def pdb(self, value):
with self.workdir:
self._pdb = "{}.pdb".format(self.name)
if isinstance(value, _BSS._SireWrappers.System):
_BSS.IO.saveMolecules(self.name, value, "pdb")
elif isinstance(value, _BSS._SireWrappers.Molecule):
_BSS.IO.saveMolecules(self.name, _BSS._SireWrappers.System(value), "pdb")
elif isinstance(value, _pmd.Structure):
_pmdwrap.saveFilesFromParmed(value, self._pdb)
else:
self._pdb = None
if value is not None:
value = _fileio.checkFileExists(value)
if value:
try:
try:
self._pdb = value
self._pdb_obj = _PDB.PDB(self.pdb)
except:
obj = _pmdwrap.openFilesAsParmed(value)
self._pdb = "{}.pdb".format(self.name)
_pmdwrap.saveFilesFromParmed(obj, self._pdb)
self._pdb_obj = _PDB.PDB(self.pdb)
self._checkfasta()
except:
self._pdb = None
if not self._pdb:
self._pdb_obj = _PDB.PDB(self.pdb) if self.pdb else None
def parametrised_files(self, val):
with self.workdir:
if val is None:
self._parametrised_files = None
self._parametrised = False
else:
val = _fileio.checkFileExists(val)
self._parametrised_files = val
self._parametrised = True
def protonated_filename(self, val):
with self.workdir:
if val is None:
self._protonated_filename = None
self._protonated = False
else:
self._protonated_filename = _fileio.checkFileExists(val)
self._molecule = _rdkit.openAsRdkit(self._protonated_filename,
removeHs=False,
minimise=self.minimise)
self._string = _rdmolfiles.MolToSmiles(self.molecule)
self._protonated = True
def fasta(self, value):
if value is not None:
value = _fileio.checkFileExists(value)
self._fasta = value
if value:
self._checkfasta()