def omega2coords(start, TG, sc_omega_plus, uc_params, num_vertices, template, g, CHECK):
sc_a,sc_b,sc_c,sc_alpha,sc_beta,sc_gamma = uc_params
path = os.path.join('templates', template)
shortest_path_dict = nx.shortest_path(TG)
SN = sorted(TG.nodes(), key = lambda x : int(re.sub('[A-Za-z]','',x)))
sequential_paths = [(SN[i],SN[i+1]) for i in range(num_vertices) if i+1 < num_vertices]
start = np.asarray(start)
cnd = nx.get_node_attributes(TG, 'cifname')
coords = [[sequential_paths[0][0], cnd[sequential_paths[0][0]], start, [(e[2]['index'],e[2]['pd'],e[2]['cifname']) for e in TG.edges(data=True) if sequential_paths[0][0] in e]]]
coords_append = coords.append
already_placed = [sequential_paths[0][0]]
already_placed_append = already_placed.append
for st in sequential_paths:
path = shortest_path_dict[st[0]][st[1]]
lp = len(path)
traverse = [(path[i],path[i+1]) for i in range(lp) if i+1 < lp]
for e0 in traverse:
s,e = e0
edict = TG[s][e]
key = [k for k in edict][0]
ind = key[0]
positive_direction = edict[key]['pd']
if (s,e) == positive_direction:
direction = 1
elif (e,s) == positive_direction:
direction = -1
else:
raise ValueError('Error in defining an edge traversal in omega_to_coords.py')
start = start + direction * sc_omega_plus[ind - 1]
if e0[1] not in already_placed:
coords_append([e0[1], cnd[e0[1]], start, [(e[2]['index'], e[2]['pd'],e[2]['cifname']) for e in TG.edges(data=True) if e0[1] in e]])
already_placed_append(e0[1])
norm_coords = []
norm_coords_append = norm_coords.append
for line in coords:
vec = []
vec_append = vec.append
v = line[0]
for dim in line[2]:
if dim < 0.0:
while dim < 0:
dim = dim + 1.0
elif dim >= 1.0:
while dim >= 1.0:
dim = dim - 1.0
vec_append(dim)
norm_coords_append([line[0],line[1],vec,line[3]])
norm_coords = sorted(norm_coords, key = lambda x : int(re.sub('[A-Za-z]','',x[0])))
path = os.path.join('templates', template)
with open(path, 'r') as tcif:
tcif = tcif.read()
tcif = filter(None, tcif.split('\n'))
if CHECK:
cpath = os.path.join('check_cifs', str(g) + '_check_scaled_' + template)
with open(cpath, 'w') as check:
for line in tcif:
s = line.split()
if not isvert(s):
if '_cell_length_a' in line:
check.write('_cell_length_a ' + str(sc_a))
elif '_cell_length_b' in line:
check.write('_cell_length_b ' + str(sc_b))
elif '_cell_length_c' in line:
check.write('_cell_length_c ' + str(sc_c))
elif '_cell_angle_alpha' in line:
check.write('_cell_angle_alpha ' + str(sc_alpha))
elif '_cell_angle_beta' in line:
check.write('_cell_angle_beta ' + str(sc_beta))
elif '_cell_angle_gamma' in line:
check.write('_cell_angle_gamma ' + str(sc_gamma))
else:
check.write(line)
check.write('\n')
else:
for n in norm_coords:
name = re.sub('[0-9]','',n[0])
v = n[2]
check.write('{:>5}{:>5}{:>20}{:>20}{:>20}{:>12}{:>8}{:>8}'.format(n[0],name,v[0],v[1],v[2],'0.00000','Uiso','1.00'))
check.write('\n')
break
return norm_coords
def write_check_cif(template, placed_nodes, placed_edges, g, sp, sc_unit_cell):
sc_a, sc_b, sc_c, sc_alpha, sc_beta, sc_gamma = sp
q = 0
tpath = os.join('templates', template)
with open(tpath, 'r') as tcif:
tcif = tcif.read()
tcif = filter(None, tcif.split('\n'))
cpath = os.path.join('check_cifs',
str(g) + '_check_scaled_placed_' + template)
with open(cpath, 'w') as check:
for line in tcif:
s = line.split()
if not isvert(s):
if '_cell_length_a' in line:
check.write('_cell_length_a ' + str(sc_a))
elif '_cell_length_b' in line:
check.write('_cell_length_b ' + str(sc_b))
elif '_cell_length_c' in line:
check.write('_cell_length_c ' + str(sc_c))
elif '_cell_angle_alpha' in line:
check.write('_cell_angle_alpha ' + str(sc_alpha))
elif '_cell_angle_beta' in line:
check.write('_cell_angle_beta ' + str(sc_beta))
elif '_cell_angle_gamma' in line:
check.write('_cell_angle_gamma ' + str(sc_gamma))
else:
check.write(line)
check.write('\n')
else:
for n in placed_edges:
q += 1
name = re.sub('[0-9]', '', n[0])
if name == 'X':
name = 'C'
index = name + str(q)
vec = np.array(list(map(float, [n[1], n[2], n[3]])))
v = np.dot(np.linalg.inv(sc_unit_cell), vec)
check.write(
