Hi Yannick,
This should be much similar now. First off, you're using some old APIs, SQT
still works but it's preferred now to go through 'Pattern'. The
SmartsPattern does all the setup needed, other implementations can be
faster and more customisable (see later) if you have many SMARTS against
one molecule but only recommended if needed.
The SMSD classes are some specific to SMSD so unless you need MCS don't use
them.
I've attached the code below but if think the real problem here is the
really SMARTS don't match molecule using Daylight's aromaticity model. All
ring atoms there are aromatic and an explicit '=' in SMARTS doesn't match
an aromatic atom ('=,:' is the way to do that).
You can try out SMARTS on CDKDepict:
http://cdkdepict-openchem.rhcloud.com/depict.html
> COC1=C(O)C=C2OC=C(C(=O)C2=C1)C3=CC=C(O)C=C3
>
[O;X1]=[#6;R1]-,:1-,:[#6;R1](=,:[#6;R1]-,:[#8]-,:c2ccccc-,:12)-[c;R1]1[c;R1][c;R1][c;R1][c;R1][c;R1]1
> Correct SMARTS
Doubly confirmed with OpenBabel
>
> *[sovereign ~/Downloads]: obgrep
> '[O;X1]=[#6;R1]-1-[#6;R1](=[#6;R1]-[#8]-c2ccccc-12)-[c;R1]1[c;R1][c;R1][c;R1][c;R1][c;R1]1'
> glycitein.sdf [sovereign ~/Downloads]: obgrep
> '[O;X1]=[#6;R1]-1-[#6;R1](=[#6;R1]-[#8]-[#6]-2=[#6]-[#6]=[#6]-[#6]=[#6]-1-2)-[#6;R1]-1=[#6;R1]-[#6;R1]=[#6;R1]-[#6;R1]=[#6;R1]-1'
> glycitein.sdf *
Here would be the normal code if SMARTS were changed. SmartsPattern does
aromaticity automatically.
*IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();*
>
> *Pattern ptrn1 =
>> SmartsPattern.create("[O;X1]=[#6;R1]-1-[#6;R1](=[#6;R1]-[#8]-c2ccccc-12)-[c;R1]1[c;R1][c;R1][c;R1][c;R1][c;R1]1",
>> null);*
>
> *Pattern ptrn2 =
>> SmartsPattern.create("[O;X1]=[#6;R1]-1-[#6;R1](=[#6;R1]-[#8]-[#6]-2=[#6]-[#6]=[#6]-[#6]=[#6]-1-2)-[#6;R1]-1=[#6;R1]-[#6;R1]=[#6;R1]-[#6;R1]=[#6;R1]-1",
>> null);*
>
>
>> *try (MDLV2000Reader mrdr = new MDLV2000Reader(new
>> FileReader("/Users/john/Downloads/glycitein.sdf"))) {*
>
> * IAtomContainer mol;*
>
> * while ((mol = mrdr.read(bldr.newInstance(IAtomContainer.class, 0, 0, 0,
>> 0))) != null) {*
>
> * System.err.println("p1: " + ptrn1.matches(mol));*
>
> * System.err.println("p2: " + ptrn2.matches(mol));*
>
> * }*
>
> *}*
>
>
Here's the code where we use a different aromaticity model. This is lower
level hence some more setup is needed.
