def features_to_pymol_strings(self, features):
"""
creates the code to visualise `ccdc.pharmacophore.Pharmacophore.Features` in PyMOL
:param list of (`ccdc.pharmacophore.Pharmacophore.Features`) features: features to be visualised
:return: str python code
"""
group_dic = {ident: [] for ident in self.feature_definitions.keys()}
pymol_out = ''
for i, feat in enumerate(features):
pymol_out += feat.to_pymol_str(i=i)
group_dic[feat.identifier].append(f"{feat.identifier}_{i}")
if feat.projected_identifier and self.protein:
resnum = feat.projected_identifier.split("/")[1]
# TODO: clean up
pymol_out += f'\ncmd.select("sele", "resi {resnum}")\ncmd.show("sticks", "sele")'
for fd in self.feature_definitions.keys():
pymol_out += PyMOLCommands.group(f"{fd}_pts", group_dic[fd])
pymol_out += PyMOLCommands.group(
"ligand_pharmacophore", [f"{a}_pts" for a in group_dic.keys()])
return pymol_out
def test_cone(self):
self.pymol_file.commands += PyMOLCommands.cone("_mycone", (0, 0, 0),
(10, 10, 10), 5,
(1, 0, 0))
self.pymol_file.commands += PyMOLCommands.load_cgo("_mycone", "mycone")
self.pymol_file.write("testdata/wrapper_pymol/test_cone.py")
def test_isosurface(self):
self.pymol_file.commands += PyMOLCommands.set_color(
"pomegranate", self.pomegranate)
self.pymol_file.commands += PyMOLCommands.isosurface(
"test_grid.grd", "mygrid", "mysurface", 4, "pomegranate")
self.pymol_file.write("testdata/wrapper_pymol/test_isosurface.py")
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 test_arrow(self):
self.pymol_file.commands += PyMOLCommands.arrow(
"_myarrow", (1, 1, 0), (4, 5, 0), (1, 0, 0), (0, 0, 1))
self.pymol_file.commands += PyMOLCommands.load_cgo(
"_myarrow", "myarrow")
self.pymol_file.write("testdata/wrapper_pymol/test_arrow.py")
def test_pseudoatom(self):
self.pymol_file.commands += PyMOLCommands.pseudoatom(
"mypseudoatom", (1, 1, 1), self.pomegranate)
self.pymol_file.commands += PyMOLCommands.pseudoatom(
"mypseudoatom2", (2, 2, 2), self.pomegranate, "31.2")
self.pymol_file.write("testdata/wrapper_pymol/test_pseudoatom.py")
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 test_line(self):
self.pymol_file.commands += PyMOLCommands.line("myline", (1, 1, 1),
(2, 2, 2),
self.pomegranate,
width=4)
self.pymol_file.commands += PyMOLCommands.line("myline2", (1, 1, 1),
(0, 0, 0),
self.pomegranate,
width=10)
self.pymol_file.write("testdata/wrapper_pymol/test_line.py")
def test_edge_detection(self):
self.selected = Grid.from_file("testdata/result/molA.grd")
edge = self.selected.edge_detection()
self.assertLess(len(edge), self.selected.count_grid())
f = PyMOLFile()
for i, n in enumerate(edge):
f.commands += PyMOLCommands.sphere(f"sphere_{i}", (0, 0, 1, 1), n,
0.1)
f.commands += PyMOLCommands.load_cgo(f"sphere_{i}",
f"sphere_{i}_obj")
f.write("testdata/grid_extension/edge_detection.py")
def test_cylinder(self):
self.pymol_file.commands += PyMOLCommands.cylinder(
"_mycylinder", (0, 0, 0), (1, 1, 1), 2, (1, 0, 0, 0.5))
self.pymol_file.commands += PyMOLCommands.load_cgo(
"_mycylinder", "mycylinder")
self.pymol_file.commands += PyMOLCommands.cylinder(
"_mycylinder2", (0, 0, 0), (10, 10, 10), 0.2, (1, 0, 0, 1),
(0.5, 0.5, 0))
self.pymol_file.commands += PyMOLCommands.load_cgo(
"_mycylinder2", "mycylinder2")
self.pymol_file.write("testdata/wrapper_pymol/test_cylinder.py")
def test_group(self):
self.pymol_file.commands += PyMOLCommands.line("myline1", (0, 0, 0),
(1, 1, 1),
self.pomegranate,
width=10)
self.pymol_file.commands += PyMOLCommands.pseudoatom(
"mypseudoatom1", (0, 0, 0), self.pomegranate)
self.pymol_file.commands += PyMOLCommands.pseudoatom(
"mypseudoatom2", (1, 1, 1), self.pomegranate)
self.pymol_file.commands += PyMOLCommands.group(
