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 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 smiles2graph(smiles):
mol = smiles2mol(smiles)
G = ChemGraph()
G.read_mol(mol.split("\n"))
return G
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 smiles2graph(smiles):
mol = smiles2mol(smiles)
G = ChemGraph()
G.read_mol(mol.split("\n"))
return G
