);
// add reactants
IMolecule reactantContainer = parseSmiles(reactantSmiles);
IMoleculeSet reactantSet = ConnectivityChecker.partitionIntoMolecules(reactantContainer);
for (int i = 0; i < reactantSet.getAtomContainerCount(); i++)
{
reaction.addReactant(reactantSet.getMolecule(i));
}
// add reactants
if (agentSmiles.length() > 0)
{
IMolecule agentContainer = parseSmiles(agentSmiles);
IMoleculeSet agentSet = ConnectivityChecker.partitionIntoMolecules(agentContainer);
for (int i = 0; i < agentSet.getAtomContainerCount(); i++)
{
reaction.addAgent(agentSet.getMolecule(i));
}
}
// add products
IMolecule productContainer = parseSmiles(productSmiles);
IMoleculeSet productSet = ConnectivityChecker.partitionIntoMolecules(productContainer);
for (int i = 0; i < productSet.getAtomContainerCount(); i++)
{
reaction.addProduct(productSet.getMolecule(i));
}
return reaction;
}
/**
* Parses a SMILES string and returns a Molecule object.
*
*@param smiles A SMILES string
*@return A Molecule representing the constitution
* given in the SMILES string
*@throws InvalidSmilesException thrown when the SMILES string is invalid
*/
@TestMethod("testAromaticSmiles,testSFBug1296113")
public IMolecule parseSmiles(String smiles) throws InvalidSmilesException {
IMolecule molecule = this.parseString(smiles);
// analyze the chirality info
for (IAtom atom : chiralityInfo.keySet()) {
TemporaryChiralityStorage chirality = chiralityInfo.get(atom);
logger.debug("Chiral atom found: ", atom);
IAtom[] atoms = chirality.atoms;
ITetrahedralChirality l4Chiral = new TetrahedralChirality(
atom,
new IAtom[]{
atoms[0], atoms[1], atoms[2], atoms[3]
},
chirality.chiralityValue == Chirality.CLOCKWISE
? Stereo.CLOCKWISE : Stereo.ANTI_CLOCKWISE
);
molecule.addStereoElement(l4Chiral);
}
if (!preservingAromaticity ) {
// perceive atom types
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(molecule.getBuilder());
int i = 0;
for (IAtom atom : molecule.atoms()) {
i++;
try {
IAtomType type = matcher.findMatchingAtomType(molecule, atom);
AtomTypeManipulator.configure(atom, type);
} catch (NoSuchAtomTypeException exception) {
logger.warn("Cannot percieve atom type for the ", i, "th atom: ", atom.getSymbol());
atom.setAtomTypeName("X");
} catch (Exception exception) {
logger.error("Caught unexpected Exception during atom typing.");
logger.debug(exception);
atom.setAtomTypeName("X");
}
}
this.addImplicitHydrogens(molecule);
this.perceiveAromaticity(molecule);
}
else {
for (IBond bond : molecule.bonds() ) {
if(!bond.getFlag(CDKConstants.ISAROMATIC) &&
bond.getAtom(0).getFlag(CDKConstants.ISAROMATIC) &&
bond.getAtom(1).getFlag(CDKConstants.ISAROMATIC)) {
bond.setFlag(CDKConstants.ISAROMATIC,true);
}
}
}
return molecule;
}
/**
* This routine parses the smiles string into a molecule but does not add hydrogens, saturate, or perceive aromaticity
* @param smiles
* @return
* @throws InvalidSmilesException
*/
private IMolecule parseString(String smiles) throws InvalidSmilesException
{
logger.debug("parseSmiles()...");
IBond bond = null;
nodeCounter = 0;
bondStatus = null;
bondIsAromatic = false;
boolean bondExists = true;
thisRing = -1;
currentSymbol = null;
molecule = builder.newInstance(IMolecule.class);
position = 0;
chiralityInfo = new HashMap<IAtom,TemporaryChiralityStorage>();
// we don't want more than 1024 rings
final int MAX_RING_COUNT = 1024;
rings = new IAtom[MAX_RING_COUNT];
ringOtherAtoms = new IAtom[MAX_RING_COUNT];
ringbonds = new IBond.Order[MAX_RING_COUNT];
for (int f = 0; f < MAX_RING_COUNT; f++) {
rings[f] = null;
ringOtherAtoms[f] = null;
ringbonds[f] = null;
}
char mychar = 'X';
char[] chars = new char[1];
IAtom lastNode = null;
Stack<IAtom> atomStack = new Stack<IAtom>();
Stack<IBond.Order> bondStack = new Stack<IBond.Order>();
IAtom atom = null;
do
{
try
{
mychar = smiles.charAt(position);
logger.debug("");
logger.debug("Processing: " + mychar);
if (lastNode != null)
{
logger.debug("Lastnode: ", lastNode.hashCode());
}
