def CascadeHandler(r):
DBG = False
casc = r.Arrow()
stages,arrow = casc.split("*")
modifiers = r.MHS()
if DBG: print "Cascade Handler: stages,arrow: ", stages, arrow
if DBG: print "Cascade Handler: modifiers: ", modifiers
#
# most of the cascades in py[cellerator] don't actually exist in cellerator
# so expand to the bottom line
#
er = expand(r)
er = map(_Handle_Reaction, er)
if DBG: print "Cascade Handler: er: ", er
okr = map(lambda u:u[-1], filter(lambda u:u[0], er))
notok = map(lambda u:u[-1], filter(lambda u:not(u[0]), er))
if DBG: print "okr: ", okr
if DBG: print "notok: ", notok
for r in notok:
print "Error: unable to convert the reaction: "+str(r)
return okr
def CascadeHandler(r):
DBG = False
casc = r.Arrow()
stages, arrow = casc.split("*")
modifiers = r.MHS()
if DBG: print "Cascade Handler: stages,arrow: ", stages, arrow
if DBG: print "Cascade Handler: modifiers: ", modifiers
#
# most of the cascades in py[cellerator] don't actually exist in cellerator
# so expand to the bottom line
#
er = expand(r)
er = map(_Handle_Reaction, er)
if DBG: print "Cascade Handler: er: ", er
okr = map(lambda u: u[-1], filter(lambda u: u[0], er))
notok = map(lambda u: u[-1], filter(lambda u: not (u[0]), er))
if DBG: print "okr: ", okr
if DBG: print "notok: ", notok
for r in notok:
print "Error: unable to convert the reaction: " + str(r)
return okr
def test_single():
assert list(expand("a.{}")) == ["a."]
assert list(expand("a.{doc}")) == ["a.doc"]
assert list(expand("a.{doc,txt}")) == ["a.doc", "a.txt"]
assert list(expand("a.{1,2,3}")) == ["a.1", "a.2", "a.3"]
assert list(expand("{good,bad} mood")) == ["good mood", "bad mood"]
assert list(expand("just {2,3} drinks")) == ["just 2 drinks", "just 3 drinks"]
assert list(expand("soft drink{,s}")) == ["soft drink", "soft drinks"]
def expand():
print '[+] Please input the location of dictionary'
loc = raw_input().replace("\'", "").strip()
while not(os.path.exists(loc)):
print "[x] {0} doesn't seem to exist, try again.".format(loc)
loc = raw_input()
print "[-] Beginning Expansion..."
e = expander.expand(loc, loc+"-EXPANDED")
e.expand()
def normalise(text):
list_tokens = split_tokens(text)
NSWs_dict = create_NSWs_dict(list_tokens)
tagged_dic = tagify(NSWs_dict)
classified_dic = classify(tagged_dic, list_tokens)
expanded_dic = expand(classified_dic, list_tokens)
normalized_text = replace_nsw(expanded_dic, list_tokens)
return normalized_text
# text = open('./vidu.txt').read()
# print(normalise(text))
def test_multiple():
assert list(expand("{a}{b}{c}{d}{e}{f}")) == ["abcdef"]
assert list(expand("{a}.{doc,txt}")) == ["a.doc", "a.txt"]
assert list(expand("{a,b}.{doc}")) == ["a.doc", "b.doc"]
assert list(expand("{a,b}.{doc,txt}")) == ["a.doc", "a.txt", "b.doc", "b.txt"]
assert list(expand("{0,1,2,3,4,5,6,7,8,9}"*5)) == [format(i, "05") for i in range(10**5)]
assert list(expand("{a}"*100)) == ["a"*100]
def classify_input(parsed_reactions, ncells, nspecie, PRINT=True):
# summarize input
#
classes = {}
for r in parsed_reactions:
reaction_class = r.arrowtype + " " + r.arrow
if reaction_class in classes:
classes[reaction_class] += 1
else:
classes[reaction_class] = 1
expanded_reactions = expander.expand(parsed_reactions)
class_names = list(classes)
if PRINT:
print_rule()
print "%5d" % (len(parsed_reactions)), "reactions input."
