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)15-11(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)/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)15-11(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)/
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
>>
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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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