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authorNavan Chauhan <navanchauhan@gmail.com>2020-07-02 20:48:33 +0530
committerNavan Chauhan <navanchauhan@gmail.com>2020-07-02 20:48:33 +0530
commit4be08f7bdd77991e9e453c1cda863c3f20c338d5 (patch)
tree083e8e91622221185a28fd50754abc2f86b1df43 /plip/visualization/visualize.py
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+from pymol import cmd
+
+from plip.basic import config, logger
+from plip.basic.supplemental import start_pymol
+from plip.visualization.pymol import PyMOLVisualizer
+
+logger = logger.get_logger()
+
+
+def visualize_in_pymol(plcomplex):
+ """Visualizes the protein-ligand pliprofiler at one site in PyMOL."""
+
+ vis = PyMOLVisualizer(plcomplex)
+
+ #####################
+ # Set everything up #
+ #####################
+
+ pdbid = plcomplex.pdbid
+ lig_members = plcomplex.lig_members
+ chain = plcomplex.chain
+ if config.PEPTIDES:
+ vis.ligname = 'PeptideChain%s' % plcomplex.chain
+ if config.INTRA is not None:
+ 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])
+
+ ########################
+ # Basic visualizations #
+ ########################
+
+ 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}')
+ cmd.set_name(current_name, pdbid)
+ cmd.hide('everything', 'all')
+ if config.PEPTIDES:
+ 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}')
+
+ # 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))
+
+ # 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')
+ 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.deselect()
+
+ vis.make_initial_selections()
+
+ vis.show_hydrophobic() # Hydrophobic Contacts
+ vis.show_hbonds() # Hydrogen Bonds
+ vis.show_halogen() # Halogen Bonds
+ vis.show_stacking() # pi-Stacking Interactions
+ vis.show_cationpi() # pi-Cation Interactions
+ vis.show_sbridges() # Salt Bridges
+ vis.show_wbridges() # Water Bridges
+ vis.show_metal() # Metal Coordination
+
+ vis.refinements()
+
+ vis.zoom_to_ligand()
+
+ vis.selections_cleanup()
+
+ vis.selections_group()
+ 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)
+
+ if config.PEPTIDES:
+ filename = "%s_PeptideChain%s" % (pdbid.upper(), plcomplex.chain)
+ if config.PYMOL:
+ vis.save_session(config.OUTPATH, override=filename)
+ elif config.INTRA is not None:
+ filename = "%s_IntraChain%s" % (pdbid.upper(), plcomplex.chain)
+ if config.PYMOL:
+ vis.save_session(config.OUTPATH, override=filename)
+ else:
+ filename = '%s_%s' % (pdbid.upper(), "_".join([hetid, plcomplex.chain, plcomplex.position]))
+ if config.PYMOL:
+ vis.save_session(config.OUTPATH)
+ if config.PICS:
+ vis.save_picture(config.OUTPATH, filename)