print "%5d" % (len(expanded_reactions)), " expanded reactions"
for class_name in class_names:
print "%5d" % (classes[class_name]), class_name, "reactions"
print "%5d" % (ncells * nspecie), " differential equations"
print_rule()
return expanded_reactions
def classify_input(parsed_reactions, ncells, nspecie, PRINT=True):
# summarize input
#
classes = {}
for r in parsed_reactions:
reaction_class=r.arrowtype+" "+r.arrow
if reaction_class in classes:
classes[reaction_class]+=1
else:
classes[reaction_class]=1
expanded_reactions = expander.expand(parsed_reactions)
class_names=list(classes)
if PRINT:
print_rule()
print "%5d" %(len(parsed_reactions)), "reactions input."
print "%5d" %(len(expanded_reactions)), " expanded reactions"
for class_name in class_names:
print "%5d" %(classes[class_name]), class_name, "reactions"
print "%5d" %(ncells*nspecie), " differential equations"
print_rule()
return expanded_reactions
def test_stray_braces():
assert list(expand(":-{")) == [":-{"]
assert list(expand("oh }{ nice")) == ["oh }{ nice"]
def test_trivial():
assert list(expand("")) == [""]
assert list(expand("hello")) == ["hello"]
def genmodel(infile, outfile, verbose=False):
(reactions, ic, rates, frozenvars, functions, assignments, filename) = readmodel(infile)
# Expand reactions
#
r = interpreter.invokeParser(reactions, dump=False)
er = expander.expand(r)
s = interpreter.makeSymbolDictionary(er, rates, ic)
try:
SBML=SBMLDocument(3,1)
except ValueError:
exit("Could not create the SBMLDocument.")
m = SBML.createModel()
m.setTimeUnits("dimensionless")
m.setSubstanceUnits("item")
m.setExtentUnits("item")
c = m.createCompartment()
c.setId('compartment')
c.setConstant(True)
c.setSize(1)
c.setSpatialDimensions(3)
c.setUnits("dimensionless")
for function in functions:
if verbose:
print "function: ", function
fnew=m.createFunctionDefinition()
fname, formula = function.split("=")
fname=fname.strip()
formula=formula.strip()
formula=formula.replace("**","^")
functionvar, functiondef=formula.split(":")
# print "functiondef:", functiondef
functionvar=functionvar.split()[-1]
# print "functionvar:", functionvar
lambdadef="lambda("+functionvar+","+functiondef+")"
# print "lambdadef: ", lambdadef
math_ast = parseL3Formula(lambdadef)
# print "math_ast=",math_ast
fnew.setId(fname)
fnew.setMath(math_ast)
species=list(ic)
sp=[]
for specie in species:
snew=m.createSpecies()
snew.setId(specie)
if specie in frozenvars:
snew.setConstant(True)
else:
snew.setConstant(False)
snew.setBoundaryCondition(False)
snew.setHasOnlySubstanceUnits(True)
amount = ic[specie]
snew.setInitialAmount(amount)
snew.setCompartment("compartment")
sp.append(snew)
# add nil species
snew=m.createSpecies()
snew.setId("Nil")
snew.setConstant(False)
snew.setBoundaryCondition(False)
snew.setHasOnlySubstanceUnits(True)
snew.setInitialAmount(0)
snew.setCompartment("compartment")
sp.append(snew)
RATES=list(rates)
ks=[]
for rate in rates:
k = m.createParameter()
k.setId(rate)
k.setConstant(True)
k.setValue(rates[rate])
k.setUnits('dimensionless')
ks.append(k)
#print assignments
i=1
for assignment in assignments:
lhs, rhs = assignment.split("=")
lhs=lhs.strip()
rhs=rhs.strip()
if verbose:
print "assignment: to:", lhs, "from:",rhs
arule = m.createAssignmentRule()
patchedlaw=rhs.replace("**","^")
math_ast = parseL3Formula(patchedlaw)
arule.setMath(math_ast)
arule.setVariable(lhs)
aid = "arule"+str(i)
i+=1
arule.setId(aid)
reacts=[]
i = 1
for line in er:
new_reaction=m.createReaction()
rid = "r"+str(i)
new_reaction.setId(rid)
new_reaction.setReversible(False)
new_reaction.setFast(False)
odeterm = interpreter.makeODETerms([line], s, frozen=frozenvars)
termkeys=list(odeterm)
# print "termkeys:", termkeys
# print "**** Reaction ", i,"\n", line.LHS(),"\n",line.MHS(),"\n",line.RHS()
S, ST = reduceStoichiometry(line.LHS(), line.LH_STOIC())
