In fact, if I convert a Structure to the aromatic form with ChemAxon (see
below),
I get the bond type 4 for the aromatic bonds. When I use your codes, either
of the aforementioned methods complain about Implicity hydrogens not being
set(See below).
You mentioned I should use General aromaticity models instead of basic.
What do you mean here? Sorry I am new to this aspect of CDK.
Thanks,
ptrn1.matches(mol) returns
Exception in thread "main" java.lang.NullPointerException: Implicit
hydrogen count was not set.
at com.google.common.base.Preconditions.checkNotNull(Preconditions.java:229)
at
org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtomInvariants.configureDaylight(
SMARTSAtomInvariants.java:292)
at
org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtomInvariants.configureDaylightWithRingInfo(
SMARTSAtomInvariants.java:247)
at org.openscience.cdk.isomorphism.matchers.smarts.SmartsMatchers.prepare(
SmartsMatchers.java:51)
at org.openscience.cdk.smiles.smarts.SmartsPattern.matchAll(
SmartsPattern.java:150)
at org.openscience.cdk.smiles.smarts.SmartsPattern.match(
SmartsPattern.java:116)
at org.openscience.cdk.isomorphism.Pattern.matches(Pattern.java:75)
test
Mrv15c1405191613332D
17 19 0 0 0 0 999 V2000
-0.3869 0.2595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1014 -0.1530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.1014 -0.9780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3869 -1.3905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3276 -0.9780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3276 -0.1530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0420 -1.3905 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7565 -0.9780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7565 -0.1530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0420 0.2595 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.4710 0.2595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1855 -0.1530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9000 0.2595 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9000 1.0845 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.1855 1.4970 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.4710 1.0845 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0420 -2.2155 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 4 0 0 0 0
2 3 4 0 0 0 0
3 4 4 0 0 0 0
4 5 4 0 0 0 0
5 6 4 0 0 0 0
1 6 4 0 0 0 0
7 8 1 0 0 0 0
8 9 1 0 0 0 0
9 10 1 0 0 0 0
5 7 1 0 0 0 0
6 10 1 0 0 0 0
12 13 4 0 0 0 0
13 14 4 0 0 0 0
14 15 4 0 0 0 0
15 16 4 0 0 0 0
11 12 4 0 0 0 0
11 16 4 0 0 0 0
9 11 1 0 0 0 0
7 17 2 0 0 0 0
M END
$$$$
On Thu, May 19, 2016 at 1:13 PM, John M <john.wilkinson...@gmail.com> wrote:
> Yep, SmartsPattern delegates to VF below but does all required setup such
> as arom perception and invariants required for SMARTS matching:
>
> https://github.com/cdk/cdk/blob/master/tool/smarts/src/main/java/org/openscience/cdk/smiles/smarts/SmartsPattern.java#L142-L172
>
> If you generated them with ChemAxon you should use the 'General'
> aromaticity model rather than 'Basic'.
>
> John
>
>
>
> Regards,
> John W May
> john.wilkinson...@gmail.com
>
> On 19 May 2016 at 19:41, Yannick .Djoumbou <y.djoum...@gmail.com> wrote:
>
>> 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 <john.wilkinson...@gmail.com>
>> 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
>>> 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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>>>>
>>>
>>
>
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