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SMILES @ and @@ chiralities are now fully read.
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* takes into account branching
* implicit hydrogens on chiral atoms are made explicit

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
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@egonw @rajarshi
egonw authored and rajarshi committed May 16, 2010
1 parent 4c2e9b7 commit 2dd575e
Showing 1 changed file with 156 additions and 19 deletions.
175 changes: 156 additions & 19 deletions src/main/org/openscience/cdk/smiles/SmilesParser.java
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Expand Up @@ -26,7 +26,9 @@
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;

Expand All @@ -41,12 +43,16 @@
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.ILigancyFourChirality;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.IPseudoAtom;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IAtomType.Hybridization;
import org.openscience.cdk.interfaces.IBond.Order;
import org.openscience.cdk.interfaces.ILigancyFourChirality.Stereo;
import org.openscience.cdk.stereo.LigancyFourChirality;
import org.openscience.cdk.tools.CDKHydrogenAdder;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
Expand Down Expand Up @@ -93,6 +99,11 @@ public class SmilesParser {
private int status = 0;
protected IChemObjectBuilder builder;

private enum Chirality {
ANTI_CLOCKWISE, // aka @
CLOCKWISE // aka @@
}

/**
* Constructor for the SmilesParser object.
*
Expand All @@ -116,11 +127,40 @@ public SmilesParser(IChemObjectBuilder builder)
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.
Expand Down Expand Up @@ -188,6 +228,22 @@ public IReaction parseReactionSmiles(String smiles) throws InvalidSmilesExceptio
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;
ILigancyFourChirality l4Chiral = new LigancyFourChirality(
atom,
new IAtom[]{
atoms[0], atoms[1], atoms[2], atoms[3]
},
chirality.chiralityValue == Chirality.CLOCKWISE
? Stereo.CLOCKWISE : Stereo.ANTI_CLOCKWISE
);
molecule.addStereoElement(l4Chiral);
}

// perceive atom types
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(molecule.getBuilder());
int i = 0;
Expand Down Expand Up @@ -225,12 +281,15 @@ private IMolecule parseString(String smiles) throws InvalidSmilesException
currentSymbol = null;
molecule = builder.newInstance(IMolecule.class);
position = 0;
chiralityInfo = new HashMap<IAtom,TemporaryChiralityStorage>();
// we don't want more than 1024 rings
rings = new IAtom[1024];
ringbonds = new IBond.Order[1024];
for (int f = 0; f < 1024; f++)
{
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;
}

Expand Down Expand Up @@ -290,7 +349,7 @@ private IMolecule parseString(String smiles) throws InvalidSmilesException
"use [" + mychar + "].");
}
}

addAtomToActiveChiralities(lastNode, atom);
molecule.addAtom(atom);
logger.debug("Adding atom ", atom.hashCode());
if ((lastNode != null) && bondExists)
Expand Down Expand Up @@ -371,7 +430,8 @@ private IMolecule parseString(String smiles) throws InvalidSmilesException
} else if (mychar == '[')
{
currentSymbol = getAtomString(smiles, position);
atom = assembleAtom(currentSymbol);
atom = assembleAtom(currentSymbol, lastNode, bondExists);
addAtomToActiveChiralities(lastNode, atom);
molecule.addAtom(atom);
logger.debug("Added atom: ", atom);
if (lastNode != null && bondExists)
Expand Down Expand Up @@ -414,11 +474,34 @@ private IMolecule parseString(String smiles) throws InvalidSmilesException
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;
}
logger.warn("Ignoring stereo information for atom");
// @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
{
Expand Down Expand Up @@ -578,6 +661,18 @@ private String getElementSymbol(String s, int pos)
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
Expand Down Expand Up @@ -631,7 +726,7 @@ private String getRingNumber(String s, int pos) throws InvalidSmilesException {
return retString;
}

private IAtom assembleAtom(String s) throws InvalidSmilesException
private IAtom assembleAtom(String s, IAtom lastNode, boolean bondExists) throws InvalidSmilesException
{
logger.debug("assembleAtom(): Assembling atom from: ", s);
IAtom atom = null;
Expand Down Expand Up @@ -754,12 +849,34 @@ private IAtom assembleAtom(String s) throws InvalidSmilesException
atom.setFormalCharge(charge);
} else if (mychar == '@')
{
if (position < s.length() - 1 && s.charAt(position + 1) == '@')
{
position++;
}
logger.warn("Ignoring stereo information for atom");
position++;
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);
Expand Down Expand Up @@ -792,33 +909,53 @@ private void handleRing(IAtom atom)
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) {

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;
}

private void addImplicitHydrogens(IMolecule container) {
/**
* 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();
Expand Down

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