if ((mychar >= 'A' && mychar <= 'Z') || (mychar >= 'a' && mychar <= 'z') ||
(mychar == '*'))
{
status = 1;
logger.debug("Found a must-be 'organic subset' element");
// only 'organic subset' elements allowed
atom = null;
if (mychar == '*')
{
currentSymbol = "*";
atom = builder.newInstance(IPseudoAtom.class, "*");
} else
{
currentSymbol = getSymbolForOrganicSubsetElement(smiles, position);
if (currentSymbol != null)
{
if (currentSymbol.length() == 1)
{
if (!(currentSymbol.toUpperCase()).equals(currentSymbol))
{
currentSymbol = currentSymbol.toUpperCase();
atom = builder.newInstance(IAtom.class,currentSymbol);
atom.setHybridization(Hybridization.SP2);
if (preservingAromaticity ) {
atom.setFlag(CDKConstants.ISAROMATIC, true);
}
} else
{
atom = builder.newInstance(IAtom.class,currentSymbol);
}
} else
{
atom = builder.newInstance(IAtom.class,currentSymbol);
}
logger.debug("Made atom: ", atom);
} else
{
throw new InvalidSmilesException(
"Found element which is not a 'organic subset' element. You must " +
"use [" + mychar + "].");
}
}
addAtomToActiveChiralities(lastNode, atom);
molecule.addAtom(atom);
logger.debug("Adding atom ", atom.hashCode());
if ((lastNode != null) && bondExists)
{
logger.debug("Creating bond between ", atom.getSymbol(), " and ", lastNode.getSymbol());
bond = builder.newInstance(IBond.class,atom, lastNode, bondStatus);
if (bondIsAromatic) {
bond.setFlag(CDKConstants.ISAROMATIC, true);
if (preservingAromaticity) {
bond.getAtom(0).setFlag(CDKConstants.ISAROMATIC, true);
bond.getAtom(1).setFlag(CDKConstants.ISAROMATIC, true);
}
}
molecule.addBond(bond);
}
bondStatus = CDKConstants.BONDORDER_SINGLE;
lastNode = atom;
nodeCounter++;
position = position + currentSymbol.length();
bondExists = true;
bondIsAromatic = false;
} else if (mychar == '=')
{
position++;
if (status == 2 || !((smiles.charAt(position) >= '0' && smiles.charAt(position) <= '9') || smiles.charAt(position) == '%'))
{
bondStatus = CDKConstants.BONDORDER_DOUBLE;
} else
{
bondStatusForRingClosure = CDKConstants.BONDORDER_DOUBLE;
}
} else if (mychar == '#')
{
position++;
if (status == 2 || !((smiles.charAt(position) >= '0' && smiles.charAt(position) <= '9') || smiles.charAt(position) == '%'))
{
bondStatus = CDKConstants.BONDORDER_TRIPLE;
} else
{
bondStatusForRingClosure = CDKConstants.BONDORDER_TRIPLE;
}
} else if (mychar == '(')
{
atomStack.push(lastNode);
logger.debug("Stack:");
Enumeration<IAtom> ses = atomStack.elements();
while (ses.hasMoreElements())
{
IAtom a = ses.nextElement();
logger.debug("", a.hashCode());
}
logger.debug("------");
bondStack.push(bondStatus);
position++;
} else if (mychar == ')')
{
lastNode = (IAtom) atomStack.pop();
logger.debug("Stack:");
Enumeration<IAtom> ses = atomStack.elements();
while (ses.hasMoreElements())
{
IAtom a = ses.nextElement();
logger.debug("", a.hashCode());
}
logger.debug("------");
bondStatus = bondStack.pop();
position++;
} else if (mychar >= '0' && mychar <= '9')
{
status = 2;
chars[0] = mychar;
currentSymbol = new String(chars);
thisRing = (Integer.valueOf(currentSymbol)).intValue();
handleRing(lastNode);
position++;
} else if (mychar == '%')
{
currentSymbol = getRingNumber(smiles, position);
thisRing = (Integer.valueOf(currentSymbol)).intValue();
handleRing(lastNode);
position += currentSymbol.length() + 1;
} else if (mychar == '[')
{
currentSymbol = getAtomString(smiles, position);
atom = assembleAtom(currentSymbol, lastNode, bondExists);
addAtomToActiveChiralities(lastNode, atom);
molecule.addAtom(atom);
logger.debug("Added atom: ", atom);
if (lastNode != null && bondExists)
{
bond = builder.newInstance(IBond.class,atom, lastNode, bondStatus);
if (bondIsAromatic) {
bond.setFlag(CDKConstants.ISAROMATIC, true);
}
molecule.addBond(bond);
logger.debug("Added bond: ", bond);
}
bondStatus = CDKConstants.BONDORDER_SINGLE;
bondIsAromatic = false;
lastNode = atom;
nodeCounter++;
position = position + currentSymbol.length() + 2;
// plus two for [ and ]
atom.setProperty(HAS_HARDCODED_HYDROGEN_COUNT, "yes");
