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Some performance tuning for SmilesGenerator. In detail: - createSMILE…
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…SWithoutCheckForMultipleMolecules public, so it can be called directly without doing partitioning - aromaticity detection optional - avoids unecessary BondTools.isStereo calls if non-chiral smiles is wished

Signed-off-by: Rajarshi Guha <rajarshi.guha@gmail.com>
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Stefan Kuhn authored and rajarshi committed Mar 25, 2010
1 parent 75dc40d commit 773d8d9
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Showing 2 changed files with 66 additions and 24 deletions.
77 changes: 53 additions & 24 deletions src/main/org/openscience/cdk/smiles/SmilesGenerator.java
View file
Expand Up @@ -273,7 +273,12 @@ public synchronized String createSMILES(IReaction reaction) throws CDKException
* SmilesGenerator in order to avoid recomputing it. Use setRings() to
* assign the SAR.
*
* @param molecule The molecule to evaluate
* @param molecule The molecule to evaluate.
* @param doubleBondConfiguration Should E/Z configurations be read at these positions? If the flag at position X is set to true,
* an E/Z configuration will be written from coordinates around bond X, if false, it will be ignored.
* If flag is true for a bond which does not constitute a valid double bond configuration, it will be
* ignored (meaning setting all to true will create E/Z indication will be pu in the smiles wherever
* possible, but note the coordinates might be arbitrary).
* @exception CDKException At least one atom has no Point2D;
* coordinates are needed for creating the chiral smiles.
* @see org.openscience.cdk.graph.invariant.CanonicalLabeler#canonLabel(IAtomContainer)
Expand All @@ -295,15 +300,20 @@ public synchronized String createChiralSMILES(IMolecule molecule, boolean[] doub
* SmilesGenerator in order to avoid recomputing it. Use setRings() to
* assign the SAR.
*
*@param molecule The molecule to evaluate
*@param chiral true=SMILES will be chiral, false=SMILES
* @param molecule The molecule to evaluate.
* @param chiral true=SMILES will be chiral, false=SMILES.
* will not be chiral.
*@exception CDKException At least one atom has no Point2D;
* @param doubleBondConfiguration Should E/Z configurations be read at these positions? If the flag at position X is set to true,
* an E/Z configuration will be written from coordinates around bond X, if false, it will be ignored.
* If flag is true for a bond which does not constitute a valid double bond configuration, it will be
* ignored (meaning setting all to true will create E/Z indication will be pu in the smiles wherever
* possible, but note the coordinates might be arbitrary).
* @exception CDKException At least one atom has no Point2D;
* coordinates are needed for crating the chiral smiles. This excpetion
* can only be thrown if chiral smiles is created, ignore it if you want a
* non-chiral smiles (createSMILES(AtomContainer) does not throw an
* exception).
*@see org.openscience.cdk.graph.invariant.CanonicalLabeler#canonLabel(IAtomContainer)
* @see org.openscience.cdk.graph.invariant.CanonicalLabeler#canonLabel(IAtomContainer)
* @return the SMILES representation of the molecule
*/
public synchronized String createSMILES(IMolecule molecule, boolean chiral, boolean doubleBondConfiguration[]) throws CDKException
Expand All @@ -315,7 +325,8 @@ public synchronized String createSMILES(IMolecule molecule, boolean chiral, bool
for (int i = 0; i < moleculeSet.getAtomContainerCount(); i++)
{
IMolecule molPart = moleculeSet.getMolecule(i);
fullSMILES.append(createSMILESWithoutCheckForMultipleMolecules(molPart, chiral, doubleBondConfiguration));
fullSMILES.append(createSMILESWithoutCheckForMultipleMolecules(
molPart, chiral, doubleBondConfiguration));
if (i < (moleculeSet.getAtomContainerCount() - 1))
{
// are there more molecules?
Expand All @@ -325,7 +336,8 @@ public synchronized String createSMILES(IMolecule molecule, boolean chiral, bool
return fullSMILES.toString();
} else
{
return (createSMILESWithoutCheckForMultipleMolecules(molecule, chiral, doubleBondConfiguration));
return (createSMILESWithoutCheckForMultipleMolecules(molecule,
chiral, doubleBondConfiguration));
}
}

Expand All @@ -338,18 +350,27 @@ public synchronized String createSMILES(IMolecule molecule, boolean chiral, bool
* SmilesGenerator in order to avoid recomputing it. Use setRings() to
* assign the SAR.
*
*@param molecule The molecule to evaluate
*@param chiral true=SMILES will be chiral, false=SMILES
* @param molecule The molecule to evaluate.
* @param chiral true=SMILES will be chiral, false=SMILES
* will not be chiral.
*@exception CDKException At least one atom has no Point2D;
* @param doubleBondConfiguration Should E/Z configurations be read at these positions? If the flag at position X is set to true,
* an E/Z configuration will be written from coordinates around bond X, if false, it will be ignored.
* If flag is true for a bond which does not constitute a valid double bond configuration, it will be
* ignored (meaning setting all to true will create E/Z indication will be pu in the smiles wherever
* possible, but note the coordinates might be arbitrary).
* @param detectAromaticity true=an aromaticity detection will be done
* (using setRings avoids ring search for that),
* false=no aromaticity detection will be done
* @exception CDKException At least one atom has no Point2D;
* coordinates are needed for creating the chiral smiles. This excpetion
* can only be thrown if chiral smiles is created, ignore it if you want a
* non-chiral smiles (createSMILES(AtomContainer) does not throw an
* exception).
*@see org.openscience.cdk.graph.invariant.CanonicalLabeler#canonLabel(IAtomContainer)
* @return the SMILES representation of the molecule
*/
private synchronized String createSMILESWithoutCheckForMultipleMolecules(IMolecule molecule, boolean chiral, boolean doubleBondConfiguration[]) throws CDKException
@TestMethod("testCreateSMILESWithoutCheckForMultipleMolecules_withDetectAromaticity,testCreateSMILESWithoutCheckForMultipleMolecules_withoutDetectAromaticity")
public synchronized String createSMILESWithoutCheckForMultipleMolecules(IMolecule molecule, boolean chiral, boolean doubleBondConfiguration[]) throws CDKException
{
if (molecule.getAtomCount() == 0)
{
Expand All @@ -375,16 +396,17 @@ private synchronized String createSMILESWithoutCheckForMultipleMolecules(IMolecu
}