# print "reactant: ", S, ST
for X,Z in zip(S, ST):
if X in termkeys:
sref=new_reaction.createReactant()
sref.setSpecies(X)
sref.setStoichiometry(float(Z))
if X in frozenvars:
sref.setConstant(True)
else:
sref.setConstant(False)
#
# some Cellerator "Reactants" are really modifiers
#
elif str(X) != "Nil":
sref=new_reaction.createModifier()
sref.setSpecies(X)
S, ST = reduceStoichiometry(line.RHS(), line.RH_STOIC())
# print "product: ", S, ST
for X,Z in zip(S, ST):
sref=new_reaction.createProduct()
sref.setSpecies(X)
sref.setStoichiometry(float(Z))
if X in frozenvars:
sref.setConstant(True)
else:
sref.setConstant(False)
for X in line.MHS():
sref=new_reaction.createModifier()
sref.setSpecies(X)
terms = [str(odeterm[X]) for X in termkeys]
# print "terms: ", terms
terms = map(lambda x: x.lstrip("-"), terms)
terms = set(terms) - set(["0"])
if len(terms)>0:
law = list(terms)[0]
else:
law = "0"
if verbose:
print "using kinetic law ", law, " for "+str(rid)+": ", line.Input()
patchedlaw=law.replace("**","^")
math_ast = parseL3Formula(patchedlaw)
kinetic_law = new_reaction.createKineticLaw()
kinetic_law.setMath(math_ast)
# print "kinetic law ", i, " is ", law, odeterm
i +=1
return (writeSBMLToString(SBML))
def generatePythonFunction(reactions,
rates,
ics,
frozenvars,
functions,
assignments,
holdrates=[],
substituteRates=False):
"""
input: reactions - list of reactions in cellerator text form
inputrates - list of rate constants in dictionary form
output: writes a function to file tmp.py that is solver-compatible
return values: (y, y0)
y: list of string names of variables ["y1", "y2",...]
y0: list of values of variables at initial time
"""
#print "solver:assignments:",assignments
#print "solver:frozenvars:",frozenvars
d = datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")
codefile = utils.uniqueFileName("tmp.py")
f = open(codefile, "w")
f.write("from math import *\n")
if len(functions) > 0:
f.write("\n")
for funct in functions:
f.write(funct + "\n")
f.write("\n")
f.write("def ode_function_rhs(y,t):\n")
f.write(" # \n")
f.write(" # this odeint(..) compatible function was \n")
f.write(" # automatically generated by Cellerator " + d + " \n")
ver = sys.version.replace("\n", " ")
f.write(" # " + ver + "\n")
f.write(" # " + sys.platform + "\n")
f.write(" # \n")
f.write(
" # =============================================================\n")
f.write(" # Model: \n #\n")
#
# there may be a whole boatload of reactions to print
# define a generator
def printable_reaction(k):
for j in xrange(k):
reaction = reactions[j]
yield " # " + reaction.strip() + "\n"
for r in printable_reaction(len(reactions)):
f.write(r)
#for reaction in reactions:
# f.write(" # " + reaction.strip() + "\n")
#
# write a whole shitload of comments with the rate constants, unless
# the rate constants are themselves written out
#
if substituteRates:
f.write(" #\n # Parameter values used: \n #\n")
for r in rates:
f.write(" # " + r + "=" + str(rates[r]) + "\n")
if len(holdrates) > 0:
f.write(" global " + holdrates[0] + "\n")
if len(frozenvars) > 0:
f.write(
" #\n # Frozen Variables (species with fixed derivatives):\n #\n"
)
for v in frozenvars:
f.write(" # " + str(v) + "\n")
f.write(
" # =============================================================\n")
results = interpreter.invokeParser(reactions, dump=False)
results = expand(results)
s = interpreter.makeSymbolDictionary(results, rates, ics)
odeterms = interpreter.makeODETerms(results, s, frozen=frozenvars)
if substituteRates:
newterms = substituteRateConstants(odeterms, rates, s, holdrates)
na = []
# rate constants also appear in assignment rules
for a in assignments:
value, assignment = a.split("=")
assignment = sympify(assignment)
newassignment = value + "=" + str(
applyReplacementRules(assignment, rates, s))
na.append(newassignment)
