def main1():
util._mkdir("../results/ec-list")
counter = 1
for line in util.parse_text_file("../rec/ec-list.smiles"):
print counter, ")", line
smiles2svg(line, "../results/ec-list/%d.svg" % counter)
counter += 1
def main():
util._mkdir("../results/svg")
#substrate = '_GAP + _GAP'
#substrate = '_GLC-6P_OCF'
#(substrate, target) = ('L-Serine', '_3-PG')
(substrate, target) = ('3-Phospho-Hydroxypyruvate', 'L-Serine')
G_subs = compounds2graph(substrate)
h_target = compounds2graph(target).hash()
h_subs = G_subs.hash()
product_html_writer = html_writer.HtmlWriter("../results/valid_products.html")
product_html_writer.write("<center>Substrate : " + strip_hash_chirality(h_subs) + "</center><br>")
product_html_writer.write("<center>Target : " + strip_hash_chirality(h_target) + "</center><br>")
product_html_writer.write_svg(G_subs.svg(Scene(400, 200, 10)), "svg/" + h_subs)
product_html_writer.write("<p>")
for (h_substrate, G_product, reaction) in generate_new_compounds({h_subs : G_subs}, False):
h_product = G_product.hash()
product_html_writer.write("<br><center>" + reaction + " : " + strip_hash_chirality(h_product) + "</center><br>")
if (strip_hash_chirality(h_product) == strip_hash_chirality(h_target)):
product_html_writer.write("<center>Target Found !!!</center><br>")
product_html_writer.write_svg(G_product.svg(Scene(400, 200, 10)), "svg/" + h_product)
product_html_writer.write("</p>")
product_html_writer.close()
return
def main1():
util._mkdir("../results/ec-list")
counter = 1
for line in util.parse_text_file("../rec/ec-list.smiles"):
print counter, ")", line
smiles2svg(line, "../results/ec-list/%d.svg" % counter)
counter += 1
def test():
init()
util._mkdir("../svg")
html_file = open("../svg/templates.html", "w")
for template in get_all_templates():
template_svg = chemconvert.hash2svg(template, svg_size, svg_size, white, grey)
html_file.write("<p>")
template_svg.embed_in_html(html_file, "../svg/", template)
html_file.write(template + "</p>")
html_file.flush()
html_file.close()
def test():
init()
util._mkdir("../svg")
html_file = open("../svg/templates.html", "w")
for template in get_all_templates():
template_svg = chemconvert.hash2svg(template, svg_size, svg_size,
white, grey)
html_file.write("<p>")
template_svg.embed_in_html(html_file, "../svg/", template)
html_file.write(template + "</p>")
html_file.flush()
html_file.close()
def verify_file(max_subgraph_size):
util._mkdir("../results/stat")
motif_filename = "../results/stat/motifs%d.txt" % max_subgraph_size
if (not os.path.exists(motif_filename)):
print "Computing motif histogram for subgraphs of size <= %d ..." % max_subgraph_size,
motifs = compute_motifs(max_subgraph_size)
print "[DONE]"
write_dictionary(motifs, motif_filename)
return motifs
else:
motifs = read_dictionary(motif_filename)
for key in motifs.keys():
motifs[key] = int(float(motifs[key]))
return motifs
def verify_file(max_subgraph_size):
util._mkdir("../results/stat")
motif_filename = "../results/stat/motifs%d.txt" % max_subgraph_size
if (not os.path.exists(motif_filename)):
print "Computing motif histogram for subgraphs of size <= %d ..." % max_subgraph_size,
motifs = compute_motifs(max_subgraph_size)
print "[DONE]"
write_dictionary(motifs, motif_filename)
return motifs
else:
motifs = read_dictionary(motif_filename)
for key in motifs.keys():
motifs[key] = int(float(motifs[key]))
return motifs
def __init__(self, filename, force_path_creation=True):
self.filename = filename
self.filepath = os.path.dirname(filename)
if (not os.path.exists(self.filepath)):
if (force_path_creation):
util._mkdir(self.filepath)
else:
raise Exception("cannot write to HTML file %s since the directory doesn't exist" % filename)
self.file = open(self.filename, "w")
self.write("<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Strict//EN\" ")
self.write("\"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd\">")
self.write("<html>\n<body>\n")
return
def convert_compounds_hash(compound_dat_filename):
compound2hash = util.parse_dat(compound_dat_filename, "UNIQUE-ID", "HASH")
util._mkdir("../mol")
for (key, smiles) in compound2hash.iteritems():
mol_filename = "../mol/" + key + ".mol"
if (not os.path.exists(mol_filename)):
print "Writing a MOL file to: " + mol_filename
if (len(smiles) > 0):
mol = chemconvert.hash2graph(smiles[0]).to_mol()
mol_file = open(mol_filename, "w")
mol_file.write(mol)
mol_file.close()
else:
print "Found the MOL file: " + mol_filename
return
def convert_compounds_hash(compound_dat_filename):
compound2hash = util.parse_dat(compound_dat_filename, "UNIQUE-ID", "HASH")