if (atom.getImplicitHydrogenCount() == null) {
// zero implicit hydrogens is implied when the Hx syntax is not used
atom.setImplicitHydrogenCount(0);
}
bondExists = true;
} else if (mychar == '.')
{
bondExists = false;
position++;
} else if (mychar == '-')
{
bondExists = true;
// a simple single bond
position++;
} else if (mychar == ':') {
bondExists = true;
bondIsAromatic = true;
position++;
} else if (mychar == '/' || mychar == '\\')
{
logger.warn("Ignoring stereo information for double bond");
position++;
} else if (mychar == '@')
{
TemporaryChiralityStorage chirality = null;
if (lastNode != null) {
chirality = new TemporaryChiralityStorage(lastNode);
} else {
chirality = new TemporaryChiralityStorage();
}
// @ or @@
if (position < smiles.length() - 1 && smiles.charAt(position + 1) == '@')
{
chirality.chiralityValue = Chirality.CLOCKWISE;
position++;
} else {
chirality.chiralityValue = Chirality.ANTI_CLOCKWISE;
}
// @H or @@H ?
if (position < smiles.length() - 1 && smiles.charAt(position + 1) == 'H') {
// because the current data model requires a ligancy four chirality to
// have 4 IAtoms, we add an explicit hydrogen
IAtom hydrogen = builder.newInstance(IAtom.class, "H");
IBond newBond = builder.newInstance(IBond.class,
atom, hydrogen, Order.SINGLE
);
molecule.addAtom(hydrogen);
molecule.addBond(newBond);
chirality.addAtom(hydrogen);
position++;
}
chiralityInfo.put(lastNode, chirality);
position++;
} else
{
throw new InvalidSmilesException("Unexpected character found: " + mychar);
}
} catch (InvalidSmilesException exc)
{
logger.error("InvalidSmilesException while parsing char (in parseSmiles()) '" +
mychar + "': " + exc.getMessage());
logger.debug(exc);
throw exc;
} catch (Exception exception)
{
logger.error("Error while parsing char '" + mychar + "': " + exception.getMessage());
logger.debug(exception);
throw new InvalidSmilesException("Error while parsing char: " + mychar, exception);
}
logger.debug("Parsing next char");
} while (position < smiles.length());
if (thisRing != -1 && ringbonds[thisRing] != null && rings[thisRing] != null)
throw new InvalidSmilesException("Rings weren't properly closed. Check ring numbers");
return molecule;
}
private String getAtomString(String smiles, int pos) throws InvalidSmilesException
{
logger.debug("getAtomString()");
StringBuffer atomString = new StringBuffer();
try
{
for (int f = pos + 1; f < smiles.length(); f++)
{
char character = smiles.charAt(f);
if (character == ']')
{
break;
} else
{
atomString.append(character);
}
}
} catch (Exception exception)
{
String message = "Problem parsing Atom specification given in brackets.\n";
message += "Invalid SMILES string was: " + smiles;
logger.error(message);
logger.debug(exception);
throw new InvalidSmilesException(message, exception);
}
return atomString.toString();
}
private int getCharge(String chargeString, int position)
{
logger.debug("getCharge(): Parsing charge from: ", chargeString.substring(position));
int charge = 0;
if (chargeString.charAt(position) == '+')
{
charge = +1;
position++;
} else if (chargeString.charAt(position) == '-')
{
charge = -1;
position++;
} else
{
return charge;
}
StringBuffer multiplier = new StringBuffer();
while (position < chargeString.length() && Character.isDigit(chargeString.charAt(position)))
{
multiplier.append(chargeString.charAt(position));
position++;
}
if (multiplier.length() > 0)
{
logger.debug("Found multiplier: ", multiplier);
try
{
charge = charge * Integer.parseInt(multiplier.toString());
} catch (Exception exception)
{
logger.error("Could not parse positive atomic charge!");
logger.debug(exception);
}
}
logger.debug("Found charge: ", charge);
return charge;
}
private int getImplicitHydrogenCount(String s, int position)
{
logger.debug("getImplicitHydrogenCount(): Parsing implicit hydrogens from: " + s);
// from the calling code, we only come here if we hit an H
//
// so if the function returns an explicit 0, it means that an
// H0 was encountered.
