Hi Paolo,
That works, thank you. I have a related question - after reading in
molecules with their coordinates, I remove hydrogens to make them implicit.
I later want to add the hydrogens back on and only optimise these, leaving
the heavy atoms alone. I tried to do this with an ethyne molecule where I
read the coordinates from an sdf file, removed the hydrogens, and added
them back on again. They are all added to the origin. I am trying and
failing to optimise the hydrogen positions without modifying the heavy
atoms. This is what I have so far:
# C atoms in positions 0 and 1
a = mol.GetConformer().GetAtomPosition(0)
b = mol.GetConformer().GetAtomPosition(1)
cmap = {0 : a, 1 : b}
AllChem.EmbedMolecule(mol, core=mol, coordMap=cmap)
AllChem.MMFFOptimizeMolecule(mol)
When I print out the coordinates I can see the heavy atoms have also been
modified. Would you be able to help me out here?
Best regards,
Puck
On Thu, 20 Aug 2020 at 13:26, Paolo Tosco <paolo.tosco.m...@gmail.com>
wrote:
> 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 <puck.vanger...@gmail.com>
> 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/
>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
--
*Puck van Gerwen*
Doktorandin / PhD candidate
Departement Chemie
Klingelbergstrasse 80
CH-4056 Basel
https://www.chemspacelab.org/
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