p4ward.run.structure_tools

p4ward.run.structure_tools.get_coords_array(pose_objs, ligase_obj)

p4ward.run.structure_tools.get_e3_modelfile(e3, model_number=1, subrec_only=False)

return the a model file corresponding to the e3 (vhl or crbn) and the model number if subrec_only == True, we get the pdb that contains only the vhl or crbn proteins if False, we get the pdb which contains the full crl model

p4ward.run.structure_tools.get_protac_dist_cuttoff(protac_objs, reclig_file, liglig_file, dist_cutoff, sampling_type, unbound_protac_num_confs)

p4ward.run.structure_tools.get_rmsd(obj1, obj2, fit=False, ca=False, backbone=True)

Use biopython to get the atomic coordinates of both objects and the pip tool rmsd.rmsd to calulate the rmsd. Returns rmsd value

p4ward.run.structure_tools.load_biopython_structures(structure_file, mol2=False)

load a structure as biopython object. If file in mol2 format, convert first using obabel. Intended for use with the ligands.

p4ward.run.structure_tools.pymol_align(target_file, moving_file, outfilename)

p4ward.run.structure_tools.pymol_combine(*args, out_filename='combined.pdb', assign_chains=True)

p4ward.run.structure_tools.structure_proximity(struct1, struct2, dist_cutoff=None)

Calculate the distance between the center of mass of two biopython struct objects and check if it is <= than a distance cutoff.

p4ward.run.structure_tools.write_charges(*charge_lists, filepath)