NAME

       prodigy - binding affinity predictor

DESCRIPTION

       usage: prodigy [-h] [--distance-cutoff DISTANCE_CUTOFF]

              [--acc-threshold  ACC_THRESHOLD]  [--temperature TEMPERATURE] [--contact_list] [--pymol_selection]
              [-q] [-np NUMBER_OF_PROCESSORS] [--selection A B [A,B C ...]]  input_path

       Binding affinity predictor based on Intermolecular Contacts (ICs).

   positional arguments:
       input_path
              Path to either: - Structure in PDB or mmCIF format - Directory containing structure files

   options:
       -h, --help
              show this help message and exit

       --distance-cutoff DISTANCE_CUTOFF
              Distance cutoff to calculate ICs

       --acc-threshold ACC_THRESHOLD
              Accessibility threshold for BSA analysis

       --temperature TEMPERATURE
              Temperature (C) for Kd prediction

       --contact_list
              Output a list of contacts

       --pymol_selection
              Output a script to highlight the interface (pymol)

       -q, --quiet
              Outputs only the predicted affinity value

       -np, --number-of-processors NUMBER_OF_PROCESSORS
              Number of processors to use (default: 1)

       Selection Options:

              By default, all intermolecular contacts are taken into consideration, a molecule being defined  as
              an isolated group of amino acids sharing a common chain identifier. In specific cases, for example
              antibody-antigen complexes, some chains should be considered as a single molecule.

              Use  the  --selection  option  to  provide collections of chains that should be considered for the
              calculation. Separate by a space the chains that are to be considered _different_  molecules.  Use
              commas to include multiple chains as part of a single group:

       --selection A B => Contacts calculated (only) between chains A and B.

       --selection A,B C => Contacts calculated (only) between
              chains A and C; and B and C.

       --selection A B C => Contacts calculated (only) between
              chains A and B; B and C; and A and C.

       --selection A B [A,B C ...]

prodigy 2.4.0                                     October 2025                                        PRODIGY(1)