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
>>>>
>>>> ------------------------------------------------------------
>>>> ------------------
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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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>>
>
>
> --
> Rajarshi Guha | http://blog.rguha.net
> NIH Center for Advancing Translational Science
>
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