Re: [Cdk-user] 'neutralizing' a molecule

2017-02-18 Thread John Mayfield 
Oh and need to watch out for cases like.

*[N+](=O)[O-]

J

On 18 February 2017 at 09:43, Egon Willighagen 
wrote:

>
> 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 
>> 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
 , 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
 

 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
>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>> ___
>> Cdk-user mailing list
>> Cdk-user@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>
>>
>
>
> --
> 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: -0001-7542-0286
> ImpactStory: https://impactstory.org/u/egonwillighagen
>
> 
>

Re: [Cdk-user] 'neutralizing' a molecule

2017-02-18 Thread Egon Willighagen 
I am also interested in implementing this in Bioclipse...

Egon

On Sat, Feb 18, 2017 at 10:12 AM, John Mayfield  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 
> 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
>>> , 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
>>> 
>>>
>>> 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  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
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>
>


 --
 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: -0001-7542-0286
 ImpactStory: https://impactstory.org/u/egonwillighagen

 
 --
 Check out the vibrant tech community on one of the world's most
 engaging tech sites, SlashDot.org! http://sdm.link/slashdot
 ___
 Cdk-user mailing list
 Cdk-user@lists.sourceforge.net

Re: [Cdk-user] 'neutralizing' a molecule

2017-02-18 Thread John Mayfield 
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  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
>> , 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
>> 
>>
>> 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 
>>> 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
 engaging tech sites, SlashDot.org! http://sdm.link/slashdot
 ___
 Cdk-user mailing list
 Cdk-user@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/cdk-user


>>>
>>>
>>> --
>>> 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: -0001-7542-0286
>>> ImpactStory: https://impactstory.org/u/egonwillighagen
>>>
>>> 
>>> --
>>> Check out the vibrant tech community on one of the world's most
>>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>>> ___
>>> Cdk-user mailing list
>>> Cdk-user@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>>
>>>
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>>

Re: [Cdk-user] 'neutralizing' a molecule

2017-02-17 Thread Rajarshi Guha 
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 
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
> , 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
> 
>
> John
>
> On 17 February 2017 at 14:00, Egon Willighagen  > 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 
>> 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
>>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>>> ___
>>> Cdk-user mailing list
>>> Cdk-user@lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>>
>>>
>>
>>
>> --
>> 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: -0001-7542-0286
>> ImpactStory: https://impactstory.org/u/egonwillighagen
>>
>> 
>> --
>> Check out the vibrant tech community on one of the world's most
>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>> ___
>> Cdk-user mailing list
>> Cdk-user@lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/cdk-user
>>
>>
>
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> ___
> Cdk-user mailing list
> Cdk-user@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/cdk-user
>
>


-- 
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
engaging tech sites, SlashDot.org! http://sdm.link/slashdot___
Cdk-user mailing list
Cdk-user@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/cdk-user

Re: [Cdk-user] 'neutralizing' a molecule

2017-02-17 Thread John Mayfield 
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
, 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


John

On 17 February 2017 at 14:00, Egon Willighagen 
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 
> 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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>
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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
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[Cdk-user] 'neutralizing' a molecule

2017-02-17 Thread Rajarshi Guha 
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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