drugforge.spectrum.calculate_rmsd

Functions

colorbyrmsd(p, target_sel, ref_sel[, quiet, ...])	Color aligned proteins by RMSD with respect to the target.
convert_chain_id(chain)	Convert a chain identifier between letter and number representations.
find_bsite_resids(pdb, pdb_ref, aligned_temp)	Find binding site residues in a protein-ligand complex based on ligand proximity.
get_binding_site_rmsd(file_mob, file_ref[, ...])	Calculate RMSD for the Binding Site residues between file_mob and file_ref The binding site is defined as all residues protein within bsite_dist Angs of the ligand in the reference protein.
get_residue_mapping(seq_ref, seq_mob)	Aligns two sequences and returns the correct start and end residue indices, ignoring gaps
rmsd_alignment(target_pdb, ref_pdb, final_pdb)	Calculate RMSD of a molecule against a reference
save_alignment_pymol(pdbs, labels, ...[, ...])	Imports the provided PDBs into a Pymol session and saves
select_best_colabfold(results_dir, seq_name, ...)	Select the best seed output (repetition) from a ColabFold run based on its RMSD wrt the reference.