def guess_bonds(r_array, type_array, threshold=0.01):
covalent_radii = cdb.get('data', 'covalentdict')
MAXRADIUS = 0.5
# Find all the pairs
ck = cKDTree(r_array)
pairs = ck.query_pairs(MAXRADIUS)
bonds = []
for i,j in pairs:
a, b = covalent_radii[type_array[i]], covalent_radii[type_array[j]]
rval = a + b
# print(rval)
thr_a = rval - threshold
thr_b = rval + threshold
#thr_a2 = thr_a * thr_a
thr_b2 = thr_b * thr_b
dr2 = ((r_array[i] - r_array[j])**2).sum()
# print(dr2)
if dr2 < thr_b2:
bonds.append((i, j))
return np.array(bonds)
def guess_bonds(r_array, type_array, threshold=0.01):
covalent_radii = cdb.get('data', 'covalentdict')
MAXRADIUS = 0.5
# Find all the pairs
ck = cKDTree(r_array)
pairs = ck.query_pairs(MAXRADIUS)
bonds = []
for i, j in pairs:
a, b = covalent_radii[type_array[i]], covalent_radii[type_array[j]]
rval = a + b
# print(rval)
thr_a = rval - threshold
thr_b = rval + threshold
#thr_a2 = thr_a * thr_a
thr_b2 = thr_b * thr_b
dr2 = ((r_array[i] - r_array[j])**2).sum()
# print(dr2)
if dr2 < thr_b2:
bonds.append((i, j))
return np.array(bonds)
def find_bonds(sys):
from chemlab.libs.ckdtree import cKDTree
ck = cKDTree(sys.r_array)
return np.unique(ck.query_pairs(0.15))
def find_bonds(sys):
from chemlab.libs.ckdtree import cKDTree
ck = cKDTree(sys.r_array)
return np.unique(ck.query_pairs(0.15))
