Re: [Rdkit-discuss] convert a smiles file to a xyz file

Have a look at write_xtb_input_file in this module: https://github.com/jensengroup/take_elementary_step/blob/master/write_input_files.py The xtb input is simple an xyz file with some additional lines below if the molecule is charged. You can simply those lines in the code. Best regards, Jan

Re: [Rdkit-discuss] Does AddConformer function lose SDF properties of conformers when adding them?

Dear Paolo, thank you very much! Now it is working as I hoped it would. My error was that I was using suppl[0] when writing out, instead of defining a new variable mol=suppl[0] and doing the copy_coords with that mol variable, as you did. Many thanks for your help! best regards, Anikó From:

[Rdkit-discuss] RDKit postgres cartridge building

Good morning, I am trying to build RDKit from source, and succeed with that following the instructions provided in the documentation. Howvere, I am trying to use the postgres cartridge, which as far as I understand is built during the main building process. but after trying to create the

Re: [Rdkit-discuss] RDKit postgres cartridge building

Hi Alfredo, My first guess would be you have another, older Postgres version on your computer and you have build against this version. Take a look at the /use/share/postgresql directory and take a look if there is another directory instead of 10/ Markus -

Re: [Rdkit-discuss] RDKit postgres cartridge building

thank you Markus for the reply, listing the /user/share/postgresql directory I can see several folder apart from 10 (9.2, 9.3, etc), I uninstalled the current postgres instalation and deleted all the folder under ´/user/share/postgresql. Afterwards I reinstalled postgres, and only 

Re: [Rdkit-discuss] RDKit postgres cartridge building

Dear Alfredo, this file contains pretty comprehensive instructions how to build and install the cartridge: https://github.com/rdkit/rdkit/blob/master/Code/PgSQL/rdkit/README Please get back to me off-list if you still have issues in getting it to work for you. Cheers, p. On 05/24/18

[Rdkit-discuss] Molecule does not have substructure match with its fragments

Hello,   I am running rdkit version 2017.09.3. I read an sdf with   supplier = SDMolSupplier('try/try.sdf')   I then took the first mol from supplier and named it mol. I then performed   fragmented = Recap.RecapDecompose(mol, minFragmentSize=3). I looped through its children with:

Re: [Rdkit-discuss] convert a smiles file to a xyz file

Thank you Prof. Jensen. I will study the module. Best, Chenyang On Thu, May 24, 2018 at 1:30 AM, Jan Halborg Jensen wrote: > Have a look at write_xtb_input_file in this module: https://github.com/ > jensengroup/take_elementary_step/blob/master/write_input_files.py > > The