def is_same(self, point, eps):
for idx in range(self._dim):
args = (self._fvec[idx], point._fvec[idx])
kwargs = {"u": "deg", "limit": self._cycle[idx]}
diff1D = fncs.angular_dist(*args, **kwargs)
if diff1D > eps: return False
return True
def abs_diff(self, point):
diff = [None for idx in range(self._dim)]
for idx in range(self._dim):
args = (self._fvec[idx], point._fvec[idx])
kwargs = {"u": "deg", "limit": self._cycle[idx]}
diff[idx] = fncs.angular_dist(*args, **kwargs)
return diff
def distance_if_smaller(self, point, ref=float("inf")):
refe2 = ref**2
dist2 = 0.0
for idx in range(self._dim):
args = (self._fvec[idx], point._fvec[idx])
kwargs = {"u": "deg", "limit": self._cycle[idx]}
dist2 += fncs.angular_dist(*args, **kwargs)**2
if dist2 > refe2: return float("inf")
return dist2**0.5
def assign_torsions(dcorr, graph1, graph2, xcc1, xcc2, symbols):
'''
only one at a time
'''
# number of non-assigned (initial)
na_i = get_not_assigned(dcorr)
# assignment based in proper torsions
minad = float("inf")
minnode1 = None
minnode2 = None
for node2, nodes1 in dcorr.items():
if type(nodes1) == int: continue
BC = None
# check neighbors
atA2, atB2, atC2, atD2 = node2, None, None, None
for atB2 in graph2.neighbors(atA2):
if type(dcorr[atB2]) != int: continue
for atC2 in graph2.neighbors(atB2):
if type(dcorr[atC2]) != int: continue
for neigh in graph2.neighbors(atC2):
if type(dcorr[neigh]) != int: continue
if len(set([atA2, atB2, atC2, neigh])) != 4: continue
atD2 = neigh
break
if atD2 is not None: break
if atD2 is not None: break
# torsion located?
if atD2 is None: continue
# Now, check A-B-C-D
atoms2 = [atA2, atB2, atC2, atD2]
xs2 = (xcc2[3 * at:3 * at + 3] for at in atoms2)
angle2 = np.rad2deg(fncs.dihedral(*xs2)) % 360
config2 = angle2 < 180
# compare torsions
for node1 in nodes1:
atoms1 = [node1, dcorr[atB2], dcorr[atC2], dcorr[atD2]]
xs1 = (xcc1[3 * at:3 * at + 3] for at in atoms1)
angle1 = np.rad2deg(fncs.dihedral(*xs1))
# difference
ad = fncs.angular_dist(-angle2, angle1, u="deg")
if ad < minad:
minad = ad
minnode1 = node1
minnode2 = node2
# Any new assignation to do??
if minnode1 is None: return dcorr, na_i
# assign
dcorr[minnode2] = minnode1
# number of non-assigned(final)
dcorr, na_j = assign_check(dcorr)
# return data
if na_j != 0 and na_j != na_i:
return assign_concatenate(dcorr, graph1, graph2)
else:
return assign_check(dcorr)
def assign_cx3(dcorr, graph1, graph2, xcc1, xcc2, symbols):
# number of non-assigned (initial)
na_i = get_not_assigned(dcorr)
# Assign in CX3 groups (CH3, CF3, CCl3, et cetera)
for node2, nodes1 in dcorr.items():
if type(nodes1) == int: continue
if len(nodes1) != 3: continue
neighbors2 = graph2.neighbors(node2)
atC = neighbors2.pop()
# check we have a C atom
if len(neighbors2) != 0: continue
if symbols[atC] != "C": continue
# determine torsion X-C-B-A
atA = None
#print("*",node2+1,atC+1)
for atB in graph2.neighbors(atC):
if type(dcorr[atB]) != int: continue
for neigh in graph2.neighbors(atB):
if type(dcorr[neigh]) != int: continue
if neigh == node2: continue
if neigh == atC: continue
atA = neigh
#print(" ",atB+1,atA+1)
break
if atA is not None: break
if atA is None: continue
# calculate dihedral
atoms2 = [node2, atC, atB, atA]
#print([i+1 for i in atoms2])
xs2 = (xcc2[3 * at:3 * at + 3] for at in atoms2)
angle2 = np.rad2deg(fncs.dihedral(*xs2))
# compare with the others
minad = float("inf")
minnode = None
for node1 in nodes1:
atoms1 = [node1, dcorr[atC], dcorr[atB], dcorr[atA]]
xs1 = (xcc1[3 * at:3 * at + 3] for at in atoms1)
angle1 = np.rad2deg(fncs.dihedral(*xs1))
# difference
ad = fncs.angular_dist(-angle2, angle1, u="deg")
if ad < minad:
minad = ad
minnode = node1
# apply
dcorr[node2] = minnode
# number of non-assigned(final)
dcorr, na_j = assign_check(dcorr)
# return data
if na_j != 0 and na_j != na_i:
return assign_concatenate(dcorr, graph1, graph2)
else:
return assign_check(dcorr)
def assign_via_improper_case1(dcorr,graph_0,graph_t,xcc_0,xcc_t):
'''
C D correlation between A1, A2, ..., An
\ /
A1 - B - An in this situation, B, C and D
/ \ are assigned so Ai-B-C-D improper
A2 ... torsion can be used
'''
# number of non-assigned (initial)
na_i = get_num_of_not_assigned(dcorr)
# Compare spatial organization (improper torsions)
for node_t,nodes_0 in dcorr.items():
if type(nodes_0) == int: continue
# check neighbors
atB2,atC2,atD2 = None,None,None
for neigh in graph_t.neighbors(node_t):
if type(dcorr[neigh]) != int: continue
atB2,atC2,atD2 = neigh,None,None
for nneigh in graph_t.neighbors(atB2):
#print(node_t+1,neigh+1,nneigh+1)
if nneigh == node_t: continue
if type(dcorr[nneigh]) != int: continue
if atC2 is None: atC2 = nneigh; continue
if atD2 is None: atD2 = nneigh; break
if atD2 is not None: break
if atD2 is None: continue
# now check spatial configuration
atoms_t = [node_t,atB2,atC2,atD2]
xs_t = (xcc_t[3*at:3*at+3] for at in atoms_t)
angle_t = np.rad2deg(fncs.dihedral(*xs_t))%360
dcorr[node_t] = set([])
# correlate to closest one
mindist, minnode = float("inf"),None
for node_0 in nodes_0:
atoms_0 = [node_0,dcorr[atB2],dcorr[atC2],dcorr[atD2]]
xs_0 = (xcc_0[3*at:3*at+3] for at in atoms_0)
angle_0 = np.rad2deg(fncs.dihedral(*xs_0))%360
dist = fncs.angular_dist(angle_0,angle_t,u="deg")
if dist < mindist:
mindist = dist
minnode = node_0
dcorr[node_t] = minnode
# break to avoid assign same node
break
# number of non-assigned(final)
dcorr,na_j = assign_check(dcorr)
# do again?
if na_i != na_j and na_j != 0:
dcorr = assign_via_improper_case1(dcorr,graph_0,graph_t,xcc_0,xcc_t)[0]
# return data
return assign_concatenate(dcorr,graph_0,graph_t)