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Re: [Cdk-user] [URGENT] Help needed for processing of aromatic compounds and Structure Search
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From: Yannick .D. <y.d...@gm...> - 2016-05-19 18:41:41
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Hi John,
Thanks a lot for the quick answer. I will be switching to the new tools. I
tried both the SMARTSpattern and the VentoFoggia. Both are working for me.
If I understood correctly, is the VentoFogia more suitable if I want to run
substructure matching on a large scale?
I also realized that some of my SMARTS patterns should be modified a bit.
It is cumbersome when they are generated with one tool and tested/used with
another.
Thanks again.
Best,
Yannick
On Thu, May 19, 2016 at 1:51 AM, John M <joh...@gm...> wrote:
> 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
> joh...@gm...
>
> On 19 May 2016 at 06:55, Yannick .Djoumbou <y.d...@gm...> 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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>
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