def compound2graph(compound):
compound = compound.upper()
if (compound in map_compound2graph):
return map_compound2graph[compound]
elif (compound.find(' + ') != -1):
G = ChemGraph()
G.ignore_attributes = False
G.add([compound2graph(c) for c in compound.split(' + ')])
return G
else:
raise ChemException("Unknown compound: %s" % compound)
def compound2graph(compound):
compound = compound.upper()
if (compound in map_compound2graph):
return map_compound2graph[compound]
elif (compound.find(' + ') != -1):
G = ChemGraph()
G.ignore_attributes = False
G.add([compound2graph(c) for c in compound.split(' + ')])
return G
else:
raise ChemException("Unknown compound: %s" % compound)
def load_mcard(filename, gzipped=False):
if (gzipped):
file = gzip.GzipFile(filename, 'r')
else:
file = open(filename, 'r')
print >> sys.stderr, "Parsing database file: %s" % filename
# Parse the Mcard SDF database file:
while True:
header = file.readline()
if (header == ""):
break
body = util.readlines_until_mark(file, "$$$$")
compound = header.split('\t')[-1].rstrip().upper()
G = ChemGraph()
G.filename = filename
try:
G.read_mol(body)
map_compound2graph[compound] = G
map_hash2compound[G.hash()] = compound
map_hash2compound_unchiral[G.hash_unchiral()] = compound
except ChemException, errstring:
print >> sys.stderr, " - Skipping this compound [%s] because of: %s" % (
compound, errstring)
pass
def load_mcard(filename, gzipped=False):
if (gzipped):
file = gzip.GzipFile(filename, 'r')
else:
file = open(filename, 'r')
print >> sys.stderr, "Parsing database file: %s" % filename
# Parse the Mcard SDF database file:
while True:
header = file.readline()
if (header == ""):
break
body = util.readlines_until_mark(file, "$$$$")
compound = header.split('\t')[-1].rstrip().upper()
G = ChemGraph()
G.filename = filename
try:
G.read_mol(body)
map_compound2graph[compound] = G
map_hash2compound[G.hash()] = compound
map_hash2compound_unchiral[G.hash_unchiral()] = compound
except ChemException, errstring:
print >> sys.stderr, " - Skipping this compound [%s] because of: %s" % (compound, errstring)
pass
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 mol2svg(mol, width=200, height=200, font_size=7):
G = ChemGraph()
G.read_mol(mol.split("\n"))
scene = svg.Scene(width, height, font_size)
G.svg(scene)
return scene
def molfile2graph(filename):
G = ChemGraph()
G.read_file(filename)
return G
def smiles2graph(smiles):
mol = smiles2mol(smiles)
G = ChemGraph()
G.read_mol(mol.split("\n"))
return G
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 mol2svg(mol, width=200, height=200, font_size=7):
G = ChemGraph()
G.read_mol(mol.split("\n"))
scene = svg.Scene(width, height, font_size)
G.svg(scene)
return scene
def molfile2graph(filename):
G = ChemGraph()
G.read_file(filename)
return G
def smiles2graph(smiles):
mol = smiles2mol(smiles)
G = ChemGraph()
G.read_mol(mol.split("\n"))
return G
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
