I am also interested in implementing this in Bioclipse...
Egon
On Sat, Feb 18, 2017 at 10:12 AM, John Mayfield <john.wilkinson...@gmail.com
> wrote:
> It's under LGPL, just a quick thing a wrote during my thesis. Might
> include in CDK proper as there's a few more things you can do.
>
> SMIRKS does let you customise these easily but actually they're not too
> bad and more efficient to inline in to code.
>
> [Cl-1:1]>>[Cl+0:1]
> [NH0+1:1]=[C+0:2][N+0:3]([H])>>[NH0+0:1][C+0:2]=[N+0:3]
>
> The second one handles cases like this:
> C[N+](C)=CN
>
> etc..
>
> On 17 February 2017 at 23:10, Rajarshi Guha <rajarshi.g...@gmail.com>
> wrote:
>
>> Indeed - thanks.
>>
>> This was actually asked by a user of the rcdk package who is dealing with
>> InChI's.
>>
>> The Java code you linked to is handy - what license is it available
>> under? if feasible, I'd like to include it in the rcdk package
>>
>> On Fri, Feb 17, 2017 at 5:38 PM, John Mayfield <
>> john.wilkinson...@gmail.com> wrote:
>>
>>> In general you shouldn't use InChI for storing (i.e. reading structures)
>>> it's unfortunate they made it possible. It is an identifier != exchange
>>> format, see Talk form Steve
>>> <http://www.hellers.com/steve/pub-talks/toronto-7-14.pdf>, Slide 8.
>>>
>>> That being said you can strip the salts and push it back through InChI
>>> (which has a neutralization algorithm - notice the formula is for the
>>> neutral form in your example), cut of the charge layer and then read it
>>> back. A disadvantage is since the layers are dependant you have to also
>>> drop the stereo as well. In this case it's actually okay to splice out the
>>> charge but in general that's not true.
>>>
>>> Charged Component:
>>> InChI=1S/C16H25N5O15P2/c17-13-7-14(19-3-18-13)21(4-20-7)15-1
>>> 1(26)9(24)6(33-15)2-32-37(28,29)36-38(30,31)35-16-12(27)10(2
>>> 5)8(23)5(1-22)34-16/h3-6,8-12,15-16,22-27H,1-2H2,(H,28,29)(H
>>> ,30,31)(H2,17,18,19)/p-2/t5-,6-,8-,9-,10+,11-,12-,15-,16?/m1/s1
>>>
>>> Neutral Component:
>>> InChI=1S/C16H25N5O15P2/c17-13-7-14(19-3-18-13)21(4-20-7)15-1
>>> 1(26)9(24)6(33-15)2-32-37(28,29)36-38(30,31)35-16-12(27)10(2
>>> 5)8(23)5(1-22)34-16/h3-6,8-12,15-16,22-27H,1-2H2,(H,28,29)(H
>>> ,30,31)(H2,17,18,19)/
>>>
>>> You'd also be surprised how far a very simple approach gets you:
>>> Neutralize.java
>>> <https://github.com/johnmay/mdk/blob/develop-1.5/tool/search-tree/src/main/java/org/openscience/cdk/isomorphism/Neutralise.java>
>>>
>>> John
>>>
>>> On 17 February 2017 at 14:00, Egon Willighagen <
>>> egon.willigha...@gmail.com> wrote:
>>>
>>>>
>>>> John suggest this list of SMARTS recently:
>>>>
>>>> http://www.daylight.com/meetings/emug00/Sayle/pkapredict.html
>>>>
>>>> And Nina mentioned code in AMBIT for SMIRKS to do the job...
>>>>
>>>> Egon
>>>>
>>>>
>>>>
>>>>
>>>> On Fri, Feb 17, 2017 at 2:51 PM, Rajarshi Guha <rajarshi.g...@gmail.com
>>>> > wrote:
>>>>
>>>>> Hi, I have a situtation where I start from an InChI for a molecule in
>>>>> salt form, and after stripping the salt, I would like to obtain the
>>>>> neutral
>>>>> form.
>>>>>
>>>>> An example is starting from
>>>>>
>>>>> InChI=1S/C16H25N5O15P2.2Na/c17-13-7-14(19-3-18-13)21(4-20-7)
>>>>> 15-11(26)9(24)6(33-15)2-32-37(28,29)36-38(30,31)35-16-12(27)
>>>>> 10(25)8(23)5(1-22)34-16;;/h3-6,8-12,15-16,22-27H,1-2H2,(H,28
>>>>> ,29)(H,30,31)(H2,17,18,19);;/q;2*+1/p-2/t5-,6-,8-,9-,10+,11-
>>>>> ,12-,15-,16?;;/m1../s1
>>>>>
>>>>> I can use ConnectivityChecker to get the largest component. But this
>>>>> has a charge of -2, with the phosphate groups missing a proton.
>>>>>
>>>>> Is there a convenience method to neutralize this molecule by adding
>>>>> protons appropriately?
>>>>>
>>>>> --
>>>>> Rajarshi Guha | http://blog.rguha.net
>>>>> NIH Center for Advancing Translational Science
>>>>>
>>>>> ------------------------------------------------------------
>>>>> ------------------
>>>>> Check out the vibrant tech community on one of the world's most
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>>>>> _______________________________________________
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>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> E.L. Willighagen
>>>> Department of Bioinformatics - BiGCaT
>>>> Maastricht University (http://www.bigcat.unimaas.nl/)
>>>> 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
>>>> ORCID: 0000-0001-7542-0286
>>>> ImpactStory: https://impactstory.org/u/egonwillighagen
>>>>
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>>>>
>>>
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>>> ------------------
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>>>
>>
>>
>> --
>> Rajarshi Guha | http://blog.rguha.net
>> NIH Center for Advancing Translational Science
>>
>
>
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--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
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
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/u/egonwillighagen
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