//detect aromaticity
if(rings == null)
{
if (ringFinder == null)
{
ringFinder = new AllRingsFinder();
}
rings = ringFinder.findAllRings(molecule);
if(useAromaticityFlag || chiral){
if(rings == null){
if (ringFinder == null)
{
ringFinder = new AllRingsFinder();
}
rings = ringFinder.findAllRings(molecule);
}
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
CDKHueckelAromaticityDetector.detectAromaticity(molecule);
}
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
CDKHueckelAromaticityDetector.detectAromaticity(molecule);
if (chiral && rings.getAtomContainerCount() > 0)
{
List v = RingPartitioner.partitionRings(rings);
Expand Down Expand Up @@ -716,6 +738,11 @@ private void addAtoms(List v, List result)
* appended to.
*@param chiral true=SMILES will be chiral, false=SMILES
* will not be chiral.
*@param doubleBondConfiguration Should E/Z configurations be read at these positions? If the flag at position X is set to true,
* an E/Z configuration will be written from coordinates around bond X, if false, it will be ignored.
* If flag is true for a bond which does not constitute a valid double bond configuration, it will be
* ignored (meaning setting all to true will create E/Z indication will be pu in the smiles wherever
* possible, but note the coordinates might be arbitrary).
*@param atomContainer the AtomContainer that the SMILES string is
* generated for.
*@param useAromaticity true=aromaticity or sp2 will trigger lower case letters, wrong=only sp2
Expand Down Expand Up @@ -747,7 +774,7 @@ private void createSMILES(IAtom a, StringBuffer line, IAtomContainer atomContain
private void createDFSTree(IAtom a, List tree, IAtom parent, IAtomContainer container)
{
tree.add(a);
List neighbours = getCanNeigh(a, container);
List neighbours = new ArrayList(getCanNeigh(a, container));
neighbours.remove(parent);
IAtom next;
a.setFlag(CDKConstants.VISITED, true);
Expand Down Expand Up @@ -1582,12 +1609,14 @@ private void parseAtom(IAtom a, StringBuffer buffer, IAtomContainer container, b
String symbol = a.getSymbol();
if (a instanceof PseudoAtom) symbol = "*";

boolean stereo = BondTools.isStereo(container, a);
boolean stereo = false;
if(chiral)
stereo = BondTools.isStereo(container, a);
boolean brackets = symbol.equals("B") || symbol.equals("C") || symbol.equals("N") || symbol.equals("O") || symbol.equals("P") || symbol.equals("S") || symbol.equals("F") || symbol.equals("Br") || symbol.equals("I") || symbol.equals("Cl");
brackets = !brackets;
//logger.debug("in parseAtom()");
//Deal with the start of a double bond configuration
if (isStartOfDoubleBond(container, a, parent, doubleBondConfiguration))
if (chiral && isStartOfDoubleBond(container, a, parent, doubleBondConfiguration))
{
buffer.append('/');
}
Expand Down Expand Up @@ -1649,7 +1678,7 @@ private void parseAtom(IAtom a, StringBuffer buffer, IAtomContainer container, b

//logger.debug("in parseAtom() after dealing with Pseudoatom or not");
//Deal with the end of a double bond configuration
if (isEndOfDoubleBond(container, a, parent, doubleBondConfiguration))
if (chiral && isEndOfDoubleBond(container, a, parent, doubleBondConfiguration))
{
IAtom viewFrom = null;
for (int i = 0; i < currentChain.size(); i++)
Expand Down
13 changes: 13 additions & 0 deletions src/test/org/openscience/cdk/smiles/SmilesGeneratorTest.java
View file
Expand Up @@ -938,5 +938,18 @@ public void testCanSmiWithConfiguredAtoms() throws CDKException, IOException {
Assert.assertTrue("The two canonical SMILES should match",o1.equals(o2));
}

@Test public void testCreateSMILESWithoutCheckForMultipleMolecules_withDetectAromaticity() throws CDKException{
IMolecule benzene = MoleculeFactory.makeBenzene();
SmilesGenerator sg = new SmilesGenerator(false);
String smileswithoutaromaticity = sg.createSMILESWithoutCheckForMultipleMolecules(benzene, false, new boolean[benzene.getBondCount()]);
Assert.assertEquals("C=1C=CC=CC=1", smileswithoutaromaticity);
}

@Test public void testCreateSMILESWithoutCheckForMultipleMolecules_withoutDetectAromaticity() throws CDKException{
IMolecule benzene = MoleculeFactory.makeBenzene();
SmilesGenerator sg = new SmilesGenerator(true);
String smileswitharomaticity = sg.createSMILESWithoutCheckForMultipleMolecules(benzene, false, new boolean[benzene.getBondCount()]);
Assert.assertEquals("c1ccccc1", smileswitharomaticity);
}
}

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