util._mkdir("../mol")
for (key, smiles) in compound2hash.iteritems():
mol_filename = "../mol/" + key + ".mol"
if (not os.path.exists(mol_filename)):
print "Writing a MOL file to: " + mol_filename
if (len(smiles) > 0):
mol = chemconvert.hash2graph(smiles[0]).to_mol()
mol_file = open(mol_filename, "w")
mol_file.write(mol)
mol_file.close()
else:
print "Found the MOL file: " + mol_filename
return
def main2():
util._mkdir("../results")
f = open("../results/hash2compound.txt", "w")
for (h, compound) in map_hash2compound.iteritems():
f.write("compound = %s\n" % compound)
f.write("hash = %s\n" % h)
f.write("$$$$\n")
f.close()
import html_writer
compound_list = sorted(map_compound2graph.keys())
util._mkdir("../results/svg")
html_writer = html_writer.HtmlWriter("../results/compounds.html")
html_writer.write("<h1><center>Known Compounds</h1></center>")
for i in range(len(compound_list)):
G = map_compound2graph[compound_list[i].upper()]
scene = G.svg(svg.Scene(300, 300, 10))
scene.add(svg.Text((30, 10), compound_list[i], 10, fill_color=magenta))
html_writer.write_svg(scene, "svg/%s" % G.hash())
html_writer.display()
def test():
util._mkdir("../results")
f = open("../results/hash2compound.txt", "w")
for (h, compound) in map_hash2compound.iteritems():
f.write("compound = %s\n" % compound)
f.write("hash = %s\n" % h)
f.write("$$$$\n")
f.close()
import html_writer
compound_list = sorted(map_compound2graph.keys())
util._mkdir("../results/svg")
html_writer = html_writer.HtmlWriter("../results/compounds.html")
html_writer.write("<h1><center>Known Compounds</h1></center>")
for i in range(len(compound_list)):
G = map_compound2graph[compound_list[i].upper()]
scene = G.svg(svg.Scene(300, 300, 10))
scene.add(svg.Text((30, 10), compound_list[i], 10, fill_color=magenta))
html_writer.write_svg(scene, "svg/%s" % G.hash())
html_writer.display()
def test(self, comp=None):
util._mkdir("../results")
util._mkdir("../results/svg")
if comp == None:
html = html_writer.HtmlWriter("../results/reaction_templates.html")
counter = 0
for rid in self.forward_reaction_list:
html.write(self.get_reaction_info(rid))
html.write_svg(self.template2svg(rid), "svg/reaction_template_%d" % counter)
counter += 1
html.display()
else:
G = compound2graph(comp)
html = html_writer.HtmlWriter("../results/reaction_example.html")
html.write("<h1>Reactions for compound: " + comp + "</h1>")
html.write("<p>")
html.write_svg(G.svg(), "svg/compound")
html.write("</p>")
counter = 0
products_set = set()
print "Products for " + comp + " : "
for (G_new, rid, mapping) in self.apply_all_reactions(G, backward=False):
products_set.add(G_new.hash(ignore_chirality=self.ignore_chirality))
print rid + ": " + graph2compound(G_new, ignore_chirality=False)
html.write(self.get_reaction_info(rid, mapping))
html.write_svg(self.template2svg(rid), "svg/reaction_template_%d" % counter)
html.write("</br>")
html.write_svg(self.reaction2svg(G, G_new, rid), "svg/product_%d" % counter)
counter += 1
product_file = open("../results/products.txt", "w")
product_file.write("\n".join(products_set))
product_file.close()
html.display()
return
def test(self, comp=None):
util._mkdir('../results')
util._mkdir('../results/svg')
if (comp == None):
html = html_writer.HtmlWriter("../results/reaction_templates.html")
counter = 0
for rid in self.forward_reaction_list:
html.write(self.get_reaction_info(rid))
html.write_svg(self.template2svg(rid), "svg/reaction_template_%d" % counter)
counter += 1
html.display()
else:
G = compound2graph(comp)
html = html_writer.HtmlWriter("../results/reaction_example.html")
html.write("<h1>Reactions for compound: " + comp + "</h1>")
html.write("<p>")
html.write_svg(G.svg(), "svg/compound")
html.write("</p>")
counter = 0
products_set = set()
print "Products for " + comp + " : "
for (G_new, rid, mapping) in self.apply_all_reactions(G, backward=False):
products_set.add(G_new.hash(ignore_chirality=self.ignore_chirality))
print rid + ": " + graph2compound(G_new, ignore_chirality=False)
html.write(self.get_reaction_info(rid, mapping))
html.write_svg(self.template2svg(rid), "svg/reaction_template_%d" % counter)
html.write("</br>")
html.write_svg(self.reaction2svg(G, G_new, rid), "svg/product_%d" % counter)
counter += 1
product_file = open("../results/products.txt", 'w')
product_file.write("\n".join(products_set))
product_file.close()
html.display()
return
def main():
util._mkdir("../results/svg")
#substrate = '_GAP + _GAP'
#substrate = '_GLC-6P_OCF'
#(substrate, target) = ('L-Serine', '_3-PG')
(substrate, target) = ('3-Phospho-Hydroxypyruvate', 'L-Serine')
