Re: [Rdkit-discuss] How to set property (e.g. energy) for each conformer?

[JP <jea...@in...>]

Interesting hack.  Well played.

Thanks.

On 24 May 2011 04:44, Greg Landrum <gre...@gm...> wrote:
> On Mon, May 23, 2011 at 12:28 PM, JP <jea...@in...> wrote:
>> How do you set a property (e.g. energy) for each conformer (instead of
>> per molecule) ?
>>
>> What I am looking for is
>> SetProp( (Mol)self, confId, (str)key, (str)val [, (bool)computed=False])
>>
>> I want to write these values in an .sdf file.
>
> There's currently no way to associate properties with a particular conformer.
> The most straightforward way to approximate this would be to combine
> the values into one hidden property and then pull them out and set
> them as the energy property before writing the SDF.
>
> Something like this (not tested):
>
> # setting properties:
> if mol.HasProp("_ConfEnergies"):
>   mol.SetProp("_ConfEnergies","%s|%d:%.4f"%(mol.GetProp("_ConfEnergies"),confId,confEnergy)
>
> # writing to the SDWriter writer :
> confEs={}
> vs = [x.split(":") for x in mol.GetProp("_ConfEnergies").split('|')]
> for id,e in vs:
>  confEs[int(id)]=e
>
> for conf in mol.GetConformers:
>  mol.SetProp("Energy",confEs[conf.GetId()]
>  writer.write(mol)
>
> Hope this helps,
> -greg
>