def bonds2graph(bonds):
graph = ChemGraph()
n = 0
m = 0
graph.add_node(atom_wildcard)
for b in bonds:
if (m == n):
graph.add_node(atom_wildcard)
m = 0
n += 1
graph.set_bond(n, m, b)
m += 1
if (m != n):
raise ChemException("length of bonds list is not N(N-1)/2: " + str(bonds))
return graph
def bonds2graph(bonds):
graph = ChemGraph()
n = 0
m = 0
graph.add_node(atom_wildcard)
for b in bonds:
if (m == n):
graph.add_node(atom_wildcard)
m = 0
n += 1
graph.set_bond(n, m, b)
m += 1
if (m != n):
raise ChemException("length of bonds list is not N(N-1)/2: " +
str(bonds))
return graph
def hash2graph(hash, update_attributes=False):
"""Converts a hash string into a ChemGraph. Works only one single molecule hashes
"""
G_total = ChemGraph()
N = 0
for (atoms, bonds) in parse_hash(hash):
G = ChemGraph()
G.resize(len(atoms))
for n in range(len(atoms)):
for m in range(n):
G.set_bond(n, m, bonds.pop(0))
for n in range(len(atoms)):
(G.nodes[n], G.valences[n], G.hydrogens[n], G.charges[n], G.chirality[n]) = parse_atom(atoms[n])
if (update_attributes):
G.update_attributes()
G.initialize_pos()
G_total.add(G)
return G_total
def hash2graph(hash, update_attributes=False):
"""Converts a hash string into a ChemGraph. Works only one single molecule hashes
"""
G_total = ChemGraph()
N = 0
for (atoms, bonds) in parse_hash(hash):
G = ChemGraph()
G.resize(len(atoms))
for n in range(len(atoms)):
for m in range(n):
G.set_bond(n, m, bonds.pop(0))
for n in range(len(atoms)):
(G.nodes[n], G.valences[n], G.hydrogens[n], G.charges[n],
G.chirality[n]) = parse_atom(atoms[n])
if (update_attributes):
G.update_attributes()
G.initialize_pos()
G_total.add(G)
return G_total
