• Script to obtain PubChem information for a CSD entry

    This script will generate a simple HTML formatted output file of PubChem information for a CSD entry. This makes use of RDKit to generate an InChi key which is used to query UniChem to obtain the PubChem ID. The PubChem ID is then used in a PubChem REST query to obtain the information. Note, the path to RDKit must be set in the top of the script (line 32).

    Example usage:

    python pubchem_info.py aabhtz aabhtz_info.html

    Please note, at least some versions of Firefox may have issues reading the image (diagram) image from the default temporary location. This can be changed by including the dir= option to the tempfile.mkstemp call on line 145.

  • Script to filter molecular conformers with unusual torsion angles

    This is a script to filter a set of conformers of a molecule or set of molecules based on the number of unusual torsion angles. Running the script with the -h or --help option will give a full usage description, but the simplest usage is the following:

    python .\conformer_filter_density.py .\2uwd_conformers.sdf .\2uwd_passed.sdf

  • Script to merge GOLD docking results

    This is a script to merge a set of GOLD docking runs into single of results file. This script was designed to be used in cases where you start with a single .conf file and then generate a set of new .conf files with start_at_ligand and finish_at_ligand options to split the docking job into multiple runs. There are a few caveats:

    1. The dockings must all have been run with the same scoring function.
    2. One of the built-in scoring functions (chemplp, goldscore, chemscore, or asp) must have been used.
    3. The final set of merged ligands (if the option is selected) will not be sorted

    Using the -h or --help option will display a usage message.