Hi Joos, I concur with Nina's view on library vs database search.
Just wondering if you had used the right code...
https://github.com/asad/SMSD/tree/master/src/org/openscience/smsd/algorithm/vflib/substructure
Kind test it with the above code.
or use
https://github.com/asad/SMSD/blob/master/src/org/openscience/smsd/Substructure.java
Asad
On 8 Sep 2011, at 10:48, [email protected] wrote:
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> Today's Topics:
>
> 1. comment about VF2 implementation from chemkit - possible bug
> (Joos Kiener)
> 2. Re: comment about VF2 implementation from chemkit - possible
> bug (Nina Jeliazkova)
> 3. Re: inchi generator and valency errors (Sam Adams)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 8 Sep 2011 11:24:41 +0200
> From: Joos Kiener <[email protected]>
> Subject: [Cdk-user] comment about VF2 implementation from chemkit -
> possible bug
> To: [email protected]
> Message-ID:
> <cahjbz72xswb6yosv0t9fcto1pzh0w9ozo1mfke5mikjgfbf...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi all,
>
> first off i guess you will be hearing more from me rather sooner than later
> but now to the actually subject. Please see:
>
> http://chembioinfo.wordpress.com/2011/03/15/benchmarking-substructure-search/
>
> for the context of this message.
>
> Currently I'm playing around with substructure search ( I have a certain
> goal in mind, more on that in later messages). Anyway UIT isn't exactly fast
> especially compared to commercial products like ChemFinder or InstantJChem
> were searches seem almost instantaneous.
>
> I was comparing UIT and the above referenced code ported from chemkit. First
> the difference in real world usage seems much less extreme than in that
> benchmark (for small molecules) or I'm misinterpreting the chart. Anyway in
> my case it takes about 60% of the time compared to UIT.
>
> Now to the subject of the message. I think there is an issue in the ported
> version. Following query returns 44 hits with chemkit and 106 with UIT.
> ChemFinder also gives 106 hits so I'm inclined to believe 106 is correct.
>
> Here the Query Molecule:
>
> CCC(C(CC(C(C)C)C)C)C
>
> Did not find or check for any other inconsistencies.
>
> Best Regards,
>
> Joos Kiener
> -------------- next part --------------
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> ------------------------------
>
> Message: 2
> Date: Thu, 8 Sep 2011 12:34:06 +0300
> From: Nina Jeliazkova <[email protected]>
> Subject: Re: [Cdk-user] comment about VF2 implementation from chemkit
> - possible bug
> To: Joos Kiener <[email protected]>
> Cc: [email protected]
> Message-ID:
> <CAE5qDd112RU46mk-goCdVVR1-Ni=3koflsdzayqztsso8z3...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> On 8 September 2011 12:24, Joos Kiener <[email protected]> wrote:
>
>> Hi all,
>>
>> first off i guess you will be hearing more from me rather sooner than later
>> but now to the actually subject. Please see:
>>
>>
>> http://chembioinfo.wordpress.com/2011/03/15/benchmarking-substructure-search/
>>
>> for the context of this message.
>>
>> Currently I'm playing around with substructure search ( I have a certain
>> goal in mind, more on that in later messages). Anyway UIT isn't exactly fast
>> especially compared to commercial products like ChemFinder or InstantJChem
>> were searches seem almost instantaneous.
>>
>>
> Just to note a comparison between a library method (as UIT) to a database
> search is not quite fair, as database search systems usually employ lot of
> pre-screening and other optimization techniques.
>
> e.g. this online search does use CDK ( but not UIT )
>
> http://apps.ideaconsult.net:8080/ambit2/query/smarts?type=smiles&search=CCC%28C%28CC%28C%28C%29C%29C%29C%29C&text=&page=0&pagesize=100
>
>
> Best regards,
> Nina
>
>
>> I was comparing UIT and the above referenced code ported from chemkit.
>> First the difference in real world usage seems much less extreme than in
>> that benchmark (for small molecules) or I'm misinterpreting the chart.
>> Anyway in my case it takes about 60% of the time compared to UIT.
>>
>> Now to the subject of the message. I think there is an issue in the ported
>> version. Following query returns 44 hits with chemkit and 106 with UIT.
>> ChemFinder also gives 106 hits so I'm inclined to believe 106 is correct.
>>
>> Here the Query Molecule:
>>
>> CCC(C(CC(C(C)C)C)C)C
>>
>> Did not find or check for any other inconsistencies.