G_subs = compounds2graph(substrate)
h_target = compounds2graph(target).hash()
h_subs = G_subs.hash()
product_html_writer = html_writer.HtmlWriter(
"../results/valid_products.html")
product_html_writer.write("<center>Substrate : " +
strip_hash_chirality(h_subs) + "</center><br>")
product_html_writer.write("<center>Target : " +
strip_hash_chirality(h_target) + "</center><br>")
product_html_writer.write_svg(G_subs.svg(Scene(400, 200, 10)),
"svg/" + h_subs)
product_html_writer.write("<p>")
for (h_substrate, G_product,
reaction) in generate_new_compounds({h_subs: G_subs}, False):
h_product = G_product.hash()
product_html_writer.write("<br><center>" + reaction + " : " +
strip_hash_chirality(h_product) +
"</center><br>")
if (strip_hash_chirality(h_product) == strip_hash_chirality(h_target)):
product_html_writer.write("<center>Target Found !!!</center><br>")
product_html_writer.write_svg(G_product.svg(Scene(400, 200, 10)),
"svg/" + h_product)
product_html_writer.write("</p>")
product_html_writer.close()
return
def __init__(self, modules_file, experiment_name, max_module_size=6):
self.modules_file = modules_file
self.experiment_name = experiment_name
self.max_module_size = max_module_size
util._mkdir("../log")
self.logfile = open("../log/pathologic_" + self.experiment_name + ".log", "w")
util._mkdir("../results")
util._mkdir("../results/pathologic_" + self.experiment_name)
self.html_writer = HtmlWriter("../results/pathologic_" + self.experiment_name + ".html")
self.html_writer.write("<h1>List of optimal and non-optimal pathways</h1>\n")
self.html_writer.write("<ul>\n")
self.line_counter = 0
self.pathfinder = None
def __init__(self, modules_file, experiment_name, max_module_size=6):
self.modules_file = modules_file
self.experiment_name = experiment_name
self.max_module_size = max_module_size
util._mkdir("../log")
self.logfile = open(
"../log/pathologic_" + self.experiment_name + ".log", "w")
util._mkdir("../results")
util._mkdir("../results/pathologic_" + self.experiment_name)
self.html_writer = HtmlWriter("../results/pathologic_" +
self.experiment_name + ".html")
self.html_writer.write(
"<h1>List of optimal and non-optimal pathways</h1>\n")
self.html_writer.write("<ul>\n")
self.line_counter = 0
self.pathfinder = None
from chemistry import *
from chemconvert import molfile2graph
import sys
from svg import Scene
import os
pathway_path = "../pathways"
mol_path = "../mol"
html_path = "../pathways/html"
#pathway = "glycolysis-2"
pathway = "glycolysis-1"
#pathway = "pentose-phosphate"
#pathway = "frucolysis"
util._mkdir(html_path + "/" + pathway)
html_filename = html_path + "/" + pathway + ".html"
html_file = open(html_filename, "w")
prev_line_bag = None
reaction_titles = []
reaction_compounds = []
line_number = 0
for line in util.parse_text_file(pathway_path + "/" + pathway + ".pth"):
line_number += 1
if (line[0:2] == "//"):
prev_line_bag = None
reaction_titles.append("*"*60 + " " + line[2:] + " " + "*"*60)
reaction_compounds.append(None)
elif (prev_line_bag == None):
prev_line_bag = bag.Bag().from_string(line)
def main():
init()
subdir = "motifs"
motif_fullpath = html_path + "/motifs"
util._mkdir(motif_fullpath)
main_html_file = open(html_path + "/motifs.html", "w")
anti_motif_list = []
for size in motif_sizes:
motifs = verify_file(size)
motifs_t = motifs_templates(motifs)
motif_hist = normalize_motifs(motifs)
motif_hist_t = normalize_motifs(motifs_t)
print "Generating all graphs of size %d ..." % size,
all_graphs = generate_all_graphs(motif_hist, size)
print "[DONE]"
results = {}
for h in all_graphs:
G = chemconvert.hash2graph(h)
template = G.template()
count = int(motifs.get(h, 0))
likelihoods = [0, 0]
for i in range(2, size + 1):
likelihoods.append(get_likelihood(G, motif_hist, i))
delta_l = likelihoods[-2] - likelihoods[-1]
if (not results.has_key(template)):
results[template] = []
results[template].append((delta_l, likelihoods, count, h))
main_html_file.write("<p>")
size_html_file = util.embed_link(main_html_file, html_path,
subdir + "/motifs%s" % size,
"Motifs of size %s" % size)
main_html_file.write("</p>")
for (template, graph_list) in results.iteritems():
size_html_file.write("<p>")
template_svg = chemconvert.hash2svg(template,
200,
200,
node_color=black,
bond_color=grey)
template_svg.embed_in_html(size_html_file, motif_fullpath,
template)
count_t = len(graph_list)
if (count_t > 0):
template_html_file = util.embed_link(
size_html_file, motif_fullpath, template,
"View all %d instances" % count_t)
for (delta_l, likelihoods, count, h) in sorted(graph_list):