'{:>5}{:>5}{:>20}{:>20}{:>20}{:>12}{:>8}{:>8}'.format(
index, name, v[0], v[1], v[2], '0.00000', 'Uiso',
'1.00'))
check.write('\n')
for n in placed_nodes:
q += 1
name = re.sub('[0-9]', '', n[0])
if name == 'X':
name = 'C'
index = name + str(q)
vec = np.array(list(map(float, [n[1], n[2], n[3]])))
v = np.dot(np.linalg.inv(sc_unit_cell), vec)
check.write(
'{:>5}{:>5}{:>20}{:>20}{:>20}{:>12}{:>8}{:>8}'.format(
index, name, v[0], v[1], v[2], '0.00000', 'Uiso',
'1.00'))
check.write('\n')
break
def omega2coords(augTG, sc_omega_plus, uc_params, num_vertices, template, g,
CHECK):
pi = np.pi
sc_a, sc_b, sc_c, sc_alpha, sc_beta, sc_gamma = uc_params
ax = sc_a
ay = 0.0
az = 0.0
bx = sc_b * np.cos(sc_gamma * pi / 180.0)
by = sc_b * np.sin(sc_gamma * pi / 180.0)
bz = 0.0
cx = sc_c * np.cos(sc_beta * pi / 180.0)
cy = (sc_c * sc_b * np.cos(sc_alpha * pi / 180.0) - bx * cx) / by
cz = (sc_c**2.0 - cx**2.0 - cy**2.0)**0.5
sc_unit_cell = np.asarray([[ax, ay, az], [bx, by, bz], [cx, cy, cz]]).T
path = os.path.join('templates', template)
with open(path, 'r') as cif:
cif = cif.read()
cif = filter(None, cif.split('\n'))
discard_coords = []
discard_coords_append = discard_coords.append
for line in cif:
s = line.split()
if isvert(s):
discard_coords_append(s)
start = np.asarray(map(float, discard_coords[0][2:5]))
shortest_path_dict = nx.shortest_path(augTG)
SN = sorted(augTG.nodes(), key=lambda x: int(re.sub('[A-Za-z]', '', x)))
sequential_paths = [(SN[i], SN[i + 1]) for i in range(num_vertices)
if i + 1 < num_vertices]
start = np.asarray(start)
cnd = nx.get_node_attributes(augTG, 'cifname')
coords = [[
sequential_paths[0][0], cnd[sequential_paths[0][0]], start,
[(e[2]['index'], e[2]['pd'], e[2]['cifname'])
for e in augTG.edges(data=True) if sequential_paths[0][0] in e]
]]
coords_append = coords.append
already_placed = [sequential_paths[0][0]]
already_placed_append = already_placed.append
for st in sequential_paths:
path = shortest_path_dict[st[0]][st[1]]
lp = len(path)
traverse = [(path[i], path[i + 1]) for i in range(lp) if i + 1 < lp]
for e0 in traverse:
s, e = e0
edict = augTG[s][e]
key = [k for k in edict][0]
ind = k[0]
positive_direction = edict[key]['pd']
if (s, e) == positive_direction:
direction = 1
elif (e, s) == positive_direction:
direction = -1
else:
print 'Error in defining an edge traversal in omega_to_coords.py'
print 'Exiting'
sys.exit()
start = start + direction * sc_omega_plus[ind - 1]
if e0[1] not in already_placed:
coords_append([
e0[1], cnd[e0[1]], start,
[(e[2]['index'], e[2]['pd'], e[2]['cifname'])
for e in augTG.edges(data=True) if e0[1] in e]
])
already_placed_append(e0[1])
norm_coords = []
norm_coords_append = norm_coords.append
for line in coords:
vec = []
vec_append = vec.append
v = line[0]
for dim in line[2]:
if dim < 0.0:
while dim < 0:
dim = dim + 1.0
elif dim >= 1.0:
while dim >= 1.0:
dim = dim - 1.0
vec_append(dim)
norm_coords_append([line[0], line[1], vec, line[3]])
norm_coords = sorted(norm_coords,
key=lambda x: int(re.sub('[A-Za-z]', '', x[0])))
path = os.path.join('templates', template)
with open(path, 'r') as tcif:
tcif = tcif.read()
tcif = filter(None, tcif.split('\n'))
if CHECK:
q = num_vertices
cpath = os.path.join('check_cifs',
str(g) + '_check_scaled_' + template)
with open(cpath, 'w') as check:
for line in tcif:
s = line.split()
if not isvert(s):
if '_cell_length_a' in line:
check.write('_cell_length_a ' + str(sc_a))
elif '_cell_length_b' in line:
check.write('_cell_length_b ' + str(sc_b))
elif '_cell_length_c' in line:
check.write('_cell_length_c ' + str(sc_c))
elif '_cell_angle_alpha' in line:
check.write('_cell_angle_alpha ' + str(sc_alpha))
elif '_cell_angle_beta' in line:
check.write('_cell_angle_beta ' + str(sc_beta))
elif '_cell_angle_gamma' in line:
check.write('_cell_angle_gamma ' + str(sc_gamma))
else:
check.write(line)
check.write('\n')
else:
for n in norm_coords:
name = re.sub('[0-9]', '', n[0])
v = n[2]
check.write(
'{:>5}{:>5}{:>20}{:>20}{:>20}{:>12}{:>8}{:>8}'.
format(n[0], name, v[0], v[1], v[2], '0.00000',
'Uiso', '1.00'))
check.write('\n')
break
return norm_coords