You can use “addCoords=True” in your addHs call.
http://rdkit.org/docs/source/rdkit.Chem.rdmolops.html#rdkit.Chem.rdmolops.AddHs
<http://rdkit.org/docs/source/rdkit.Chem.rdmolops.html#rdkit.Chem.rdmolops.AddHs>
Sunhwan
> On Aug 21, 2020, at 6:11 AM, Puck van Gerwen <puck.vanger...@gmail.com> wrote:
>
> 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
> <mailto: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
> <mailto: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/ <https://www.chemspacelab.org/>
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> <mailto:Rdkit-discuss@lists.sourceforge.net>
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>> <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/ <https://www.chemspacelab.org/>
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
