def trajectory(self):
"""
Particles' coordinates at the current time
Returns
-------
stream : :class:`MDAnalysis.lib.util.NamedStream`
A stream in the format that can be parsed by :class:`ESPReader`
"""
# time
_xyz = str(self.system.time) + '\n'
# number of particles
_xyz += str(len(self.system.part)) + '\n'
# box edges
_xyz += str(self.system.box_l) + '\n'
# configuration
for _p in self.system.part:
_xyz += str(_p.pos) + '\n'
for _p in self.system.part:
_xyz += str(_p.v) + '\n'
for _p in self.system.part:
_xyz += str(_p.f) + '\n'
return NamedStream(StringIO(_xyz), "__.ESP")
def _pharmacohore_from_mdanalysis(
self,
frame_num: int,
load_mol_system: bool = False,
load_ligand: bool = False) -> StructuredBasedPharmacophore:
""" Derive a pharmacophore for a single frame of an MdAnalysis Universe object.
Parameters
----------
frame_num : int
The index number of the frame from which the pharmacophore will be derived.
load_mol_system: bool, default=False
If true the receptor will be stored in the pharmacophore object.
load_ligand: bool, default=False
If true the ligand will be stored in the pharmacophore object.
"""
if not isinstance(frame_num, int):
raise OpenPharmacophoreTypeError("Frame number must be an integer")
stream = StringIO()
pdb_stream = NamedStream(stream, "output.pdb")
atoms = self._trajectory.select_atoms("all")
atoms.write(pdb_stream,
frames=self._trajectory.trajectory[[frame_num]])
pharmacophore = StructuredBasedPharmacophore.from_pdb(
pdb_stream,
radius=1.0,
ligand_id=None,
hydrophobics="plip",
load_mol_system=load_mol_system,
load_ligand=load_ligand)
return pharmacophore
def setUp(self):
self.universe = MDAnalysis.Universe(PSF, DCD)
stream = StringIO()
self.namedfile = NamedStream(stream, self.filename)
def namedfile(self):
return NamedStream(StringIO(), self.filename)
def benzene_universe():
return mda.Universe(NamedStream(io.StringIO(benz), 'benzene.pdb'))
