p4ward.run.megadock

p4ward.run.megadock.capture_scores(run_docking_output_file, ligase_obj)

Grab all original megadock scores from run_docking_output_file and generate the ProteinPose objs from the docking run.

Parameters:

• run_docking_output_file – file generated my megadock output

• ligase_obj – object representing the ligase

p4ward.run.megadock.cluster(ligase_obj, protac_objs, clustering_type, clustering_cutoff_redund, clustering_cutoff_trend, cluster_redund_repr, rescore_poses)

cluster protein_poses’ triad points for redundancy or trend using hieragglo with ward linkage

p4ward.run.megadock.prep_structures(receptor_obj, ligase_obj)

Combine and prepare the protein files with their ligands for docking using pymol combine

p4ward.run.megadock.rotate_atoms(atom_coords, ref_rotation, pose_rotation)

Move atoms using information captured from the megadock output file.

p4ward.run.megadock.run_docking(program_path, receptor_file, ligase_file, num_threads, run_docking_output_file, num_predictions, num_predictions_per_rotation, num_rotational_angles, log_file)

Run the megadock main step