def makeconnect(self):
distmat = moltools.distmat(self)
self._connect = numpy.zeros((len(self), len(self)),
bool)
for i in range(len(self)):
for j in range(i):
if self.atoms[i].no == 1 or self.atoms[j].no == 1:
self.connect[i][j] = self.connect[j][i] = distmat[i][j] < self.__maxbondlen_h
else:
self.connect[i][j] = self.connect[j][i] = distmat[i][j] < self.__maxbondlen
def findneighbor(self, mol, r6):
coords = mol.coords
# FIXME: we need not calculate the full distance matrix
# FIXME: we need not calculate distmat for each r6
dismat = moltools.distmat(mol)
for molidx, molresult in enumerate(getr6result(coords, r6, dismat, self.shakedata)):
newmol = mol.copy()
for idx, coord in molresult.items():
newmol.change_coord(idx, coord)
rmol, rene = self._minimizemol(newmol)
if rmol is None:
continue
self.mutex.acquire() # r/w _step_count
self._step_count += 1
self.mutex.release()
logstr = " Step %5i Comb %02i-%02i %42.4f " % (self._step_count, self.r6s[r6], molidx, rene)
yield rmol, rene, logstr
if self.maxsteps > 0 and self._step_count >= self.maxsteps:
return