>>
>> Best Regards,
>>
>> Joos Kiener
>>
>>
>> ------------------------------------------------------------------------------
>> Doing More with Less: The Next Generation Virtual Desktop
>> What are the key obstacles that have prevented many mid-market businesses
>> from deploying virtual desktops? How do next-generation virtual desktops
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> ------------------------------
>
> Message: 3
> Date: Thu, 8 Sep 2011 10:48:40 +0100
> From: Sam Adams <[email protected]>
> Subject: Re: [Cdk-user] inchi generator and valency errors
> To: Nina Jeliazkova <[email protected]>
> Cc: Sam Adams <[email protected]>, [email protected]
> Message-ID:
> <CALiCMJ5ZrZ=aw3mn682n+l+6w8m5muodqhb+cwx8a_r1ta0...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> InChI generation should work with either implicit or explicit hydrogens.
>
> It looks like there's a bug in the passing of aromatic bonds from CDK to
> InChI (do I remember correctly that CDK's aromaticity handling get adjusted
> a couple of years ago?). Anyway, delete lines 294-295 from InChIGenerator
> should fix the things.
>
> https://github.com/egonw/cdk/blob/master/src/main/org/openscience/cdk/inchi/InChIGenerator.java#L294:
> if (bond.getFlag(CDKConstants.ISAROMATIC)) {
> * *order = INCHI_BOND_TYPE.ALTERN;
>
> I haven't got CDK on my machine at the moment, so it would be quicker for
> someone else to makes the changes.
>
> Cheers,
>
> Sam
>
>
> On 4 September 2011 07:39, Nina Jeliazkova <[email protected]>wrote:
>
>>
>>
>> On 4 September 2011 09:25, Egon Willighagen
>> <[email protected]>wrote:
>>
>>> cc:Sam (author of the CDK-InChI bridge)
>>>
>>> On Sun, Sep 4, 2011 at 7:52 AM, Nina Jeliazkova
>>> <[email protected]> wrote:
>>>> This usually happens, when the molecule does not contain explicit
>>>> hydrogens.
>>>
>>> I was not aware of that. Doesn't sound very useful. We don't have a
>>> unit test for this yet, right? That tests for InChI generation for a
>>> compound with and without explicit hydrogens, do we?
>>>
>>> Does this happen for any compound?
>>>
>>
>> Aromatics only.
>>
>> I came into this issue only recently, when working on metabolite generation
>> in Toxtree, haven't tested on a large scale.
>>
>>
>>>
>>>> e.g. the test below fails with exactly the same message : "Accepted
>>> unusual
>>>> valence(s): C(3); Cannot process aromatic bonds"
>>>> SmilesParser p = new
>>>> SmilesParser(NoNotificationChemObjectBuilder.getInstance());
>>>> IMolecule mol = p.parseSmiles("CN1C=NC2=C1C(=O)N(C(=O)N2C)C");
>>>> /*
>>>> CDKHydrogenAdder ha =
>>>>
>>> CDKHydrogenAdder.getInstance(NoNotificationChemObjectBuilder.getInstance());
>>>> ha.addImplicitHydrogens(mol);
>>>> AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol);
>>>> */
>>>> InChIGeneratorFactory factory = InChIGeneratorFactory.getInstance();
>>>> InChIGenerator gen = factory.getInChIGenerator(mol);
>>>> INCHI_RET ret = gen.getReturnStatus();
>>>> if (ret != INCHI_RET.OKAY) {
>>>> throw new Exception(String.format("InChI failed: %s [%s]",
>>>> ret.toString(),gen.getMessage()));
>>>> }
>>>> String inchi = gen.getInchi();
>>>>
>>> Assert.assertEquals("InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3",
>>>> inchi);
>>>
>>> I'll try to use this to create a unit test. I'll also make one for
>>> methane... wondering how widespread this issue is...
>>>
>>
>> Alkanes work fine.
>>
>> Nina
>>
>>
>>>
>>>> Uncomment the hydrogen adder code and the test will succeed.
>>>> I haven't investigated whether the explicit H requirement is the normal
>>>> InChI behaviour or something in the cdk-inchi interaction, perhaps
>>> others
>>>> could help. Otherwise, I agree the current behaviour is not quite
>>>> convenient.
>>>
>>> Sam, do you know what is going on?
>>>
>>> Egon
>>>
>>>
>>> --
>>> Dr E.L. Willighagen
>>> Postdoctoral Researcher
>>> Institutet f?r milj?medicin
>>> Karolinska Institutet (http://ki.se/imm)
>>> Homepage: http://egonw.github.com/
>>> LinkedIn: http://se.linkedin.com/in/egonw
>>> Blog: http://chem-bla-ics.blogspot.com/
>>> PubList: http://www.citeulike.org/user/egonw/tag/papers
>>>
>>
>>
>>
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> Doing More with Less: The Next Generation Virtual Desktop
> What are the key obstacles that have prevented many mid-market businesses
> from deploying virtual desktops? How do next-generation virtual desktops
> provide companies an easier-to-deploy, easier-to-manage and more affordable
> virtual desktop model.http://www.accelacomm.com/jaw/sfnl/114/51426474/
>
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> End of Cdk-user Digest, Vol 64, Issue 5
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