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 < >

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

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]

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

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