Re: [Rdkit-discuss] separate module by breaking bonds

[Yingfeng W. <ywa...@gm...>]

Greg,

Thank you very much.

I think I need to add masses of all atoms for getting the mass of the whole
fragment. Am I right?

Yingfeng


On Fri, May 31, 2013 at 1:22 AM, Greg Landrum <gre...@gm...>wrote:

> Hi,
>
> On Fri, May 31, 2013 at 7:02 AM, Yingfeng Wang <ywa...@gm...> wrote:
>
>> I am looking for a simple way to separate a module by breaking bonds.
>>
>> Say, I have a compound with the following inchi format,
>>
>>
>> InChI=1S/C10H9N3O/c1-7-11-10(14)9(13-12-7)8-5-3-2-4-6-8/h2-6H,1H3,(H,11,12,14)
>>
>> I want to separate it into two parts by removing one or two bonds. And I
>> want to enumberate all possibilities. May I use BreakBRICSBonds by
>> specifying argument 'bonds'?
>>
>> Actually, BreakBRICSBonds returns a Mol, how do I know mass of each part
>> after bonds are removed?
>>
>>
> Once you have a molecule that is made up of different pieces, you can get
> it as separate molecules using Chem.GetMolFrags:
>
> Here's a demo using your example:
> In [42]: m
> =Chem.MolFromInchi('InChI=1S/C10H9N3O/c1-7-11-10(14)9(13-12-7)8-5-3-2-4-6-8/h2-6H,1H3,(H,11,12,14)')
>
> In [43]: broken = BRICS.BreakBRICSBonds(m)
>
> In [44]: frags = Chem.GetMolFrags(broken,asMols=True)
>
> In [45]: frags
> Out[45]: (<rdkit.Chem.rdchem.Mol at 0x1e62398>, <rdkit.Chem.rdchem.Mol at
> 0x2335d70>)
>
> In [47]: [Chem.MolToSmiles(x,True) for x in frags]
> Out[47]: ['[14*]c1nnc(C)nc1O', '[16*]c1ccccc1']
>
>
> If you want to exhaustively explore breaking bonds or pairs of bonds, I'd
> suggest using an EditableMol instead of the BRICS code (which is really
> designed for breaking a particular set of bonds).
>
> In [53]: m =Chem.MolFromSmiles('c1ccccc1c2ncccc2')
>
> In [54]: em = Chem.EditableMol(m)
>
> In [55]: em.RemoveBond(5,6)
>
> In [56]: nm = em.GetMol()
>
> In [57]: frags = Chem.GetMolFrags(nm,asMols=True)
>
> In [58]: [Chem.MolToSmiles(x,True) for x in frags]
> Out[58]: ['c1ccccc1', 'c1ccncc1']
>
> There are a number of examples of using EditableMol in the archives of
> this list (searchable here:
> http://www.mail-archive.com/rdk...@li.../) and in
> the RDkit documentation.
>
> hope this helps,
> -greg
>
>