if (likelihoods[-1] <= log_zero
and likelihoods[-2] <= log_zero):
continue
elif (likelihoods[-1] <= log_zero):
bond_color = red
anti_motif_list.append(h)
else:
#bond_color = (0, 255 * math.exp(-delta_l), 255 * (1 - math.exp(-delta_l)))
bond_color = green
motif_svg = chemconvert.hash2svg(h, 150, 150, black,
bond_color)
motif_svg.set_attribute("height", 200)
if (True): # add
#motif_svg.add(svg.Text((35, 25), h, 12, green))
l_string = ",".join(
["%.1f" % l for l in likelihoods[2:]])
motif_svg.add(
svg.Text((10, 160),
"ΔL = %.1f" % delta_l,
font_size=12))
motif_svg.add(
svg.Text((10, 175), l_string, font_size=12))
if (count > 0):
#motif_svg.add(svg.Text((35, 75), "diff = %.1f" % (l1-l0), 12, black))
motif_svg.add(
svg.Text((10, 190),
"count = %d" % count,
font_size=12))
motif_svg.embed_in_html(template_html_file,
motif_fullpath, h)
else:
template_html_file.write("<p>")
motif_svg.embed_in_html(template_html_file,
motif_fullpath, h)
template_html_file.write("<a href=\"" + h + ".svg\">" +
h + "</a>")
template_html_file.write(", count = %d" % count)
for i in range(2, size + 1):
template_html_file.write(", L(%d) = %.1f" %
(i, likelihoods[i]))
template_html_file.write("</p>")
template_html_file.close()
else:
size_html_file.write("No instances")
size_html_file.write("</p>")
size_html_file.close()
main_html_file.close()
util.write_text_file(anti_motif_list, "../results/stat/anti_motifs.txt")
return
def main():
init()
subdir = "motifs"
motif_fullpath = html_path + "/motifs"
util._mkdir(motif_fullpath)
main_html_file = open(html_path + "/motifs.html", "w")
anti_motif_list = []
for size in motif_sizes:
motifs = verify_file(size)
motifs_t = motifs_templates(motifs)
motif_hist = normalize_motifs(motifs)
motif_hist_t = normalize_motifs(motifs_t)
print "Generating all graphs of size %d ..." % size,
all_graphs = generate_all_graphs(motif_hist, size)
print "[DONE]"
results = {}
for h in all_graphs:
G = chemconvert.hash2graph(h)
template = G.template()
count = int(motifs.get(h, 0))
likelihoods = [0, 0]
for i in range(2, size+1):
likelihoods.append(get_likelihood(G, motif_hist, i))
delta_l = likelihoods[-2] - likelihoods[-1]
if (not results.has_key(template)):
results[template] = []
results[template].append((delta_l, likelihoods, count, h))
main_html_file.write("<p>")
size_html_file = util.embed_link(main_html_file, html_path, subdir + "/motifs%s" % size, "Motifs of size %s" % size)
main_html_file.write("</p>")
for (template, graph_list) in results.iteritems():
size_html_file.write("<p>")
template_svg = chemconvert.hash2svg(template, 200, 200, node_color=black, bond_color=grey)
template_svg.embed_in_html(size_html_file, motif_fullpath, template)
count_t = len(graph_list)
if (count_t > 0):
template_html_file = util.embed_link(size_html_file, motif_fullpath, template, "View all %d instances" % count_t)
for (delta_l, likelihoods, count, h) in sorted(graph_list):
if (likelihoods[-1] <= log_zero and likelihoods[-2] <= log_zero):
continue
elif (likelihoods[-1] <= log_zero):
bond_color = red
anti_motif_list.append(h)
else:
#bond_color = (0, 255 * math.exp(-delta_l), 255 * (1 - math.exp(-delta_l)))
bond_color = green
motif_svg = chemconvert.hash2svg(h, 150, 150, black, bond_color)
motif_svg.set_attribute("height", 200)
if (True): # add
#motif_svg.add(svg.Text((35, 25), h, 12, green))
l_string = ",".join(["%.1f" % l for l in likelihoods[2:]])
motif_svg.add(svg.Text((10, 160), "ΔL = %.1f" % delta_l, font_size=12))
motif_svg.add(svg.Text((10, 175), l_string, font_size=12))
if (count > 0):
#motif_svg.add(svg.Text((35, 75), "diff = %.1f" % (l1-l0), 12, black))
motif_svg.add(svg.Text((10, 190), "count = %d" % count, font_size=12))
motif_svg.embed_in_html(template_html_file, motif_fullpath, h)
else:
template_html_file.write("<p>")
motif_svg.embed_in_html(template_html_file, motif_fullpath, h)
template_html_file.write("<a href=\"" + h + ".svg\">" + h + "</a>")
template_html_file.write(", count = %d" % count)
for i in range(2, size+1):
template_html_file.write(", L(%d) = %.1f" % (i, likelihoods[i]))
template_html_file.write("</p>")
template_html_file.close()
else:
size_html_file.write("No instances")
size_html_file.write("</p>")
size_html_file.close()
main_html_file.close()
util.write_text_file(anti_motif_list, "../results/stat/anti_motifs.txt")
return
#!/usr/bin/python
""" This is a script that runs through a CSV file of pairs of compounds and
tests if they are part of an optimality module (the wild-type path between
them is one of the possible shortest paths).
"""
import util
import sys
import bag
