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 visualise(g, gname, peaks):
# visualise
gobj_name = f"{gname}_grid"
surface_objname = f"surface_{gobj_name}"
vis = f"testdata/grid_extension/{gname}.py"
gpath = f"testdata/grid_extension/{gname}.grd"
g.write(gpath)
f = PyMOLFile()
f.commands += PyMOLCommands.load(fname=f"{gname}.grd",
objname=gobj_name)
f.commands += PyMOLCommands.isosurface(
grd_name=gobj_name,
isosurface_name=surface_objname,
level=5,
color="yellow")
for i, p in enumerate(peaks):
f.commands += PyMOLCommands.sphere(objname=f"peak_obj_{i}",
rgba=[1, 1, 1, 1],
coords=p,
radius=0.5)
f.commands += PyMOLCommands.load_cgo(obj=f"peak_obj_{i}",
objname=f"peak_{i}")
f.write(vis)
def _write_pymol_isosurfaces(self, dict, relpath, identifier, dict_type):
"""
Loads grids and generates isosurfaces
:param dict: interaction grid dictionary
:param relpath: result containing directory
:param identifier: hotspot identifier
:param dict_type: superstar, fhm or weighted_superstar
:type dict: dict
:type relpath: str
:type identifier: str
:type dict_type: str
:return: pymol commands
:rtype: str
"""
cmd = ""
default_level = 5
# load grids and create isosurfaces
group_members = []
for p in dict.keys():
if dict_type == 'fhm':
objname = f'{p}_{identifier}'
fname = f'{relpath}/{p}{self.settings.grid_extension}'
else:
objname = f'{dict_type}_{p}_{identifier}'
fname = f'{relpath}/{dict_type}_{p}{self.settings.grid_extension}'
cmd += PyMOLCommands.load(fname=fname, objname=objname)
# surface_10_apolar_hotspotid
surface_objname = f'surface_{objname}'
cmd += PyMOLCommands.isosurface(grd_name=objname,
isosurface_name=surface_objname,
level=default_level,
color=self.settings.colour_dict[p])
cmd += PyMOLCommands.pymol_set(setting_name='transparency',
value=self.settings.transparency,
selection=surface_objname)
group_members.extend([objname, f"surface_{objname}"])
cmd += PyMOLCommands.group(group_name=identifier,
members=group_members)
return cmd
def test_load(self):
self.pymol_file.commands += PyMOLCommands.load("test_protein.pdb",
"myprotein")
self.pymol_file.write("testdata/wrapper_pymol/test_load.py")
def test_grid(self):
self.pymol_file.commands += PyMOLCommands.load("test_grid.grd",
"mygrid")
self.pymol_file.write("testdata/wrapper_pymol/test_grid.py")
def pymol_visulisation(self, outdir=None, fname="pymol_file.py"):
if not outdir:
outdir = os.getcwd()
if not os.path.exists(outdir):
os.mkdir(outdir)
if self.ligands:
with MoleculeWriter(os.path.join(outdir, "ligands.mol2")) as w:
for ligand in self.ligands:
try:
w.write(ligand.molecule)
except AttributeError:
w.write(ligand)
if self.protein:
with MoleculeWriter(os.path.join(outdir, "protein.mol2")) as w:
w.write(self.protein.molecule)
self.pymol_out = PyMOLFile()
if self.ligands:
self.pymol_out.commands += PyMOLCommands.load(
"ligands.mol2", "ligands")
if self.protein:
self.pymol_out.commands += PyMOLCommands.load(
"protein.mol2", "protein")
# write out point spheres and projection sphere and lines if applicable
self.pymol_out.commands += self.features_to_pymol_strings(
self.detected_features)
if self.feature_point_grids:
for identifier, g in self.feature_point_grids.items():
g.write(os.path.join(outdir, f"{identifier}.grd"))
point_colour = rgb_to_decimal(
self.feature_definitions[identifier].colour)
self.pymol_out.commands += PyMOLCommands.set_color(
f"{identifier}_color", point_colour)
self.pymol_out.commands += PyMOLCommands.load(
f"{identifier}.grd", f"{identifier}_grid")
self.pymol_out.commands += PyMOLCommands.isosurface(
f"{identifier}_grid",
f"surface_{identifier}",
level=1,
color=f"{identifier}_color")
self.pymol_out.commands += PyMOLCommands.group(
"feature_grids", self.feature_point_grids.keys())
self.pymol_out.commands += PyMOLCommands.group(
"feature_grids",
[f"surface_{a}" for a in self.feature_point_grids])
min_value = 0
surface_dic = {
self.identifier: {
'feature_grids':
[f"surface_{g}" for g in self.feature_point_grids.keys()]
}
}
surface_value_dic = {
self.identifier: {
"feature_grids":
max([
round(g.extrema[1], 1)
for g in self.feature_point_grids.values()
])
}
}
self.pymol_out.commands += PyMOLCommands.isoslider(
surface_dic, surface_value_dic)
self.pymol_out.write(os.path.join(outdir, fname))
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")