//
// Howvever, H is equivalent to H1. In the latter, the calling code has
// to increment the positon by 1, but in the former it shouldn't. So we
// need a way to differentiate these two cases. We do so by returning
// -1 if we get just H, and 1 if we see H1.
//
// This is a horrible kludge :( We need a JavaCC parser!
int count = 0; // for the case of no H which is same as H0
if (s.charAt(position) == 'H')
{
StringBuffer multiplier = new StringBuffer();
while (position < (s.length() - 1) && Character.isDigit(s.charAt(position + 1)))
{
multiplier.append(s.charAt(position + 1));
position++;
}
if (multiplier.length() > 0)
{
try
{
count = Integer.parseInt(multiplier.toString());
} catch (Exception exception)
{
logger.error("Could not parse number of implicit hydrogens from the multiplier: " + multiplier);
logger.debug(exception);
}
} else count = -1; // since H == H1
}
return count;
}
private String getElementSymbol(String s, int pos)
{
logger.debug("getElementSymbol(): Parsing element symbol (pos=" + pos + ") from: " + s);
// try to match elements not in the organic subset.
// first, the two char elements
if (pos < s.length() - 1)
{
String possibleSymbol = ("" + s.charAt(pos)).toUpperCase() + s.charAt(pos + 1);
logger.debug("possibleSymbol: ", possibleSymbol);
if (PeriodicTable.getAtomicNumber(possibleSymbol) != null) {
return possibleSymbol;
}
}
// if that fails, the one char elements
String possibleSymbol = s.substring(pos, pos + 1);
logger.debug("possibleSymbol: ", possibleSymbol);
if (("HKUVYW".indexOf(possibleSymbol) >= 0))
{
return possibleSymbol;
}
// if that failed too, then possibly a organic subset element
return getSymbolForOrganicSubsetElement(s, pos);
}
private void addAtomToActiveChiralities(IAtom chiAtom, IAtom atom) {
for (IAtom chiralAtom : chiralityInfo.keySet()) {
if (chiralAtom == atom)
// but not if the new atom is the chiral atom itself
continue;
if (chiAtom != chiralAtom)
// ok, the atom does not belong to this chirality
continue;
TemporaryChiralityStorage chirality = chiralityInfo.get(chiralAtom);
if (chirality.counter < 4) chirality.addAtom(atom);
}
}
/**
* Gets the ElementSymbol for an element in the 'organic subset' for which
* brackets may be omited. <p>
*
* See: <a href="http://www.daylight.com/dayhtml/smiles/smiles-atoms.html">
* http://www.daylight.com/dayhtml/smiles/smiles-atoms.html</a> .