from pathfinder import PathFinder
from chemconvert import compound2graph
util._mkdir('../log')
logfile = open('../log/pathcounter.log', 'a')
substrates = []
substrates.append(('Acetyl-CoA', range(1, 4)))
substrates.append(('Phosphoenolpyruvate', range(1, 4)))
substrates.append(('Pyruvate', range(1, 4)))
substrates.append(('D-Glyceraldehyde-3P', range(1, 4)))
substrates.append(('3-Phosphoglycerate', range(1, 4)))
substrates.append(('oxaloacetate', range(1, 4)))
substrates.append(('fumarate', range(1, 4)))
pairs = []
pairs.append(('D-fructose-6P_ring', 'D-glucolactone-6P', range(1, 5)))
pairs.append(('D-fructose-6P', 'D-ribose-5P', range(1, 5)))
pairs.append(('D-Glyceraldehyde-3P', '3-Phosphoglycerate', range(1, 5)))
pairs.append(('3-Phosphoglycerate', 'Phosphoenolpyruvate', range(1, 5)))
pairs.append(('fumarate', 'oxaloacetate', range(1, 5)))
pairs.append(('oxaloacetate', 'pyruvate', range(1, 5)))
#!/usr/bin/python
import sys
import os
import util
from chemconvert import hash2graph
from html_writer import HtmlWriter
from svg import Scene
html = HtmlWriter("../results/hash_list.html")
util._mkdir("../results/hash_list")
for line in util.parse_text_file(sys.argv[1]):
print line
graph = hash2graph(line)
graph.initialize_pos()
scene = graph.svg(Scene(200, 200, font_size=12))
html.write_svg(scene, "../results/hash_list/" + line)
html.display()
def main():
Pentose_target_compounds = ['D-Xylulose-5P', 'D-Ribulose-5P', 'D-Ribose-5P']
PP_compounds = \
['D-Xylulose-5P',\
'D-Ribulose-5P',\
'D-Ribose-5P',\
'D-Erythrose-4P',\
'D-Sedoheptulose-7P',\
'D-Fructose-6P',\
'D-Glyceraldehyde-3P']
Glycolysis_compounds = \
['Dihydroxyacetone-3P',\
'D-Glyceraldehyde-3P',\
'Bisphosphoglycerate',\
'3-Phosphoglycerate',\
'2-Phosphoglycerate',\
'Phosphoenolpyruvate',\
'Pyruvate']
TCA_compounds = \
['Oxaloacetate',\
'Citrate',\
'cis-Aconitate',\
'D-Isocitrate',\
'2-Ketoglutarate',\
#succinyl-CoA\
'Succinate',\
'Fumarate',\
'Malate',\
]
Biosynthese_compounds = PP_compounds + Glycolysis_compounds + TCA_compounds
pathway_list = []
# fast test
pathway_list.append(("TEST", ['2-Phosphoglycerate'], ['Bisphosphoglycerate'], None))
# Optimality Modules:
pathway_list.append(("Glucose to Fructose", ['D-glucose-6P'], ['D-fructose-6P'], None))
pathway_list.append(("Fructose to Glucose", ['D-fructose-6P'], ['D-glucose-6P'], None))
pathway_list.append(("oxaloacetate+acetyl-CoA to citrate", ['oxaloacetate + acetyl-CoA'], ['citrate'], None))
pathway_list.append(("cis-aconitate to succinate", ['cis-aconitate'], ['succinate'], None))
pathway_list.append(("D-xylose to D-xylulose-5P", ['D-Xylose'], ['D-Xylulose-5P'], None))
pathway_list.append(("D-arabitol to D-xylulose-5P", ['D-Arabitol'], ['D-Xylulose-5P'], None))
pathway_list.append(("L-arabinose to D-xylulose-5P", ['L-Arabinose'], ['D-Xylulose-5P'], None))
pathway_list.append(("L-xylulose to D-xylulose-5P", ['L-Xylulose'], ['D-Xylulose-5P'], None))
pathway_list.append(("ribitol to D-xylulose-5P", ['Ribitol'], ['D-Xylulose-5P'], None))
pathway_list.append(("D-ribose to D-xylulose-5P", ['D-Ribose'], ['D-Xylulose-5P'], None))
pathway_list.append(("Oxaloacetate to 2-Ketoglutarate", ['Oxaloacetate'], ['2-Ketoglutarate'], None))
pathway_list.append(("Citrate to 2-Ketoglutarate", ['Citrate'], ['2-Ketoglutarate'], None))
pathway_list.append(("Pentose Phosphate", ['D-Xylulose-5P + D-Xylulose-5P + D-Ribose-5P'], ['D-Fructose-6P + D-Fructose-6P + D-Glyceraldehyde-3P'], None))
#pathway_list.append(("Pentose Phosphate", ['D-Xylulose-5P + D-Ribose-5P'], ['D-Glyceraldehyde-3P + D-Sedoheptulose-7P'], None))
pathway_list.append(("D-glucose to D-ribulose-5P", ['D-Glucose'], ['D-Ribulose-5P'], None))
pathway_list.append(("D-glucose to D-fructose-16P", ['D-Glucose'], ['D-Fructose-16P'], None))
pathway_list.append(("D-fructose-6P to GAP+DHAP", ['D-Fructose-6P'], ['D-Glyceraldehyde-3P + Dihydroxyacetone-3P'], None))
pathway_list.append(("GAP to 3-PG", ['D-Glyceraldehyde-3P'], ['3-Phosphoglycerate'], None))
pathway_list.append(("GAP to 2-PG", ['D-Glyceraldehyde-3P'], ['2-Phosphoglycerate'], None))
pathway_list.append(("BPG to 3-PG", ['Bisphosphoglycerate'], ['3-Phosphoglycerate'], None))
pathway_list.append(("BPG to 2-PG", ['Bisphosphoglycerate'], ['2-Phosphoglycerate'], None))
pathway_list.append(("BPG to PEP", ['Bisphosphoglycerate'], ['Phosphoenolpyruvate'], None))
pathway_list.append(("3-PG to PYR", ['3-Phosphoglycerate'], ['Pyruvate'], None))
# Biosynthesis
pathway_list.append(("3-PG to L-Serine", ['3-Phosphoglycerate'], ['L-Serine'], None))
pathway_list.append(("L-Serine to Glycine", ['L-Serine'], ['Glycine'], None))
