def _single_write(self, path, hr):
hr.out_dir = Helper.get_out_dir(join(path, hr.identifier))
self._write_grids(hr)
self._write_protein(hr.out_dir, hr.protein)
relpath = f'{hr.identifier}'
self._write_pymol_objects(relpath, hr)
def _single_write(self, path, hr):
hr.out_dir = Helper.get_out_dir(join(path, hr.identifier))
self._write_grids(hr)
self._write_protein(hr.out_dir, hr.protein)
if basename(path) == 'out' and self.zip_results==False:
relpath = join(basename(path), f'{hr.identifier}')
else:
relpath = f'{hr.identifier}'
self._write_pymol_objects(relpath, hr)
def to_grid(target, pdb):
out_dir = "Z:/patel_set/{}/{}".format(target, pdb)
mols = MoleculeReader(
join(out_dir, "reference_pharmacophore", "aligned_mols.mol2"))
p = PharmacophoreModel.from_ligands(ligands=mols, identifier="test")
result = Results(super_grids=p.dic,
protein=Protein.from_file(
join(out_dir, "hs", "{}.pdb".format(pdb))))
out = Helper.get_out_dir(join(out_dir, "reference_pharmacophore", "grids"))
settings = HotspotWriter.Settings()
settings.isosurface_threshold = [2, 5, 10]
with HotspotWriter(path=out, zip_results=True, settings=settings) as w:
w.write(result)
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 write(self, hr):
"""
writes the Fragment Hotspot Maps result to the output directory and create the pymol visualisation file
:param `hotspots.result.Result` hr: a Fragment Hotspot Maps result or list of results
>>> 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)
"""
if isinstance(hr, list):
self.settings.grids = list(hr[0].super_grids.keys())
self.settings.container = "hotspot_boundaries"
self.number_of_hotspots = len(hr)
self.out_dir = Helper.get_out_dir(
join(self.path, self.settings.container))
self._write_protein(hr[0].protein)
if hr[0].pharmacophore:
self.settings.pharmacophore = True
# hts = [h.hotspot_result for h in hr]
self._write_pymol(hr, self.zipped)
for i, hotspot in enumerate(hr):
self.out_dir = Helper.get_out_dir(
join(self.path, self.settings.container, str(i)))
self.settings.isosurface_threshold = [
round(hotspot.threshold, 1)
]
bi = (Grid.super_grid(
2, hotspot.best_island).max_value_of_neighbours() >
hotspot.threshold)
self._write_grids(hotspot.super_grids,
buriedness=None,
mesh=bi)
self._write_protein(hotspot.protein)
if hotspot.pharmacophore:
self._write_pharmacophore(hotspot.pharmacophore)
self._write_pymol(hotspot, False)
self.out_dir = dirname(self.out_dir)
if self.zipped:
self.compress(
join(dirname(self.out_dir), self.settings.container))
else:
self.settings.grids = list(hr.super_grids.keys())
# self.settings.container = "out"
self.number_of_hotspots = 1
self.out_dir = Helper.get_out_dir(
join(self.path, self.settings.container))
self._write_grids(hr.super_grids, buriedness=hr.buriedness)
self._write_protein(hr.protein)
if hr.pharmacophore:
self.settings.pharmacophore = True
self._write_pharmacophore(hr.pharmacophore)
self._write_pymol(hr, self.zipped)
if self.zipped:
self.compress(
join(dirname(self.out_dir), self.settings.container))