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)