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