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

[Greg L. <gre...@gm...>]

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