pathway_list.append(("Pyruvate to L-Alanine", ['Pyruvate'], ['L-Alanine'], None))
pathway_list.append(("Synthesis of L-Serine", Biosynthese_compounds, ['L-Serine'], None))
pathway_list.append(("Synthesis of L-Alanine", Biosynthese_compounds, ['L-Alanine'], None))
pathway_list.append(("Synthesis of Glycine", Biosynthese_compounds, ['Glycine'], None))
pathway_list.append(("Synthesis of L-Aspartate", Biosynthese_compounds, ['L-Aspartate'], None))
pathway_list.append(("Synthesis of L-Glutamate", Biosynthese_compounds, ['L-Glutamate'], None))
# Pentose utilization
pathway_list.append(("L-Arabinose to Pentose Phosphate", ['L-Arabinose'], Pentose_target_compounds, None))
pathway_list.append(("D-Xylose to Pentose Phosphate", ['D-Xylose'], Pentose_target_compounds, None))
pathway_list.append(("D-Ribose to Pentose Phosphate", ['D-Ribose'], Pentose_target_compounds, None))
pathway_list.append(("Ribitol to Pentose Phosphate", ['Ribitol'], Pentose_target_compounds, None))
pathway_list.append(("D-Arabitol to Pentose Phosphate", ['D-Arabitol'], Pentose_target_compounds, None))
# Glycolysis
pathway_list.append(("GAP to PYR", ['D-Glyceraldehyde-3P'], ['Pyruvate'], 'PP'))
pathway_list.append(("GAP to DHAP", ['D-Glyceraldehyde-3P'], ['Dihydroxyacetone-3P'], 'PP'))
pathway_list.append(("GAP to PEP", ['D-Glyceraldehyde-3P + H2O'], ['Phosphoenolpyruvate + H2O'], 'PP'))
pathway_list.append(("GAP to 2-PG", ['D-Glyceraldehyde-3P'], ['2-Phosphoglycerate'], 'PP'))
pathway_list.append(("GLC to GAP", ['D-Glucose'], ['D-Glyceraldehyde-3P + D-Glyceraldehyde-3P'], 'PP'))
pathway_list.append(("GLC to PYR", ['Glucose'], ['Pyruvate + Pyruvate'], 'PP'))
pathway_list.append(("GLC-36P to GAP", ['D-Glucose-36P'], ['D-Glyceraldehyde-3P + D-Glyceraldehyde-3P'], 'PP'))
pathway_list.append(("GLC-6P to GAP", ['D-Glucose-6P'], ['D-Glyceraldehyde-3P + D-Glyceraldehyde-3P'], 'PP'))
pathway_list.append(("GLC-6P to BPG", ['D-Glucose-6P'], ['Bisphosphoglycerate + Bisphosphoglycerate'], 'PP'))
pathway_list.append(("GLC-6P to 3-PG", ['D-Glucose-6P'], ['3-Phosphoglycerate + 3-Phosphoglycerate'], 'PP'))
pathway_list.append(("GLC-6P to 2-PG", ['D-Glucose-6P'], ['2-Phosphoglycerate + 2-Phosphoglycerate'], 'PP'))
pathway_list.append(("GLC-6P to PEP", ['D-Glucose-6P'], ['Phosphoenolpyruvate + Phosphoenolpyruvate'], 'PP'))
pathway_list.append(("2-PG to PYR", ['2-Phosphoglycerate'], ['Pyruvate'], 'PP'))
pathway_list.append(("3-PG to PYR", ['3-Phosphoglycerate'], ['Pyruvate'], 'PP'))
pathway_list.append(("BPG to PYR", ['Bisphosphoglycerate'], ['Pyruvate'], 'PP'))
pathway_list.append(("BPG to PEP", ['Bisphosphoglycerate'], ['Phosphoenolpyruvate'], 'PP'))
# Arren's project
pathway_list.append(("Glyoxylate + GAP to Pentose", ['Glyoxylate + D-Glyceraldehyde-3P'], Pentose_target_compounds, None))
pathway_list.append(("Glyoxylate + PYR to Pentose", ['Glyoxylate + Pyruvate'], Pentose_target_compounds, None))
pathway_list.append(("Glycolate + GAP to Pentose", ['Glycolate + D-Glyceraldehyde-3P'], Pentose_target_compounds, None))
pathway_list.append(("Glycolate + PYR to Pentose", ['Glycolate + Pyruvate'], Pentose_target_compounds, None))
pathway_names = [pathway[0] for pathway in pathway_list]
pathway_map = {}
for pathway in pathway_list:
pathway_map[pathway[0]] = pathway[1:]
if (len(sys.argv) > 1):
pathway_name = pathway_names[int(sys.argv[1]) - 1]
else:
pathway_name = TkListSelection(pathway_names, "Choose a pathway:")
if (pathway_name == None):
sys.exit(0)
(substrates, products, pruning_method) = pathway_map[pathway_name]
pathfinder = PathFinder(carbon_only=False, pruning_method=pruning_method, ignore_chirality=True)
print "-"*80 + "\nChosen pathway name is %s\n" % pathway_name + "-"*80
util._mkdir("../results")
util._mkdir("../results/" + pathway_name)
html_writer = HtmlWriter("../results/" + pathway_name + ".html")
html_writer.write("<h1><center>%s</center></h1>\n" % pathway_name)
html_writer.write("<ul>\n")
for i in range(len(substrates)):
for j in range(len(products)):
##(subs, prod) = pathfinder.balance_reaction(substrates[i], products[j])
(subs, prod) = (substrates[i], products[j])
pathway_prefix = "pathway_%d_%d" % (i, j)
util._mkdir("../results/" + pathway_name + "/" + pathway_prefix)
pathfinder.solve_pathway(subs, prod, html_writer, pathway_name, pathway_prefix, max_levels=6, stop_after_first_solution=True)
html_writer.flush()
html_writer.write("</ul>\n")
html_writer.display()
return
#!/usr/bin/python
import sys
import os
import util
from chemconvert import hash2graph
from html_writer import HtmlWriter
