Matt Ragoza
Matt Ragoza
That could make sense as well, since a single heavy-atom molecule is a bit of an exception, where it doesn't necessarily signal partial initialization/further downstream processing needed when the coordinates...
If you set the config option `output: output_mols: True`, then the 3D molecules will be written to sdf files in the directory `{out_dir}/molecules/`. Computed metrics for the generated molecules will...
Yes, the files ending in `lig_gen_fit_add_gna.sdf` are the generated molecules after minimization in the binding pocket with gnina. Here are all the output identifier types and what they mean: ```...
Does the script run successfully after updating rdkit?
Ok, I have not yet nailed down the exact version(s) of rdkit that cause issues (I am using 2022.03.4), but I know that conda often fails to exactly resolve the...
How did you install the dependencies?
There are known compatibility issues between pip/conda molgrid and conda openbabel. You should use the `environment.yaml` file that is now provided in the repo to create a conda environment (preferably...
The last dependency you need is [gnina](https://github.com/gnina/gnina), which is used for the final minimization and affinity prediction with respect to the conditional receptor. I just updated the main branch with...
@RMeli I pushed a commit so that we use `GNINA_CMD` if it is defined in the environment, otherwise just `gnina` is run.
If you have not yet been able to install the dependencies, please try the detailed installation instructions I have just updated in the README.md and let me know how it...