diff options
Diffstat (limited to 'plip/visualization/visualize.py')
| -rw-r--r-- | plip/visualization/visualize.py | 62 |
1 files changed, 37 insertions, 25 deletions
diff --git a/plip/visualization/visualize.py b/plip/visualization/visualize.py index 4cd7a14..a551798 100644 --- a/plip/visualization/visualize.py +++ b/plip/visualization/visualize.py @@ -20,54 +20,63 @@ def visualize_in_pymol(plcomplex): lig_members = plcomplex.lig_members chain = plcomplex.chain if config.PEPTIDES: - vis.ligname = 'PeptideChain%s' % plcomplex.chain + vis.ligname = "PeptideChain%s" % plcomplex.chain if config.INTRA is not None: - vis.ligname = 'Intra%s' % plcomplex.chain + vis.ligname = "Intra%s" % plcomplex.chain ligname = vis.ligname hetid = plcomplex.hetid metal_ids = plcomplex.metal_ids - metal_ids_str = '+'.join([str(i) for i in metal_ids]) + metal_ids_str = "+".join([str(i) for i in metal_ids]) ######################## # Basic visualizations # ######################## - start_pymol(run=True, options='-pcq', quiet=not config.VERBOSE and not config.SILENT) + start_pymol( + run=True, options="-pcq", quiet=not config.VERBOSE and not config.SILENT + ) vis.set_initial_representations() cmd.load(plcomplex.sourcefile) - current_name = cmd.get_object_list(selection='(all)')[0] - logger.debug(f'setting current_name to {current_name} and pdbid to {pdbid}') + current_name = cmd.get_object_list(selection="(all)")[0] + logger.debug(f"setting current_name to {current_name} and pdbid to {pdbid}") cmd.set_name(current_name, pdbid) - cmd.hide('everything', 'all') + cmd.hide("everything", "all") if config.PEPTIDES: - cmd.select(ligname, 'chain %s and not resn HOH' % plcomplex.chain) + cmd.select(ligname, "chain %s and not resn HOH" % plcomplex.chain) else: - cmd.select(ligname, 'resn %s and chain %s and resi %s*' % (hetid, chain, plcomplex.position)) - logger.debug(f'selecting ligand for PDBID {pdbid} and ligand name {ligname}') - logger.debug(f'resn {hetid} and chain {chain} and resi {plcomplex.position}') + cmd.select( + ligname, + "resn %s and chain %s and resi %s*" % (hetid, chain, plcomplex.position), + ) + logger.debug(f"selecting ligand for PDBID {pdbid} and ligand name {ligname}") + logger.debug(f"resn {hetid} and chain {chain} and resi {plcomplex.position}") # Visualize and color metal ions if there are any if not len(metal_ids) == 0: vis.select_by_ids(ligname, metal_ids, selection_exists=True) - cmd.show('spheres', 'id %s and %s' % (metal_ids_str, pdbid)) + cmd.show("spheres", "id %s and %s" % (metal_ids_str, pdbid)) # Additionally, select all members of composite ligands if len(lig_members) > 1: for member in lig_members: resid, chain, resnr = member[0], member[1], str(member[2]) - cmd.select(ligname, '%s or (resn %s and chain %s and resi %s)' % (ligname, resid, chain, resnr)) - - cmd.show('sticks', ligname) - cmd.color('myblue') - cmd.color('myorange', ligname) - cmd.util.cnc('all') + cmd.select( + ligname, + "%s or (resn %s and chain %s and resi %s)" + % (ligname, resid, chain, resnr), + ) + + cmd.show("sticks", ligname) + cmd.color("myblue") + cmd.color("myorange", ligname) + cmd.util.cnc("all") if not len(metal_ids) == 0: - cmd.color('hotpink', 'id %s' % metal_ids_str) - cmd.hide('sticks', 'id %s' % metal_ids_str) - cmd.set('sphere_scale', 0.3, ligname) + cmd.color("hotpink", "id %s" % metal_ids_str) + cmd.hide("sticks", "id %s" % metal_ids_str) + cmd.set("sphere_scale", 0.3, ligname) cmd.deselect() vis.make_initial_selections() @@ -91,9 +100,9 @@ def visualize_in_pymol(plcomplex): vis.additional_cleanup() if config.DNARECEPTOR: # Rename Cartoon selection to Line selection and change repr. - cmd.set_name('%sCartoon' % plcomplex.pdbid, '%sLines' % plcomplex.pdbid) - cmd.hide('cartoon', '%sLines' % plcomplex.pdbid) - cmd.show('lines', '%sLines' % plcomplex.pdbid) + cmd.set_name("%sCartoon" % plcomplex.pdbid, "%sLines" % plcomplex.pdbid) + cmd.hide("cartoon", "%sLines" % plcomplex.pdbid) + cmd.show("lines", "%sLines" % plcomplex.pdbid) if config.PEPTIDES: filename = "%s_PeptideChain%s" % (pdbid.upper(), plcomplex.chain) @@ -104,7 +113,10 @@ def visualize_in_pymol(plcomplex): if config.PYMOL: vis.save_session(config.OUTPATH, override=filename) else: - filename = '%s_%s' % (pdbid.upper(), "_".join([hetid, plcomplex.chain, plcomplex.position])) + filename = "%s_%s" % ( + pdbid.upper(), + "_".join([hetid, plcomplex.chain, plcomplex.position]), + ) if config.PYMOL: vis.save_session(config.OUTPATH) if config.PICS: |