def pathway2text(self, G_subs, expanded_reaction_list):
num_reactions = len(expanded_reaction_list)
num_compounds = len(expanded_reaction_list) + 1
i = 0
G = G_subs.clone()
rid = None
s = ""
while True:
if (i == len(expanded_reaction_list)):
break
(rid, mapping, reaction_list) = expanded_reaction_list[i]
s += str(G) + " (" + graph2compound(G, self.ignore_chirality) + ") - " + str(rid) + " : " + str(mapping) + "\n"
for reaction in reaction_list:
s += "\t" + str(G) + " (" + graph2compound(G, self.ignore_chirality) + ") - " + str(reaction.tostring(mapping)) + "\n"
reaction.apply(G, mapping)
G.update_attributes()
if (self.ignore_chirality):
G.reset_chiralities()
i += 1
s += str(G) + " (" + graph2compound(G, self.ignore_chirality) + ")\n"
return (s, G)
def pathway2text(self, G_subs, expanded_reaction_list):
num_reactions = len(expanded_reaction_list)
num_compounds = len(expanded_reaction_list) + 1
i = 0
G = G_subs.clone()
rid = None
s = ""
while True:
if (i == len(expanded_reaction_list)):
break
(rid, mapping, reaction_list) = expanded_reaction_list[i]
s += str(G) + " (" + graph2compound(
G, self.ignore_chirality) + ") - " + str(rid) + " : " + str(
mapping) + "\n"
for reaction in reaction_list:
s += "\t" + str(G) + " (" + graph2compound(
G, self.ignore_chirality) + ") - " + str(
reaction.tostring(mapping)) + "\n"
reaction.apply(G, mapping)
G.update_attributes()
if (self.ignore_chirality):
G.reset_chiralities()
i += 1
s += str(G) + " (" + graph2compound(G, self.ignore_chirality) + ")\n"
return (s, G)
def reaction2svg(self, G_old, G_new, rid):
font_size = 10
scene = svg.Scene(800, 300)
scene.add(G_old.svg(svg.Scene(300, 300)))
scene.add(svg.Text((30, font_size), graph2compound(G_old, self.ignore_chirality), font_size, fill_color=magenta))
scene.add(svg.Text((325, 120), self.reaction_templates[rid]['NAME'], font_size=font_size, fill_color=red))
scene.add(svg.ChemicalArrow((380, 150), (420, 150), stroke_width=2))
scene.add(G_new.svg(svg.Scene(300, 300)), (500, 0))
scene.add(svg.Text((530, font_size), graph2compound(G_new, self.ignore_chirality), font_size, fill_color=magenta))
# scene.justify()
scene.border(True)
return scene
def reaction2svg(self, G_old, G_new, rid):
font_size = 10
scene = svg.Scene(800, 300)
scene.add(G_old.svg(svg.Scene(300, 300)))
scene.add(
svg.Text((30, font_size), graph2compound(G_old, self.ignore_chirality), font_size, fill_color=magenta)
)
scene.add(svg.Text((325, 120), self.reaction_templates[rid]["NAME"], font_size=font_size, fill_color=red))
scene.add(svg.ChemicalArrow((380, 150), (420, 150), stroke_width=2))
scene.add(G_new.svg(svg.Scene(300, 300)), (500, 0))
scene.add(
svg.Text((530, font_size), graph2compound(G_new, self.ignore_chirality), font_size, fill_color=magenta)
)
# scene.justify()
scene.border(True)
return scene
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
