def set_rotatable_bonds_from_file(self,mol):
assert mol.allAtoms.bonds[0]
assert hasattr(self, 'activeInFile')
mol.allAtoms.bonds[0].possibleTors = 0
mol.allAtoms.bonds[0].activeTors = 0
for ll in self.activeInFile:
# 0 1 2 3 4 5 6 7
#ex: ll = ['REMARK', '1', 'A', 'between', 'atoms:', 'N1_1', 'and', 'C31_39']
name1, index1 = ll[5].split('_') #index1 is NOT usable ['N1','1']@@
name2, index2 = ll[7].split('_') #index2 is NOT ['C31','39']
#at1 = mol.allAtoms[int(index1)-1]
at1 = mol.allAtoms.get(name1)[0]
#if len(ats1)==1:
# at1 = ats1[0]
#else:
#?WHAT TO DO IF more than one?
# ?check for bonded atom named at2
ATS2 = mol.allAtoms.get(name2)
if len(ATS2)==1:
at2 = ATS2[0]
else:
for at in ATS2:
if at.isBonded(at1):
at2 = at
break
#at2 = mol.allAtoms[int(index2)-1]
bnd = AtomSet([at1,at2]).bonds[0]
bnd.possibleTors = 1
bnd.activeTors = 1 #?verify 'A'
if ll[2]=='I':
bnd.activeTors = 0
def set_rotatable_bonds_from_file(self, mol):
assert mol.allAtoms.bonds[0]
assert hasattr(self, 'activeInFile')
mol.allAtoms.bonds[0].possibleTors = 0
mol.allAtoms.bonds[0].activeTors = 0
for ll in self.activeInFile:
# 0 1 2 3 4 5 6 7
#ex: ll = ['REMARK', '1', 'A', 'between', 'atoms:', 'N1_1', 'and', 'C31_39']
name1, index1 = ll[5].split(
'_') #index1 is NOT usable ['N1','1']@@
name2, index2 = ll[7].split('_') #index2 is NOT ['C31','39']
#at1 = mol.allAtoms[int(index1)-1]
at1 = mol.allAtoms.get(name1)[0]
#if len(ats1)==1:
# at1 = ats1[0]
#else:
#?WHAT TO DO IF more than one?
# ?check for bonded atom named at2
ATS2 = mol.allAtoms.get(name2)
if len(ATS2) == 1:
at2 = ATS2[0]
else:
for at in ATS2:
if at.isBonded(at1):
at2 = at
break
#at2 = mol.allAtoms[int(index2)-1]
bnd = AtomSet([at1, at2]).bonds[0]
bnd.possibleTors = 1
bnd.activeTors = 1 #?verify 'A'
if ll[2] == 'I':
bnd.activeTors = 0
