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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)
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