>
>
>
>
>
>
>
>
>
>
>
>
> *IChemObjectBuilder bldr = SilentChemObjectBuilder.getInstance();Pattern
> ptrn1 =
> VentoFoggia.findSubstructure(SMARTSParser.parse("[O;X1]=[#6;R1]-1-[#6;R1](=[#6;R1]-[#8]-c2ccccc-12)-[c;R1]1[c;R1][c;R1][c;R1][c;R1][c;R1]1",
> null));Pattern ptrn2 =
> VentoFoggia.findSubstructure(SMARTSParser.parse("[O;X1]=[#6;R1]-1-[#6;R1](=[#6;R1]-[#8]-[#6]-2=[#6]-[#6]=[#6]-[#6]=[#6]-1-2)-[#6;R1]-1=[#6;R1]-[#6;R1]=[#6;R1]-[#6;R1]=[#6;R1]-1",
> null));Aromaticity arom = new Aromaticity(ElectronDonation.piBonds(),
> Cycles.all(6));try (MDLV2000Reader mrdr = new
> MDLV2000Reader(new FileReader("/Users/john/Downloads/glycitein.sdf"))) {
> IAtomContainer mol; while ((mol =
> mrdr.read(bldr.newInstance(IAtomContainer.class, 0, 0, 0, 0))) != null) {
> arom.apply(mol); SmartsMatchers.prepare(mol, true);
> System.err.println("p1: " + ptrn1.matches(mol));
> System.err.println("p2: " + ptrn2.matches(mol)); }}*
Regards,
John W May
john.wilkinson...@gmail.com
On 19 May 2016 at 06:55, Yannick .Djoumbou <y.djoum...@gmail.com> wrote:
> Hi all,
>
> I am having some issues with the CDK library.
>
> I have the molecule "glycitein" in the attached file (glycitein.sdf). I
> am running the SMARTSQueryTool to perform structure search. The SMARTS
> patterns are the following:
>
>
> P1:
> [O;X1]=[#6;R1]-1-[#6;R1](=[#6;R1]-[#8]-c2ccccc-12)-[c;R1]1[c;R1][c;R1][c;R1][c;R1][c;R1]1
>
>
> P2:
> [O;X1]=[#6;R1]-1-[#6;R1](=[#6;R1]-[#8]-[#6]-2=[#6]-[#6]=[#6]-[#6]=[#6]-1-2)-[#6;R1]-1=[#6;R1]-[#6;R1]=[#6;R1]-[#6;R1]=[#6;R1]-1
>
> For each of those, the query tool returns false, which is
> really surprising. I imagine it still has to do with the Aromaticity
> detection or a related issue. I have tried many things and it seems that
> they do not always work as they should.
>
> 1) I therefore preprocessed the molecule using the code below (from a
> previous chat I had on a forum):
>
> SMSDNormalizer.percieveAtomTypesAndConfigureAtoms(molecule);
>
> CDKHydrogenAdder.getInstance(molecule.getBuilder())
>
> .addImplicitHydrogens(molecule);
>
> for (IBond bond : molecule.bonds()) {
>
> if (bond.getFlag(CDKConstants.SINGLE_OR_DOUBLE)) {
>
> bond.setFlag(CDKConstants.ISAROMATIC, true);
>
> bond.getAtom(0).setFlag(CDKConstants.ISAROMATIC, true);
>
> bond.getAtom(1).setFlag(CDKConstants.ISAROMATIC, true);
>
>
> }
>
> }
>
>
> SMSDNormalizer.aromatizeMolecule(molecule);
>
>
> I attached the resulting structure in SDF format as returned by CDK
> ((glycitein_processed.sdf)), which in most editors is shown as in the
> attached picture. It seems that all the aromatic bonds (marked as 4) in the
> SDF are perceived as single bonds.
>
> Therefore, the result of the structure search is still "FALSE".
>
> By the way, trying a combination of AtomContainerManipulator (to perceive
> atom types) and Aromaticity
> <http://cdk.github.io/cdk/1.5/docs/api/org/openscience/cdk/aromaticity/Aromaticity.html>
> did not help either
>
>
>
> 2) Instead of aromatizing, I removed the SMSDNormalizer lines, and added
> the following:
>
> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule
> );
>
> Kekulization.kekulize(molecule);
>
>
> The SDF of the resulting molecule is the same. The result also.
>
>
> How can I process these molecules efficiently?
>
>
> I am writing a function that will take SDF files, and run
> the SMARTSQueryTool to match certain patterns. Therefore, I need an
> efficient way to preprocess these molecules.
>
>
> Can someone help me out here?
>
>
> Thank you in advance.
>
>
> Best,
>
>
>
>
>
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