"mygroup", ["myline1", "mypseudoatom1", "mypseudoatom2"])
self.pymol_file.write("testdata/wrapper_pymol/test_group.py")
def test_sphere(self):
self.pymol_file.commands += PyMOLCommands.sphere("_mysphere",
self.pomegranate,
(0, 0, 0),
radius=2)
self.pymol_file.commands += PyMOLCommands.load_cgo(
"_mysphere", "mysphere")
self.pymol_file.commands += PyMOLCommands.sphere("_mysphere1",
self.pomegranate,
(1, 1, 1),
radius=1)
self.pymol_file.commands += PyMOLCommands.load_cgo(
"_mysphere1", "mysphere1")
self.pymol_file.write("testdata/wrapper_pymol/test_sphere.py")
def to_pymol_str(self):
pymol_out = ""
pymol_out += PyMOLCommands.sphere("peak_obj", (1, 1, 1, 1),
coords=self.point,
radius=1)
pymol_out += PyMOLCommands.load_cgo("peak_obj", "peak")
ligand_peak_features = []
for i, feat in enumerate(self.features):
pymol_out += feat.to_pymol_str(i=i)
ligand_peak_features.append(f"{feat.identifier}_{i}")
pymol_out += PyMOLCommands.group("ligand_peak_features",
ligand_peak_features)
return pymol_out
def __init__(self,
path,
grid_extension=".grd",
zip_results=True,
settings=None):
if settings is None:
self.settings = self.Settings()
else:
self.settings = settings
if grid_extension in self.settings.supported_grids:
self.settings.grid_extension = grid_extension
else:
self.settings.grid_extension = ".grd"
print(
"WARNING: Invalid grid file format provided. Default: '.grd' will be used"
)
self.path = self.get_out_dir(path)
self.zip_results = zip_results
self.pymol_out = PyMOLFile()
if self.zip_results:
# unzip and change working directory
self.pymol_out.commands += PyMOLCommands.unzip_dir(
self.settings.container)
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 write(self, hr):
"""
writes the Fragment Hotspot Maps result to the output directory and create the pymol visualisation file
:param hr: a Fragment Hotspot Maps result or list of results
:type hr: `hotspots.result.Result`
>>> from hotspots.calculation import Runner
>>> from hotspots.hs_io import HotspotWriter
>>> r = Runner
>>> result = r.from_pdb("1hcl")
>>> out_dir = <path_to_out>
>>> with HotspotWriter(out_dir) as w:
>>> w.write(result)
"""
container = Helper.get_out_dir(join(self.path,
self.settings.container))
if isinstance(hr, list):
print(hr)
if len({h.identifier for h in hr}) != len(hr):
# if there are not unique identifiers, create some.
for i, h in enumerate(hr):
h.identifier = f"hotspot-{i}"
for h in hr:
self._single_write(container, h)
else:
if not hr.identifier:
hr.identifier = "hotspot"
self._single_write(container, hr)
self._write_pymol_isoslider(hr)
self.pymol_out.commands += PyMOLCommands.background_color(
self.settings.bg_color)
self.pymol_out.commands += PyMOLCommands.push_to_wd()
if self.zip_results:
self.compress()
self.pymol_out.write(join(self.path, "pymol_file.py"))
def test_neighbourhood(self):
# check the catchment critera
neighbours = Grid.neighbourhood(i=0,
j=0,
k=0,
high=self.buriedness.nsteps,
catchment=1)
self.assertEqual(3, len(neighbours))
neighbours1 = Grid.neighbourhood(i=5,
j=5,
k=5,
high=self.buriedness.nsteps,
catchment=1)
self.assertEqual(6, len(neighbours1))
f = PyMOLFile()
for i, n in enumerate(neighbours + neighbours1):
f.commands += PyMOLCommands.sphere(f"sphere_{i}", (0, 0, 1, 1), n,
0.1)
f.commands += PyMOLCommands.load_cgo(f"sphere_{i}",
f"sphere_{i}_obj")
f.commands += PyMOLCommands.sphere("centre", (1, 0, 0, 1), (5, 5, 5),
0.1)
f.commands += PyMOLCommands.load_cgo("centre", "centre_obj")
f.commands += PyMOLCommands.sphere("centre1", (1, 0, 0, 1), (0, 0, 0),
0.1)
f.commands += PyMOLCommands.load_cgo("centre1", "centre1_obj")
f.write("testdata/grid_extension/neighbourhood.py")
def _write_pymol_isoslider(self, hr):
"""
