Re: [Rdkit-discuss] Keeping 3D coordinates from sdf file

[Paolo T. <pao...@gm...>]

Hi Puck,

When you read a SDF file using a SDMolSupplier RDKit will retain 3D coordinates. You can access them from the mol Conformer (a molecule can have multiple Conforrmers; one is generated for you when you read a set of coordinates):

mol.GetConformer().GetAtomPosition(atom_idx)

If you wish to retain hydrogen atoms, make sure to set removeHs=False when creating the supplier.

Cheers,
p.

> On 20 Aug 2020, at 12:54, Puck van Gerwen <puc...@gm...> wrote:
> 
> Dear rdkit, 
> 
> I am wondering whether after reading a molecule from an sdf file, it is possible to keep the original 3d coordinates that were in that sdf file? I will modify the molecules (fragment bonds and saturate with hydrogen) but as much as possible I want to keep the original coordinates. For example, if I had H3C-CH=CH2 and I break the first bond to remove H3C (to saturate to CH4) leaving CH=CH2 (to saturate to H2C=CH2), would it be possible to keep the original C coordinates rather than generate conformations and so on?
> 
> I appreciate the assistance.
> Best regards,
> -- 
> Puck van Gerwen
> Doktorandin / PhD candidate 
> Departement Chemie 
> Klingelbergstrasse 80
> CH-4056 Basel
> https://www.chemspacelab.org/
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