Oh and need to watch out for cases like.
*[N+](=O)[O-]
J
On 18 February 2017 at 09:43, Egon Willighagen <[email protected]>
wrote:
>
> I am also interested in implementing this in Bioclipse...
>
> Egon
>
> On Sat, Feb 18, 2017 at 10:12 AM, John Mayfield <
> [email protected]> 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 <[email protected]>
>> 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 <
>>> [email protected]> 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 <
>>>> [email protected]> 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 <
>>>>> [email protected]> 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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>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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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