class Reaction:
def __init__(self, reaction_id=None, block=None):
self.reaction_id = reaction_id
self.ligand = self.reaction_id
self.equation = None # str
self.subs = []
self.prods = []
self.reactiongraph = None
self.height = 0
self.width = 0
self.mappings = []
# self.arita_mapping = None
# self.kegg_mapping = None
# self.astar_mapping = None
self.rpairs = []
if reaction_id:
self.parse_reaction(block)
self.read_reactants()
# self.compute_mapping_colors()
def parse_reaction(self, block=None):
data = block
if not block:
f = open(Kegg.Kegg.REACTION_FILE)
data = f.readlines()
f.close()
self.equation = ""
lastkeyword = None
reac = False
for line in data:
line = line.rstrip()
if not line:
continue
if not line.startswith(" "):
lastkeyword = line.split()[0]
if line.startswith("ENTRY") and self.reaction_id in line:
reac = True
elif "///" in line and reac == True:
break
elif reac and ("EQUATION" in line or (line.startswith(" ") and lastkeyword == "EQUATION")):
self.equation += line[12:].strip() + " "
eq = True
elif lastkeyword == "RPAIR" and reac:
self.rpairs.append(line[12:].split()[1])
words = self.equation.strip().split()
self.subs = []
self.prods = []
ptr = self.subs
for i in range(len(words)):
w = words[i]
if w == "+":
continue
elif w.isdigit():
wnext = words[i + 1]
if re.search(r"C[0-9]{5}", wnext):
for k in range(0, int(w) - 1):
wnext = re.findall(r"C[0-9]{5}", wnext)[0]
ptr.append(wnext)
elif w == "<=>":
ptr = self.prods
elif re.search(r"C[0-9]{5}", w):
w = re.findall(r"C[0-9]{5}", w)[0]
ptr.append(w)
def read_reactants(self):
left = 50
max_right = 0
top = 50
max_bottom = 0
for i in range(len(self.subs)):
m = Molecule(self.subs[i], self, left, top)
self.subs[i] = m
top = m.max_y + 50
if max_right < m.max_x:
max_right = m.max_x
if max_bottom < m.max_y:
max_bottom = m.max_y
left = max_right + 100
top = 50
for i in range(len(self.prods)):
m = Molecule(self.prods[i], self, left, top)
self.prods[i] = m
top = m.max_y + 50
if max_right < m.max_x:
max_right = m.max_x
if max_bottom < m.max_y:
max_bottom = m.max_y
self.subs = [m for m in self.subs if m.graph and m.graph.atoms] # filter atomless molecules
self.prods = [m for m in self.prods if m.graph and m.graph.atoms] # filter atomless molecules
# trimmed formula containing only non-empty molecules
self.trim_formula = (
" + ".join([m.ligand for m in self.subs]) + " <=> " + " + ".join([m.ligand for m in self.prods])
)
self.height = max_bottom + 50
self.width = max_right + 50
def read_mapping(self, t="ASTAR", fname=None):
if t == "ASTAR":
self.mappings.append(Mapping(self))
self.mappings[-1].read_astar_mapping(fname)
elif t == "KEGG":
self.mappings.append(Mapping(self))
self.mappings[-1].read_kegg_mapping(fname)
elif t == "ARITA":
self.mappings.append(Mapping(self))
self.mappings[-1].read_arita_mapping(fname)
def read_reactiongraph(self, mapfile=None):
self.reactiongraph = ReactionGraph(self)
self.reactiongraph.read(mapfile)
def compute_mapping_colors(self):
pass
def write_header(self, f):
f.write(
'<?xml version="1.0"?>\n<!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.0//EN" "http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd">\n\n<svg fill-opacity="1" xmlns:xlink="http://www.w3.org/1999/xlink" color-rendering="auto" color-interpolation="auto" stroke="black" text-rendering="auto" stroke-linecap="square" width="%d" stroke-miterlimit="10" stroke-opacity="1" shape-rendering="auto" fill="black" stroke-dasharray="none" font-weight="normal" stroke-width="1" height="%d" xmlns="http://www.w3.org/2000/svg" font-family="'Dialog'" font-style="normal" stroke-linejoin="miter" font-size="12" stroke-dashoffset="0" image-rendering="auto">\n'
