binana package

binana.run(args=None)[source]

Gets all the interactions between a ligand and receptor, per the parameters specified in args. If args is not None, it should look like this:

[
    "-receptor", "receptor.pdb",
    "-ligand", "ligand.pdb",
    "-close_contacts_dist1_cutoff", "2.5",
    "-close_contacts_dist2_cutoff", "4",
    "-electrostatic_dist_cutoff", "4",
    "-active_site_flexibility_dist_cutoff", "4",
    "-hydrophobic_dist_cutoff", "4",
    "-hydrogen_bond_dist_cutoff", "4",
    "-hydrogen_halogen_bond_angle_cutoff", "40",
    "-halogen_bond_dist_cutoff", "5.5",
    "-pi_padding_dist", "0.75",
    "-pi_pi_interacting_dist_cutoff", "7.5",
    "-pi_stacking_angle_tolerance", "30",
    "-T_stacking_angle_tolerance", "30",
    "-T_stacking_closest_dist_cutoff", "5",
    "-cation_pi_dist_cutoff", "6",
    "-salt_bridge_dist_cutoff", "5.5",
    "-metal_coordination_dist_cutoff", "3.5"
]

If any of the parameters above are omitted, default values will be used. This function is most useful when using BINANA as a Python library (i.e., not JavaScript).

Parameters

args (list, optional) – A list of strings corresponding to parameter name/value pairs. The parameter names must start with a hyphen. If None, uses sys.argv (command line arguments). Defaults to None.