def main():
root = Tk()
if (len(sys.argv) > 1):
mol_filename = sys.argv[1]
else:
#print >> sys.stderr, "Syntax: %s <mol file> [<svg file>]" % sys.argv[0]
mol_filename = askopenfilename(parent=root,
title="Pick a MOL file to plot",
filetypes=[("MOL files", "*.mol"),
("All Files", "*")])
if (mol_filename == ''):
sys.exit(-1)
if (len(sys.argv) > 2):
svg_filename = sys.argv[2]
else:
svg_filename = None
if (not os.path.isfile(mol_filename)):
print >> sys.stderr, "File not found: " + mol_filename
sys.exit(-2)
#file = open(mol_filename)
try:
G = molfile2graph(mol_filename)
except Exception, strerror:
root.title("ERROR")
Message(root, text=strerror, width=100).pack()
Button(root, text="OK", command=root.destroy).pack()
root.mainloop()
sys.exit(-1)
def main():
root = Tk()
if (len(sys.argv) > 1):
mol_filename = sys.argv[1]
else:
#print >> sys.stderr, "Syntax: %s <mol file> [<svg file>]" % sys.argv[0]
mol_filename = askopenfilename(parent=root, title="Pick a MOL file to plot", filetypes=[("MOL files", "*.mol"),("All Files", "*")])
if (mol_filename == ''):
sys.exit(-1)
if (len(sys.argv) > 2):
svg_filename = sys.argv[2]
else:
svg_filename = None
if (not os.path.isfile(mol_filename)):
print >> sys.stderr, "File not found: " + mol_filename
sys.exit(-2)
#file = open(mol_filename)
try:
G = molfile2graph(mol_filename)
except Exception, strerror:
root.title("ERROR")
Message(root, text=strerror, width=100).pack()
Button(root, text="OK", command=root.destroy).pack()
root.mainloop()
sys.exit(-1)
def init():
global html_path
html_path = "../results"
global compound2smiles
compound2smiles = util.parse_dat("../metacyc/compounds.dat", "UNIQUE-ID",
"SMILES")
global atom_types
atom_types = ['C', 'N', 'O', 'P', 'S']
#global bond_types; bond_types = range(5)
global bond_types
bond_types = range(4)
global motif_sizes
motif_sizes = range(2, 7)
global log_zero
log_zero = -800.0
global compound2graph
compound2graph = {}
for compound in compound2smiles.keys():
try:
compound2graph[compound] = chemconvert.molfile2graph("../mol/" +
compound +
".mol")
except Exception:
pass
return
def init():
global html_path; html_path = "../results"
global compound2smiles;
compound2smiles = util.parse_dat("../metacyc/compounds.dat", "UNIQUE-ID", "SMILES")
global atom_types; atom_types = ['C', 'N', 'O', 'P', 'S']
#global bond_types; bond_types = range(5)
global bond_types; bond_types = range(4)
global motif_sizes; motif_sizes = range(2, 7)
global log_zero; log_zero = -800.0
global compound2graph; compound2graph = {}
for compound in compound2smiles.keys():
try:
compound2graph[compound] = chemconvert.molfile2graph("../mol/" + compound + ".mol")
except Exception:
pass
return
reaction_titles.append("*"*60 + " " + line[2:] + " " + "*"*60)
reaction_compounds.append(None)
elif (prev_line_bag == None):
prev_line_bag = bag.Bag().from_string(line)
else:
curr_line_bag = bag.Bag().from_string(line)
common_bag = curr_line_bag.intersection(prev_line_bag)
side_bags = [prev_line_bag - common_bag, curr_line_bag - common_bag, common_bag] # left-side, right-side, common
side_strings = ["", "", ""]
side_graphs = (ChemGraph(), ChemGraph(), ChemGraph())
for side in range(3):
side_strings[side] += str(side_bags[side])
for (compound, cnt) in sorted(side_bags[side].itercounts()):
for i in range(cnt):
side_graphs[side].add(molfile2graph(mol_path + "/" + compound + ".mol"))
if (side_graphs[0].node_bag() != side_graphs[1].node_bag()):
raise Exception("Unbalanced reaction at lines %d - %d\n%s = %s (common: %s)" %\
(line_number-1, line_number, side_strings[0], side_strings[1], side_strings[2]))
reaction_titles.append("%s = %s (common: %s)" % tuple(side_strings))
reaction_compounds.append(side_graphs)
prev_line_bag = curr_line_bag
# now deduce the reactions from the ChemGraphs
Gref = None # a full graph that is the reference for drawing the global reaction
Gprev = None # a full graph that remembers the last right-hand graph (aligned with the reference graph)
total_reaction_list = [] # a list of 3-tuples that indicate which bonds have changes and by how much