% (self.width, self.height)
)
f.write(" <g>\n")
def write_end(self, f):
f.write(" </g>\n")
f.write("</svg>\n")
def write_background(self, f):
f.write(
' <g fill="rgb(238,238,238)" stroke="rgb(238,238,238)">\n <rect width="%d" x="0" height="%d" y="0" stroke="none" />\n </g>\n'
% (self.width, self.height)
)
def write_svg(self):
f = open("./" + self.reaction_id + ".svg", "w")
self.write_header(f)
for m in self.subs + self.prods:
m.write_svg(f)
f.write("\n")
self.write_end(f)
f.close()
def atoms(self):
return [a for m in self.subs + self.prods for a in m.graph.atoms]
def get_atoms(self, mol_id, atom_id):
mol = None
atom = None
try:
mols = [m for m in self.subs + self.prods if m.mol_id == mol_id]
except:
print "wanted mol", mol_id, ". have:", self.equation
try:
atoms = [a for m in mols for a in m.graph.atoms if a.id == int(atom_id)]
except:
print "wanted atom", atom_id, "have:"
for a in mols[0].graph.atoms:
print a.id
return
return atoms
# checks whether atom numbering in rpair and mol-file are same
# def atom_numbering_consistent(self):
# for mol in self.subs + self.prods:
# # read from rpair!
# Mapping.read_rpair_data()
def has_hydrogens(self):
for c in self.subs + self.prods:
for a in c.graph.atoms:
if a.symbol == "H" or a.symbol == "H+":
return True
return False
def is_balanced(self):
subatoms = sorted("".join([a.symbol for m in self.subs for a in m.graph.atoms]))
prodatoms = sorted("".join([a.symbol for m in self.prods for a in m.graph.atoms]))
return subatoms == prodatoms
def __str__(self):
return self.reaction_id
class Reaction:
def __init__(self, reaction_id=None, block=None):
self.reaction_id = reaction_id
self.ligand = self.reaction_id
self.equation = None #str
self.subs = []
self.prods = []
self.reactiongraph = None
self.height = 0
self.width = 0
self.mappings = []
# self.arita_mapping = None
# self.kegg_mapping = None
# self.astar_mapping = None
self.rpairs = []
if reaction_id:
self.parse_reaction(block)
self.read_reactants()
# self.compute_mapping_colors()
def parse_reaction(self, block=None):
data = block
if not block:
f = open(Kegg.Kegg.REACTION_FILE)
data = f.readlines()
f.close()
self.equation = ""
lastkeyword = None
reac = False
for line in data:
line = line.rstrip()
if not line:
continue
if not line.startswith(" "):
lastkeyword = line.split()[0]
if line.startswith("ENTRY") and self.reaction_id in line:
reac = True
elif "///" in line and reac == True:
break
elif reac and ("EQUATION" in line or
(line.startswith(" ")
and lastkeyword == "EQUATION")):
self.equation += line[12:].strip() + " "
eq = True
elif lastkeyword == "RPAIR" and reac:
self.rpairs.append(line[12:].split()[1])
words = self.equation.strip().split()
self.subs = []
self.prods = []
ptr = self.subs
for i in range(len(words)):
w = words[i]
if w == "+":
continue
elif w.isdigit():
wnext = words[i + 1]
if re.search(r'C[0-9]{5}', wnext):
for k in range(0, int(w) - 1):
wnext = re.findall(r'C[0-9]{5}', wnext)[0]
ptr.append(wnext)
elif w == "<=>":
ptr = self.prods
elif re.search(r'C[0-9]{5}', w):
w = re.findall(r'C[0-9]{5}', w)[0]
ptr.append(w)
def read_reactants(self):
left = 50
max_right = 0
top = 50
max_bottom = 0
for i in range(len(self.subs)):
m = Molecule(self.subs[i], self, left, top)
self.subs[i] = m
top = m.max_y + 50
if max_right < m.max_x:
max_right = m.max_x
if max_bottom < m.max_y:
max_bottom = m.max_y
left = max_right + 100
top = 50
for i in range(len(self.prods)):
m = Molecule(self.prods[i], self, left, top)
self.prods[i] = m
