def create_pymol_file(residues, pdb):
f = PyMOLFile()
f.commands += PyMOLCommands.load(f"{pdb.upper()}.pdb", pdb)
f.commands += PyMOLCommands.hide("sticks")
for residue in residues:
f.commands += PyMOLCommands.select("sele", f"resi {residue[3:]}")
f.commands += PyMOLCommands.show("stick", "sele")
f.commands += PyMOLCommands.load(f"{pdb}_ref.mol2", "lig")
return f
def _write_pymol_objects(self, relpath, hr, load_prot=True):
"""
generates pymol commands associated with an indivdual hotspot
:param relpath: path to the directory holding associated files
:param hr: hotspot result
:type relpath: str
:type hr: `hotspots.results.Results`
"""
self.pymol_out.commands += self._write_pymol_isosurfaces(
hr.super_grids, relpath, hr.identifier, "fhm")
if self.settings.output_superstar and hr.superstar:
self.pymol_out.commands += self._write_pymol_isosurfaces(
hr.superstar, relpath, hr.identifier, "superstar")
if self.settings.output_weighted and hr.weighted_superstar:
self.pymol_out.commands += self._write_pymol_isosurfaces(
hr.weighted_superstar, relpath, hr.identifier, "weighted")
if self.settings.output_buriedness and hr.buriedness:
default_level = 3
objname = f'buriedness_{hr.identifier}'
fname = f'{relpath}/buriedness{self.settings.grid_extension}'
self.pymol_out.commands += PyMOLCommands.load(fname=fname,
objname=objname)
# surface_10_apolar_hotspotid
surface_objname = f'surface_{objname}'
self.pymol_out.commands += PyMOLCommands.isosurface(
grd_name=objname,
isosurface_name=surface_objname,
level=default_level,
color=self.settings.colour_dict["buriedness"])
self.pymol_out.commands += PyMOLCommands.pymol_set(
setting_name='transparency',
value=self.settings.transparency,
selection=surface_objname)
group_members = [
f'buriedness_{hr.identifier}',
f'surface_buriedness_{hr.identifier}'
]
self.pymol_out.commands += PyMOLCommands.group(
group_name=hr.identifier, members=group_members)
# generate grid labels
labels = hr.grid_labels()
for p, dic in labels.items():
i = 0
group_me = []
for coord, value in dic.items():
objname = f"PS_{p}_{hr.identifier}_{i}"
group_me.append(objname)
self.pymol_out.commands += PyMOLCommands.pseudoatom(
objname=objname, coords=coord, label=f'{round(value, 1)}')
group_me.append(objname)
i += 1
self.pymol_out.commands += PyMOLCommands.group(
f'label_{p}_{hr.identifier}', group_me)
self.pymol_out.commands += PyMOLCommands.group(
f"labels_{hr.identifier}",
[f'label_{p}_{hr.identifier}' for p in hr.super_grids.keys()])
# load up the protein
if load_prot:
self.pymol_out.commands += PyMOLCommands.load(
f'{relpath}/protein.pdb', f'protein_{hr.identifier}')
if len(self.settings.protein_color_dic) > 0:
self.pymol_out += PyMOLCommands.color(
"slate", f'protein_{hr.identifier}')
self.pymol_out.commands += PyMOLCommands.show(
"cartoon", f'protein_{hr.identifier}')
self.pymol_out.commands += PyMOLCommands.hide(
"line", f'protein_{hr.identifier}')
self.pymol_out.commands += PyMOLCommands.show("sticks", "organic")