generates the commands for an isoslider
:param hr: a hotspot result
:type hr: `hotspots.results.Results`
"""
# Isosurface obj's take the name: "surface_{probe ID}_{hotpsot ID}"
# e.g. "surface_apolar_hotspotA"
if not isinstance(hr, list):
hr = [hr]
# the hotspot grids are always output
surface_dic = {h.identifier: {'fhm': [f"surface_{g}_{h.identifier}" for g in h.super_grids.keys()]}
for h in hr}
surface_value_dic = {h.identifier: {"fhm": max([round(g.extrema[1], 1) for g in h.super_grids.values()])}
for h in hr}
for h in hr:
if self.settings.output_superstar and h.superstar:
surface_dic[h.identifier].update({'superstar': [f"surface_superstar_{g}_{h.identifier}"
for g in h.superstar.keys()]})
surface_value_dic[h.identifier].update({'superstar': max([round(g.extrema[1], 1)
for g in h.superstar.values()])})
if self.settings.output_weighted and h.weighted_superstar:
surface_dic[h.identifier].update({'weighted': [f"surface_weighted_superstar_{g}_{h.identifier}"
for g in h.weighted_superstar.keys()]})
surface_value_dic[h.identifier].update({'weighted': max([round(g.extrema[1], 1)
for g in h.weighted_superstar.values()])})
if self.settings.output_buriedness and h.buriedness:
surface_dic[h.identifier].update({'buriedness': [f"surface_buriedness_{h.identifier}"]})
surface_value_dic[h.identifier].update({'buriedness': 8})
min_value = 0
print(surface_dic)
print(surface_value_dic)
self.pymol_out.commands += PyMOLCommands.isoslider(surface_dic, surface_value_dic)
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 _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")
def to_pymol_str(self, i=0, label=True, transparency=0.6):
pymol_out = ""
point_colour = rgb_to_decimal(self.colour)
point_colour = utilities.Colour(point_colour[0], point_colour[1],
point_colour[2], transparency)
feat_ID = f"{self.identifier}_{i}"
group = []
coords = (self.point[0].centre[0], self.point[0].centre[1],
self.point[0].centre[2])
radius = self.point[0].radius
point_objname = f"{self.identifier}_point_{i}"
pymol_out += PyMOLCommands.sphere(point_objname,
point_colour,
coords,
radius=radius)
pymol_out += PyMOLCommands.load_cgo(point_objname,
f"{point_objname}_obj")
group.append(f"{point_objname}_obj")
if self.score != 0 and label:
score_name = f"{point_objname}_score"
pymol_out += PyMOLCommands.pseudoatom(
objname=score_name,
coords=coords,
label=f'{round(self.score, 1)}')
group.append(score_name)
rank_name = f"{self.identifier}_rank_{i}"
pymol_out += PyMOLCommands.pseudoatom(objname=rank_name,
coords=coords,
label=str(i + 1))
group.append(rank_name)
if self.projected:
proj_coords = (self.projected[0].centre[0],
self.projected[0].centre[1],
self.projected[0].centre[2])
projection_objname = f"{self.identifier}_projection_{i}"
line_objname = f"{self.identifier}_line_{i}"
group.extend([projection_objname, line_objname])
if self.projected_value != 0 and label:
proj_score_name = f"{point_objname}_proj_score"
pymol_out += PyMOLCommands.pseudoatom(
objname=proj_score_name,
coords=proj_coords,
label=f'{round(self.projected_value, 1)}')
group.append(proj_score_name)
projected_colour = adjust_lightness(self.colour, percentage=30)
projected_colour = utilities.Colour(projected_colour[0],
projected_colour[1],
projected_colour[2],
transparency)
projected_radius = self.projected[0].radius
pymol_out += PyMOLCommands.sphere(projection_objname,
projected_colour,
proj_coords,
radius=projected_radius)
pymol_out += PyMOLCommands.load_cgo(projection_objname,
f"{projection_objname}_obj")
pymol_out += PyMOLCommands.line(line_objname,
coords,
proj_coords,
rgb=projected_colour)
pymol_out += PyMOLCommands.group(feat_ID, group)
return pymol_out
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))