charges_to_add=None,
root=0,
outputfilename=outputfilename,
cleanup='')
#rebuild torTree
allAts = mol.allAtoms
for b in allAts.bonds[0]:
if b.activeTors: b.activeTors = 0
torscount = 0
tM = mol.torTree.torsionMap
for i in range(len(tM)):
bnum0, bnum1 = tM[i].bond
a0 = allAts.get(lambda x: x.number == bnum0 + 1)[0]
a0.tt_ind = bnum0
a1 = allAts.get(lambda x: x.number == bnum1 + 1)[0]
a1.tt_ind = bnum1
b = AtomSet([a0, a1]).bonds[0]
if hasattr(b, 'possibleTors'):
assert b.possibleTors
else:
b.possibleTors = 1
b.activeTors = 1
torscount = torscount + 1
mol.torscount = torscount
mol.ROOT = mol.allAtoms[0]
mol.ROOT.rnum0 = 0
mol.LPO.write(outputfilename)
# To execute this command type:
# repair_ligand4.py -f pdbqt_filename [-o outputfilename] -v
allAts = mol.allAtoms
for b in allAts.bonds[0]:
if b.activeTors: b.activeTors = 0
torscount = 0
tM = mol.torTree.torsionMap
for i in range(len(tM)):
bnum0, bnum1 = tM[i].bond
a0 = allAts.get(lambda x: x.number==bnum0 + 1)[0]
a0.tt_ind = bnum0
a1 = allAts.get(lambda x: x.number==bnum1 + 1)[0]
a1.tt_ind = bnum1
b = AtomSet([a0,a1]).bonds[0]
if hasattr(b, 'possibleTors'):
assert b.possibleTors
else:
b.possibleTors = 1
b.activeTors = 1
torscount = torscount + 1
mol.torscount = torscount
mol.ROOT = mol.allAtoms[0]
mol.ROOT.rnum0 = 0
mol.LPO.write(outputfilename)
# To execute this command type:
# repair_ligand4.py -f pdbqt_filename [-o outputfilename] -v