from svg import Scene
html = HtmlWriter("../results/hash_list.html")
util._mkdir("../results/hash_list")
for line in util.parse_text_file(sys.argv[1]):
print line
graph = hash2graph(line)
graph.initialize_pos()
scene = graph.svg(Scene(200, 200, font_size=12))
html.write_svg(scene, "../results/hash_list/" + line)
html.display()
def main():
Pentose_target_compounds = [
'D-Xylulose-5P', 'D-Ribulose-5P', 'D-Ribose-5P'
]
PP_compounds = \
['D-Xylulose-5P',\
'D-Ribulose-5P',\
'D-Ribose-5P',\
'D-Erythrose-4P',\
'D-Sedoheptulose-7P',\
'D-Fructose-6P',\
'D-Glyceraldehyde-3P']
Glycolysis_compounds = \
['Dihydroxyacetone-3P',\
'D-Glyceraldehyde-3P',\
'Bisphosphoglycerate',\
'3-Phosphoglycerate',\
'2-Phosphoglycerate',\
'Phosphoenolpyruvate',\
'Pyruvate']
TCA_compounds = \
['Oxaloacetate',\
'Citrate',\
'cis-Aconitate',\
'D-Isocitrate',\
'2-Ketoglutarate',\
#succinyl-CoA\
'Succinate',\
'Fumarate',\
'Malate',\
]
Biosynthese_compounds = PP_compounds + Glycolysis_compounds + TCA_compounds
pathway_list = []
# fast test
pathway_list.append(
("TEST", ['2-Phosphoglycerate'], ['Bisphosphoglycerate'], None))
# Optimality Modules:
pathway_list.append(
("Glucose to Fructose", ['D-glucose-6P'], ['D-fructose-6P'], None))
pathway_list.append(
("Fructose to Glucose", ['D-fructose-6P'], ['D-glucose-6P'], None))
pathway_list.append(("oxaloacetate+acetyl-CoA to citrate",
['oxaloacetate + acetyl-CoA'], ['citrate'], None))
pathway_list.append(
("cis-aconitate to succinate", ['cis-aconitate'], ['succinate'], None))
pathway_list.append(
("D-xylose to D-xylulose-5P", ['D-Xylose'], ['D-Xylulose-5P'], None))
pathway_list.append(("D-arabitol to D-xylulose-5P", ['D-Arabitol'],
['D-Xylulose-5P'], None))
pathway_list.append(("L-arabinose to D-xylulose-5P", ['L-Arabinose'],
['D-Xylulose-5P'], None))
pathway_list.append(("L-xylulose to D-xylulose-5P", ['L-Xylulose'],
['D-Xylulose-5P'], None))
pathway_list.append(
("ribitol to D-xylulose-5P", ['Ribitol'], ['D-Xylulose-5P'], None))
pathway_list.append(
("D-ribose to D-xylulose-5P", ['D-Ribose'], ['D-Xylulose-5P'], None))
pathway_list.append(("Oxaloacetate to 2-Ketoglutarate", ['Oxaloacetate'],
['2-Ketoglutarate'], None))
pathway_list.append(
("Citrate to 2-Ketoglutarate", ['Citrate'], ['2-Ketoglutarate'], None))
pathway_list.append(
("Pentose Phosphate", ['D-Xylulose-5P + D-Xylulose-5P + D-Ribose-5P'],
['D-Fructose-6P + D-Fructose-6P + D-Glyceraldehyde-3P'], None))
#pathway_list.append(("Pentose Phosphate", ['D-Xylulose-5P + D-Ribose-5P'], ['D-Glyceraldehyde-3P + D-Sedoheptulose-7P'], None))
pathway_list.append(
("D-glucose to D-ribulose-5P", ['D-Glucose'], ['D-Ribulose-5P'], None))
pathway_list.append(("D-glucose to D-fructose-16P", ['D-Glucose'],
['D-Fructose-16P'], None))
pathway_list.append(("D-fructose-6P to GAP+DHAP", ['D-Fructose-6P'],
['D-Glyceraldehyde-3P + Dihydroxyacetone-3P'], None))
pathway_list.append(
("GAP to 3-PG", ['D-Glyceraldehyde-3P'], ['3-Phosphoglycerate'], None))
pathway_list.append(
("GAP to 2-PG", ['D-Glyceraldehyde-3P'], ['2-Phosphoglycerate'], None))
pathway_list.append(
("BPG to 3-PG", ['Bisphosphoglycerate'], ['3-Phosphoglycerate'], None))
pathway_list.append(
("BPG to 2-PG", ['Bisphosphoglycerate'], ['2-Phosphoglycerate'], None))
pathway_list.append(
("BPG to PEP", ['Bisphosphoglycerate'], ['Phosphoenolpyruvate'], None))
pathway_list.append(
("3-PG to PYR", ['3-Phosphoglycerate'], ['Pyruvate'], None))
# Biosynthesis
pathway_list.append(
("3-PG to L-Serine", ['3-Phosphoglycerate'], ['L-Serine'], None))
pathway_list.append(
("L-Serine to Glycine", ['L-Serine'], ['Glycine'], None))
pathway_list.append(
("Pyruvate to L-Alanine", ['Pyruvate'], ['L-Alanine'], None))
pathway_list.append(
("Synthesis of L-Serine", Biosynthese_compounds, ['L-Serine'], None))
pathway_list.append(
("Synthesis of L-Alanine", Biosynthese_compounds, ['L-Alanine'], None))
pathway_list.append(
("Synthesis of Glycine", Biosynthese_compounds, ['Glycine'], None))
pathway_list.append(("Synthesis of L-Aspartate", Biosynthese_compounds,
['L-Aspartate'], None))
pathway_list.append(("Synthesis of L-Glutamate", Biosynthese_compounds,
['L-Glutamate'], None))
# Pentose utilization
pathway_list.append(("L-Arabinose to Pentose Phosphate", ['L-Arabinose'],
Pentose_target_compounds, None))
pathway_list.append(("D-Xylose to Pentose Phosphate", ['D-Xylose'],
Pentose_target_compounds, None))
pathway_list.append(("D-Ribose to Pentose Phosphate", ['D-Ribose'],
Pentose_target_compounds, None))
pathway_list.append(("Ribitol to Pentose Phosphate", ['Ribitol'],
Pentose_target_compounds, None))
