def main():
mol = read.readxyz(file(sys.argv[1]))
loop = detectloop.loopdetect(mol)[0]
loopc = loopclosure.LoopClosure()
shakedata = loopclosure.getshakedata(mol, loop)
loopc.shakedata = shakedata
loopc.forcefield = "oplsaa"
loopc.log_level = 0
for r6 in peptide.Peptide(mol).getr6s(loop):
for mol, ene in loopc.findneighbor(mol, r6):
print ene
def init_loop(self):
if self.loopatoms is None:
if self.loopfile:
self.loopatoms = 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.loopfile)).readlines()], [])
if self.loopatoms is None:
loops = detectloop.loopdetect(self.seedmol)
try:
self.loopatoms = detectloop.pick_largest_simpleloop(loops)
except Exception, e:
self.log(str(e))
return False
def test_1(self):
mol = read.readxyz(StringIO.StringIO(in_str))
res = detectloop.loopdetect(mol)
res.sort()
self.assertEqual(res, [[0, 1, 3, 6, 9, 12], [2, 18, 20, 23, 26, 29]])
def getlooptor(mol, loop):
if loop is None:
loops = detectloop.loopdetect(mol)
assert len(loops) == 1
loop = loops[0]
return tools.calclooptor(mol, loop)
