def is_valid(self, mol, ene):
if ene < self.legal_min_ene:
return "L"
if self.chiral_idxs and tuple(chiral.chiral_types(mol, self.chiral_idxs)) != self._chirals:
return "C"
if self.check_minimal and not tinker.isminimal(mol, self.forcefield):
return "M"
return "V"
def is_valid(self, mol, ene):
if ene < self.legal_min_ene:
return 'L'
if self.chiral_idxs \
and tuple(chiral.chiral_types(mol, self.chiral_idxs)) \
!= self._chirals:
return 'C'
if self.check_minimal and not tinker.isminimal(mol, self.forcefield):
return 'M'
return 'V'
def init_check(self):
if self.chiral_idxs is None:
if self.chiral_index_file:
self.chiral_idxs = sum(
[
[int(x) - 1 for x in line.split() if line.strip() and line[0] != "#"]
for line in file(os.path.join(self.olddir, self.chiral_index_file)).readlines()
],
[],
)
if self.chiral_idxs:
self._chirals = tuple(chiral.chiral_types(self.seedmol, self.chiral_idxs))
if self.head_tail == "auto":
if self.moltypekey == "peptide":
self.head_tail = -1
else:
self.head_tail = 0
else:
self.head_tail = int(self.head_tail)
if self.is_achiral == "auto":
if self.moltypekey == "peptide":
self.is_achiral = False
else:
self.is_achiral = True
else:
self.is_achiral = self.config.getboolean("DEFAULT", "is_achiral")
if self.loopstep == "auto":
if self.moltypekey == "peptide" or self.is_chain:
self.loopstep = 0
else:
self.loopstep = 1
else:
self.loopstep = int(self.loopstep)
if self.cmptors is None:
if self.cmptorsfile:
self.cmptors = [
[int(x) - 1 for x in line.split() if line.strip() and line[0] != "#"]
for line in file(self.cmptorsfile).readlines()
]
if self.cmptors is None:
if self.is_chain:
self.cmptors = [self.loopatoms[i : i + 4] for i in range(len(self.loopatoms) - 3)]
else:
self.cmptors = [(self.loopatoms * 2)[i : i + 4] for i in range(len(self.loopatoms))]
for x in self.cmptors:
assert len(x) == 4
return True
def init_check(self):
if self.chiral_idxs is None:
if self.chiral_index_file:
self.chiral_idxs = sum([[int(x) - 1 \
for x in line.split()
if line.strip() and line[0] != '#']
for line in file(os.path.join(self.olddir,
self.chiral_index_file)).readlines()], [])
if self.chiral_idxs:
self._chirals = tuple(chiral.chiral_types(self.seedmol, self.chiral_idxs))
if self.head_tail is None:
if self.moltypekey == 'peptide':
self.head_tail = -1
else:
self.head_tail = 0
if self.is_achiral is None:
if self.moltypekey == 'peptide':
self.is_achiral = False
else:
self.is_achiral = True
if self.loopstep == -1:
if self.moltypekey == 'peptide' or self.is_chain:
self.loopstep = 0
else:
self.loopstep = 1
if self.cmptors is None:
if self.cmptorsfile:
self.cmptors = [[int(x)-1 for x in line.split()
if line.strip() and line[0] != '#']
for line in file(self.cmptorsfile).readlines()]
if self.cmptors is None:
if self.is_chain:
self.cmptors = \
[self.loopatoms[i:i+4] for i in range(len(self.loopatoms)-3)]
else:
self.cmptors = \
[(self.loopatoms*2)[i:i+4] for i in range(len(self.loopatoms))]
for x in self.cmptors:
assert len(x) == 4
return True