pathway_list.append(("D-Arabitol to Pentose Phosphate", ['D-Arabitol'],
Pentose_target_compounds, None))
# Glycolysis
pathway_list.append(
("GAP to PYR", ['D-Glyceraldehyde-3P'], ['Pyruvate'], 'PP'))
pathway_list.append(("GAP to DHAP", ['D-Glyceraldehyde-3P'],
['Dihydroxyacetone-3P'], 'PP'))
pathway_list.append(("GAP to PEP", ['D-Glyceraldehyde-3P + H2O'],
['Phosphoenolpyruvate + H2O'], 'PP'))
pathway_list.append(
("GAP to 2-PG", ['D-Glyceraldehyde-3P'], ['2-Phosphoglycerate'], 'PP'))
pathway_list.append(("GLC to GAP", ['D-Glucose'],
['D-Glyceraldehyde-3P + D-Glyceraldehyde-3P'], 'PP'))
pathway_list.append(
("GLC to PYR", ['Glucose'], ['Pyruvate + Pyruvate'], 'PP'))
pathway_list.append(("GLC-36P to GAP", ['D-Glucose-36P'],
['D-Glyceraldehyde-3P + D-Glyceraldehyde-3P'], 'PP'))
pathway_list.append(("GLC-6P to GAP", ['D-Glucose-6P'],
['D-Glyceraldehyde-3P + D-Glyceraldehyde-3P'], 'PP'))
pathway_list.append(("GLC-6P to BPG", ['D-Glucose-6P'],
['Bisphosphoglycerate + Bisphosphoglycerate'], 'PP'))
pathway_list.append(("GLC-6P to 3-PG", ['D-Glucose-6P'],
['3-Phosphoglycerate + 3-Phosphoglycerate'], 'PP'))
pathway_list.append(("GLC-6P to 2-PG", ['D-Glucose-6P'],
['2-Phosphoglycerate + 2-Phosphoglycerate'], 'PP'))
pathway_list.append(("GLC-6P to PEP", ['D-Glucose-6P'],
['Phosphoenolpyruvate + Phosphoenolpyruvate'], 'PP'))
pathway_list.append(
("2-PG to PYR", ['2-Phosphoglycerate'], ['Pyruvate'], 'PP'))
pathway_list.append(
("3-PG to PYR", ['3-Phosphoglycerate'], ['Pyruvate'], 'PP'))
pathway_list.append(
("BPG to PYR", ['Bisphosphoglycerate'], ['Pyruvate'], 'PP'))
pathway_list.append(
("BPG to PEP", ['Bisphosphoglycerate'], ['Phosphoenolpyruvate'], 'PP'))
# Arren's project
pathway_list.append(
("Glyoxylate + GAP to Pentose", ['Glyoxylate + D-Glyceraldehyde-3P'],
Pentose_target_compounds, None))
pathway_list.append(
("Glyoxylate + PYR to Pentose", ['Glyoxylate + Pyruvate'],
Pentose_target_compounds, None))
pathway_list.append(
("Glycolate + GAP to Pentose", ['Glycolate + D-Glyceraldehyde-3P'],
Pentose_target_compounds, None))
pathway_list.append(
("Glycolate + PYR to Pentose", ['Glycolate + Pyruvate'],
Pentose_target_compounds, None))
pathway_names = [pathway[0] for pathway in pathway_list]
pathway_map = {}
for pathway in pathway_list:
pathway_map[pathway[0]] = pathway[1:]
if (len(sys.argv) > 1):
pathway_name = pathway_names[int(sys.argv[1]) - 1]
else:
pathway_name = TkListSelection(pathway_names, "Choose a pathway:")
if (pathway_name == None):
sys.exit(0)
(substrates, products, pruning_method) = pathway_map[pathway_name]
pathfinder = PathFinder(carbon_only=False,
pruning_method=pruning_method,
ignore_chirality=True)
print "-" * 80 + "\nChosen pathway name is %s\n" % pathway_name + "-" * 80
util._mkdir("../results")
util._mkdir("../results/" + pathway_name)
html_writer = HtmlWriter("../results/" + pathway_name + ".html")
html_writer.write("<h1><center>%s</center></h1>\n" % pathway_name)
html_writer.write("<ul>\n")
for i in range(len(substrates)):
for j in range(len(products)):
##(subs, prod) = pathfinder.balance_reaction(substrates[i], products[j])
(subs, prod) = (substrates[i], products[j])
pathway_prefix = "pathway_%d_%d" % (i, j)
util._mkdir("../results/" + pathway_name + "/" + pathway_prefix)
pathfinder.solve_pathway(subs,
prod,
html_writer,
pathway_name,
pathway_prefix,
max_levels=6,
stop_after_first_solution=True)
html_writer.flush()
html_writer.write("</ul>\n")
html_writer.display()
return
#!/usr/bin/python
""" This is a script that runs through a CSV file of pairs of compounds and
tests if they are part of an optimality module (the wild-type path between
them is one of the possible shortest paths).
"""
import util
import sys
import bag
from pathfinder import PathFinder
from chemconvert import compound2graph
util._mkdir('../log')
logfile = open('../log/pathcounter.log', 'a')
substrates = []
substrates.append(('Acetyl-CoA', range(1,4)))
substrates.append(('Phosphoenolpyruvate', range(1,4)))
substrates.append(('Pyruvate', range(1,4)))
substrates.append(('D-Glyceraldehyde-3P', range(1,4)))
substrates.append(('3-Phosphoglycerate', range(1,4)))
substrates.append(('oxaloacetate', range(1,4)))
substrates.append(('fumarate', range(1,4)))
pairs = []
pairs.append(('D-fructose-6P_ring', 'D-glucolactone-6P', range(1,5)))
pairs.append(('D-fructose-6P', 'D-ribose-5P', range(1,5)))
pairs.append(('D-Glyceraldehyde-3P', '3-Phosphoglycerate', range(1,5)))
pairs.append(('3-Phosphoglycerate', 'Phosphoenolpyruvate', range(1,5)))
pairs.append(('fumarate', 'oxaloacetate', range(1,5)))