*/
private String getSymbolForOrganicSubsetElement(String s, int pos)
{
logger.debug("getSymbolForOrganicSubsetElement(): Parsing organic subset element from: ", s);
if (pos < s.length() - 1)
{
String possibleSymbol = s.substring(pos, pos + 2);
if (("ClBr".indexOf(possibleSymbol) >= 0))
{
return possibleSymbol;
}
}
if ("BCcNnOoFPSsI".indexOf((s.charAt(pos))) >= 0)
{
return s.substring(pos, pos + 1);
}
if ("fpi".indexOf((s.charAt(pos))) >= 0)
{
logger.warn("Element ", s, " is normally not sp2 hybridisized!");
return s.substring(pos, pos + 1);
}
logger.warn("Subset element not found!");
return null;
}
/**
* Gets the RingNumber attribute of the SmilesParser object
*/
private String getRingNumber(String s, int pos) throws InvalidSmilesException {
logger.debug("getRingNumber()");
pos++;
// Two digits impossible due to end of string
if (pos >= s.length() - 1)
throw new InvalidSmilesException("Percent sign ring closure numbers must be two-digit.");
String retString = s.substring(pos, pos + 2);
if (retString.charAt(0) < '0' || retString.charAt(0) > '9' ||
retString.charAt(1) < '0' || retString.charAt(1) > '9')
throw new InvalidSmilesException("Percent sign ring closure numbers must be two-digit.");
return retString;
}
private IAtom assembleAtom(String s, IAtom lastNode, boolean bondExists) throws InvalidSmilesException
{
logger.debug("assembleAtom(): Assembling atom from: ", s);
IAtom atom = null;
int position = 0;
String currentSymbol = null;
StringBuffer isotopicNumber = new StringBuffer();
char mychar;
logger.debug("Parse everythings before and including element symbol");
do
{
try
{
mychar = s.charAt(position);
logger.debug("Parsing char: " + mychar);
if ((mychar >= 'A' && mychar <= 'Z') || (mychar >= 'a' && mychar <= 'z'))
{
currentSymbol = getElementSymbol(s, position);
if (currentSymbol == null)
{
throw new InvalidSmilesException(
"Expected element symbol, found null!"
);
} else
{
logger.debug("Found element symbol: ", currentSymbol);
position = position + currentSymbol.length();
if(Character.isLowerCase(mychar)) {
if (currentSymbol.length() == 1) {
currentSymbol = currentSymbol.toUpperCase();
}
atom = builder.newInstance(IAtom.class,currentSymbol);
atom.setHybridization(Hybridization.SP2);
Integer hcount = atom.getImplicitHydrogenCount() == CDKConstants.UNSET ? 0 : atom.getImplicitHydrogenCount();
if (hcount > 0) {
atom.setImplicitHydrogenCount(hcount - 1);
}
if (preservingAromaticity )
atom.setFlag(CDKConstants.ISAROMATIC, true);
}
else
{
atom = builder.newInstance(IAtom.class,currentSymbol);
}
logger.debug("Made atom: ", atom);
}
break;
} else if (mychar >= '0' && mychar <= '9')
{
isotopicNumber.append(mychar);
position++;
} else if (mychar == '*')
{
currentSymbol = "*";
atom = builder.newInstance(IPseudoAtom.class, currentSymbol);
logger.debug("Made atom: ", atom);
position++;
break;
} else
{
throw new InvalidSmilesException("Found unexpected char: " + mychar);
}
} catch (InvalidSmilesException exc)
{
logger.error("InvalidSmilesException while parsing atom string '" + s + "': " + exc.getMessage());
logger.debug(exc);
throw exc;
} catch (Exception exception)
{
logger.error("Could not parse atom string: ", s);
logger.debug(exception);
throw new InvalidSmilesException("Could not parse atom string '" + s + "': " + exception.getMessage(), exception);
}
} while (position < s.length());
if (isotopicNumber.toString().length() > 0)
{
try
{
atom.setMassNumber(Integer.parseInt(isotopicNumber.toString()));
} catch (Exception exception)
{
logger.error("Could not set atom's isotope number '" + isotopicNumber + "'");
logger.debug(exception);
}
}
logger.debug("Parsing part after element symbol (like charge): ", s.substring(position));
int charge = 0;
int implicitHydrogens = 0;
while (position < s.length())
{
try
{
mychar = s.charAt(position);
logger.debug("Parsing char: " + mychar);
if (mychar == 'H')
{
// count implicit hydrogens
implicitHydrogens = getImplicitHydrogenCount(s, position);
position++;
// we check if H was followed by a number. if it wasn't, then the return value
// of getImplicitHydrogens is -1. See comments in that method
if (implicitHydrogens >= 0)
{
position++;
}
if (implicitHydrogens == -1) implicitHydrogens = 1;
atom.setImplicitHydrogenCount(implicitHydrogens);
} else if (mychar == '+' || mychar == '-')
{
charge = getCharge(s, position);
position++; // skip the +
// skip all digits following the +
while (position < s.length() && Character.isDigit(s.charAt(position))) {
position++;
}
atom.setFormalCharge(charge);
} else if (mychar == '@')
{
TemporaryChiralityStorage chirality = null;
if (lastNode != null && bondExists) {
chirality = new TemporaryChiralityStorage(lastNode);
} else {
chirality = new TemporaryChiralityStorage();
}
if (position < s.length() - 1 && s.charAt(position + 1) == '@')
{
chirality.chiralityValue = Chirality.CLOCKWISE;
position++;
} else {
chirality.chiralityValue = Chirality.ANTI_CLOCKWISE;
}
// @H or @@H ?
