[Rdkit-discuss] how to append conformer number to molecule name in SDF output file?

[Francois BERENGER]

Hello,

I am generating conformers.

When I write them out, I'd like that they are named like this:

molName_001
molName_002
...

So that, down the line, I know with which conformer of which molecule
I am working with.

So: "parent" molecule name followed by one '_' then the conformer Id
in a fixed format.

Is it possible to do so with a Chem.SDWriter?

Thanks a lot,
Francois.

[Greg Landrum]

Sure you can do this by setting the molecule's "_Name" property before each
call to SDWriter.write().
Here's a short example:

In [15]: sio = StringIO()

In [16]: w = Chem.SDWriter(sio)

In [17]: basen = m.GetProp('_Name')

In [18]: for conf in m.GetConformers():
...: cid = conf.GetId()
...: nm = "{}-{}".format(basen,cid)
...: m.SetProp('_Name',nm)
...: w.write(m,confId=cid)
...:

In [19]: w.flush()

In [20]: print(sio.getvalue()[:20])
mol1-0
RDKit

This just adds a conformation ID to the end of whatever the molecule's name
starts out as.

Hope this helps,
-greg



On Wed, Jun 14, 2017 at 5:00 AM, Francois BERENGER <

Post by Francois BERENGER
Hello,
I am generating conformers.
molName_001
molName_002
...
So that, down the line, I know with which conformer of which molecule
I am working with.
So: "parent" molecule name followed by one '_' then the conformer Id
in a fixed format.
Is it possible to do so with a Chem.SDWriter?
Thanks a lot,
Francois.
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