top = m.max_y + 50
if max_right < m.max_x:
max_right = m.max_x
if max_bottom < m.max_y:
max_bottom = m.max_y
self.subs = [m for m in self.subs
if m.graph and m.graph.atoms] # filter atomless molecules
self.prods = [m for m in self.prods if m.graph and m.graph.atoms
] # filter atomless molecules
# trimmed formula containing only non-empty molecules
self.trim_formula = " + ".join([
m.ligand for m in self.subs
]) + " <=> " + " + ".join([m.ligand for m in self.prods])
self.height = max_bottom + 50
self.width = max_right + 50
def read_mapping(self, t="ASTAR", fname=None):
if t == "ASTAR":
self.mappings.append(Mapping(self))
self.mappings[-1].read_astar_mapping(fname)
elif t == "KEGG":
self.mappings.append(Mapping(self))
self.mappings[-1].read_kegg_mapping(fname)
elif t == "ARITA":
self.mappings.append(Mapping(self))
self.mappings[-1].read_arita_mapping(fname)
def read_reactiongraph(self, mapfile=None):
self.reactiongraph = ReactionGraph(self)
self.reactiongraph.read(mapfile)
def compute_mapping_colors(self):
pass
def write_header(self, f):
f.write(
"<?xml version=\"1.0\"?>\n<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.0//EN\" \"http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd\">\n\n<svg fill-opacity=\"1\" xmlns:xlink=\"http://www.w3.org/1999/xlink\" color-rendering=\"auto\" color-interpolation=\"auto\" stroke=\"black\" text-rendering=\"auto\" stroke-linecap=\"square\" width=\"%d\" stroke-miterlimit=\"10\" stroke-opacity=\"1\" shape-rendering=\"auto\" fill=\"black\" stroke-dasharray=\"none\" font-weight=\"normal\" stroke-width=\"1\" height=\"%d\" xmlns=\"http://www.w3.org/2000/svg\" font-family=\"'Dialog'\" font-style=\"normal\" stroke-linejoin=\"miter\" font-size=\"12\" stroke-dashoffset=\"0\" image-rendering=\"auto\">\n"
% (self.width, self.height))
f.write(" <g>\n")
def write_end(self, f):
f.write(" </g>\n")
f.write("</svg>\n")
def write_background(self, f):
f.write(
' <g fill="rgb(238,238,238)" stroke="rgb(238,238,238)">\n <rect width="%d" x="0" height="%d" y="0" stroke="none" />\n </g>\n'
% (self.width, self.height))
def write_svg(self):
f = open("./" + self.reaction_id + ".svg", "w")
self.write_header(f)
for m in self.subs + self.prods:
m.write_svg(f)
f.write("\n")
self.write_end(f)
f.close()
def atoms(self):
return [a for m in self.subs + self.prods for a in m.graph.atoms]
def get_atoms(self, mol_id, atom_id):
mol = None
atom = None
try:
mols = [m for m in self.subs + self.prods if m.mol_id == mol_id]
except:
print "wanted mol", mol_id, ". have:", self.equation
try:
atoms = [
a for m in mols for a in m.graph.atoms if a.id == int(atom_id)
]
except:
print "wanted atom", atom_id, "have:"
for a in mols[0].graph.atoms:
print a.id
return
return atoms
# checks whether atom numbering in rpair and mol-file are same
# def atom_numbering_consistent(self):
# for mol in self.subs + self.prods:
# # read from rpair!
# Mapping.read_rpair_data()
def has_hydrogens(self):
for c in self.subs + self.prods:
for a in c.graph.atoms:
if a.symbol == "H" or a.symbol == "H+":
return True
return False
def is_balanced(self):
subatoms = sorted("".join(
[a.symbol for m in self.subs for a in m.graph.atoms]))
prodatoms = sorted("".join(
[a.symbol for m in self.prods for a in m.graph.atoms]))
return subatoms == prodatoms
def __str__(self):
return self.reaction_id
def read_reactiongraph(self, mapfile=None):
self.reactiongraph = ReactionGraph(self)
self.reactiongraph.read(mapfile)
def read_reactiongraph(self, mapfile=None):
self.reactiongraph = ReactionGraph(self)
self.reactiongraph.read(mapfile)