On 1 March 2011 10:49, Thomas Strunz <beginn...@hotmail.de> wrote:
> Hi all,
>
> the Isomorphism class has an init method:
>
> public void init(IMolecule reactant, IMolecule product, boolean
> removeHydrogen, boolean cleanAndConfigureMolecule) throws CDKException {
> this.removeHydrogen = removeHydrogen;
> init(new MolHandler(reactant, removeHydrogen,
> cleanAndConfigureMolecule),
> new MolHandler(product, removeHydrogen,
> cleanAndConfigureMolecule));
> }
>
> The molecules I pass into this method have no explicit hydrogens and are
> configured so both flags removeHydrogen and cleanAndConfigureMolecule I
> should be able to set them to false.
> The issue is the removeHydrogen flag. If I set it to "false" it cripples
> performance compared to "true". However even with flag set to true UIT is
> faster!
>
> MolHandler Constructor:
>
> public MolHandler(IAtomContainer container, boolean removeHydrogen,
> boolean cleanMolecule) {
> String molID = container.getID();
> this.removeHydrogen = removeHydrogen;
> this.atomContainer = container;
> if (removeHydrogen) {
> try {
> this.atomContainer =
> ExtAtomContainerManipulator.removeHydrogensExceptSingleAndPreserveAtomID(atomContainer);
> <- remove Hydrogen set to true
> } catch (Exception ex) {
> logger.error(ex);
> }
> } else {
> this.atomContainer =
> container.getBuilder().newInstance(IAtomContainer.class, atomContainer); <-
> remove Hydrogen set to false. this is pointless IMHO. do nothing.
> }
>
> if (cleanMolecule) {
> try {
> if (!isPseudoAtoms()) {
> atomContainer =
> canonLabeler.getCanonicalMolecule(atomContainer);
> }
> // percieve atoms, set valency etc
>
> ExtAtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(atomContainer);
> //Add implicit Hydrogens
> CDKHydrogenAdder adder =
> CDKHydrogenAdder.getInstance(atomContainer.getBuilder());
> adder.addImplicitHydrogens(atomContainer);
> // figure out which atoms are in aromatic rings:
>
> CDKHueckelAromaticityDetector.detectAromaticity(atomContainer);
> } catch (CDKException ex) {
> logger.error(ex);
> }
> }
> atomContainer.setID(molID);
> }
>
> I tried to determine what actually is done in both code-path.
>
> Setting removeHydrogen to "true":
> Bascially clones all atoms (except H) and all bonds (except does that were
> connected to H) into a new Molecule and sets implicit hydrogen. In my case
> this is just a waste of CPU time.
>
> Setting removeHydrogen to "false":
> Executes following line of code:
> this.atomContainer =
> container.getBuilder().newInstance(IAtomContainer.class, atomContainer);
>
> What is the point of this? IMHO it's 100% pointless and a waste of CPU
> time. I'm not sure why this cripples performance because what it ends up
> doing is this:
>
> public AtomContainer(IAtomContainer container)
> {
> this.atomCount = container.getAtomCount();
> this.bondCount = container.getBondCount();
> this.lonePairCount = container.getLonePairCount();
> this.singleElectronCount = container.getSingleElectronCount();
> this.atoms = new IAtom[this.atomCount];
> this.bonds = new IBond[this.bondCount];
> this.lonePairs = new ILonePair[this.lonePairCount];
> this.singleElectrons = new
> ISingleElectron[this.singleElectronCount];
>
> stereoElements = new ArrayList<IStereoElement>(atomCount/2);
>
> for (int f = 0; f < container.getAtomCount(); f++) {
> atoms[f] = container.getAtom(f);
> container.getAtom(f).addListener(this);
> }
> for (int f = 0; f < this.bondCount; f++) {
> bonds[f] = container.getBond(f);
> container.getBond(f).addListener(this);
> }
> for (int f = 0; f < this.lonePairCount; f++) {
> lonePairs[f] = container.getLonePair(f);
> container.getLonePair(f).addListener(this);
> }
> for (int f = 0; f < this.singleElectronCount; f++) {
> singleElectrons[f] = container.getSingleElectron(f);
> container.getSingleElectron(f).addListener(this);
> }
> }
>
> So it also copies the whole Molecule into a new AtomContainer. Not sure why
> this is so much slower but it is besides being pointless. The number of hits
> found is identical to setting removeHydrogens to true or using UIT.
> I'm not sure why everyone says UIT is much slower. It is theoretically but
> in my case it is not probably because of the useless work done as indicated
> above.
>
To share a bit of our recent benchmarking experience, we actually found CDK
UIT is faster than SMSD for substructure searching (haven't tested MCSS).
Nina
>
> Any comments? Am I missing something?
>
> Regards,
>
> Thomas
>
>
>
>
> ------------------------------------------------------------------------------
> Free Software Download: Index, Search & Analyze Logs and other IT data in
> Real-Time with Splunk. Collect, index and harness all the fast moving IT
> data
> generated by your applications, servers and devices whether physical,
> virtual
> or in the cloud. Deliver compliance at lower cost and gain new business
> insights. http://p.sf.net/sfu/splunk-dev2dev
> _______________________________________________
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>
>
------------------------------------------------------------------------------
Free Software Download: Index, Search & Analyze Logs and other IT data in
Real-Time with Splunk. Collect, index and harness all the fast moving IT data
generated by your applications, servers and devices whether physical, virtual
or in the cloud. Deliver compliance at lower cost and gain new business
insights. http://p.sf.net/sfu/splunk-dev2dev
_______________________________________________
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user