if (position < s.length() - 1 && s.charAt(position + 1) == 'H') {
// because the current data model requires a ligancy four chirality to
// have 4 IAtoms, we add an explicit hydrogen
IAtom hydrogen = builder.newInstance(IAtom.class, "H");
IBond newBond = builder.newInstance(IBond.class,
atom, hydrogen, Order.SINGLE
);
molecule.addAtom(hydrogen);
molecule.addBond(newBond);
chirality.addAtom(hydrogen);
position++;
}
chiralityInfo.put(atom, chirality);
position++;
} else
{
throw new InvalidSmilesException("Found unexpected char: " + mychar);
}
} catch (InvalidSmilesException exc)
{
logger.error("InvalidSmilesException while parsing atom string: ", s);
logger.debug(exc);
throw exc;
} catch (Exception exception)
{
logger.error("Could not parse atom string: ", s);
logger.debug(exception);
throw new InvalidSmilesException("Could not parse atom string: " + s, exception);
}
}
return atom;
}
/**
* We call this method when a ring (depicted by a number) has been found.
*/
private void handleRing(IAtom atom)
{
logger.debug("handleRing():");
IBond.Order bondStat = bondStatusForRingClosure;
if (BondManipulator.isHigherOrder(ringbonds[thisRing], bondStat))
bondStat = ringbonds[thisRing];
IBond bond = null;
IAtom partner = null;
IAtom thisNode = rings[thisRing];
IAtom templateAtom = ringOtherAtoms[thisRing];
// lookup
if (thisNode != null)
{
partner = thisNode;
replaceTemplateAtomInStereos(templateAtom, atom);
if (chiralityInfo.containsKey(atom))
addAtomToActiveChiralities(atom, partner);
bond = builder.newInstance(IBond.class,atom, partner, bondStat);
if (bondIsAromatic) {
bond.setFlag(CDKConstants.ISAROMATIC, true);
}
molecule.addBond(bond);
bondIsAromatic = false;
rings[thisRing] = null;
ringbonds[thisRing] = null;
ringOtherAtoms[thisRing] = null;
} else
{
/*
* First occurence of this ring:
* - add current atom to list
*/
rings[thisRing] = atom;
ringOtherAtoms[thisRing] = builder.newInstance(IAtom.class);
addAtomToActiveChiralities(atom, ringOtherAtoms[thisRing]);
ringbonds[thisRing] = bondStatusForRingClosure;
}
bondStatusForRingClosure = IBond.Order.SINGLE;
}
/**
* Replaces the <code>templateAtom</code> by <code>atom</code> in all currently defined stereochemistries.
*
* @param templateAtom {@link IAtom} to replace
* @param atom new {@link IAtom}
*/
private void replaceTemplateAtomInStereos(IAtom templateAtom, IAtom atom) {
for (TemporaryChiralityStorage chirality : chiralityInfo.values()) {
for (int i=0; i<4; i++) {
if (chirality.atoms[i] == templateAtom)
chirality.atoms[i] = atom;
}
}
}
private void addImplicitHydrogens(IMolecule container) {
try {
logger.debug("before H-adding: ", container);
Iterator<IAtom> atoms = container.atoms().iterator();
while (atoms.hasNext()) {
IAtom nextAtom = atoms.next();
if (nextAtom.getProperty(HAS_HARDCODED_HYDROGEN_COUNT) == null) {
hAdder.addImplicitHydrogens(container, nextAtom);
}
}
logger.debug("after H-adding: ", container);
} catch (Exception exception) {
logger.error("Error while calculation Hcount for SMILES atom: ", exception.getMessage());
}
}
private void perceiveAromaticity(IMolecule m) {
IMoleculeSet moleculeSet = ConnectivityChecker.partitionIntoMolecules(m);