assignments = na
else: # better this way because applyReplacementRules grows superquadratically
newterms = odeterms
ks = rates.keys()
ks.sort()
f.write(" # rate constants\n")
for k in ks:
if k in holdrates:
continue
v = rates[k]
nextline = " " + k + " = " + str(v) + "\n"
f.write(nextline)
(y, yprime, ics) = makeODEfunc(newterms, s, ics)
y = map(str, y)
yprime = map(str, yprime)
f.write("# pick up values from previous iteration\n")
n = len(y)
for i in range(n):
nextline = " " + y[i] + " = " + "max(0, y[" + str(i) + "])\n"
#
nextline = nextline.replace("{", "[").replace("}", "]")
#
f.write(nextline)
if (len(assignments) > 0):
f.write("# apply boundary conditions / assignment rules \n")
for a in assignments:
f.write(" " + a + "\n")
f.write("# calculate derivatives of all variables\n")
f.write(" yp=[0 for i in range(" + str(n) + ")]\n")
for i in range(n):
nextline = " yp[" + str(i) + "] = " + yprime[i] + "\n"
#
#
#
nextline = nextline.replace("{", "[").replace("}", "]")
#
#
f.write(nextline)
#print "solver:",nextline
f.write(" return yp\n")
f.close()
#sys.exit()
return (y, ics, codefile)
def interpret(filename, ofile="", dumpparser=False, format="ODE", frozen=[], \
symbolic=False):
if "-time" in sys.argv:
start = clock()
DBG = False
if DBG: print "interpret: Starting"
output=[]
dump = dumpparser or ("-dump" in sys.argv)
SYMBOLIC = symbolic or "-symbolic" in sys.argv
freeze=[]
if ("-frozen" in sys.argv):
i=(sys.argv).index("-frozen")+1
while i<len(sys.argv):
next = sys.argv[i]
if str(next)[0]=="-": break
freeze.append(next)
i+=1
elif type(frozen)==type([]):
freeze = frozen
if DBG: print "interpret: calling Parser"
(results, rates, functions, frozen, assignments, ICS) = runparser(filename, trace=dump)
#
# combine frozen variables on command line with those in model file
#
freeze = list (set (freeze + frozen))
# print rates
if DBG: print "interpret: expanding"
if "-time" in sys.argv:
parsetime = clock()-start
print "(parse time): %20.10f" %(parsetime)
start = clock()
results = expand(results)
if DBG: print "interpret: making Symbol Dicitionary"
s=makeSymbolDictionary(results, rates, ICS)
if DBG: print "interpret: making ODE Terms"
odeterms = makeODETerms(results, s, frozen=freeze)
if DBG: print "interpret: printing terms"
# print odeterms
if "-format" in sys.argv:
i = (sys.argv).index("-format")+1
if i < len(sys.argv):
format = sys.argv[i]
else:
print "Error: interpret: expecting format string after -format keyword."
format = "ODE"
fmt = str(format).upper()
if not fmt in ["ODE","DICT","CODE", "PYTHON", "LATEX", "JACOBIAN", "STEADYSTATE"]:
print "Error: interpret: invalid format='"+str(fmt)+"' requested."
raise SystemExit("Resubmit job with correct value for keyword -format")
k=0
if fmt in ["CODE","PYTHON"]:
output.append("from math import *")
if len(functions)>0:
for f in functions:
output.append(f)
output.append("def f(y,t):")
for x in rates:
output.append(" "+str(x)+" = "+str(rates[x]))
for x in assignments:
output.append(" "+str(x))
for x in odeterms:
line = " y["+str(k)+"] = " + str(x)
output.append(line)
k += 1
k = 0
elif fmt == "DICT":
output=odeterms
return (output)
# if symbolic: return output
elif fmt == "JACOBIAN":
output = jacobian(odeterms)
return (output)
# if symbolic: return output
elif fmt == "STEADYSTATE":
output = steadystate(odeterms, rates, SYMBOLIC)
elif fmt == "LATEX":
output.append("\\documentclass[12pt,letterpaper]{article}")
output.append("\\usepackage[latin1]{inputenc}")
output.append("\\usepackage{amsmath, amsfonts, amssymb}")
output.append("\\author{py[cellerator]}")
output.append("\\date{\\today}")
output.append("\\title{Automatically Generated Equations}")
output.append("\\begin{document}")
output.append("\\maketitle")
output.append("\\begin{align*}")
for f in functions:
output.append(latex(f))
if fmt == "ODE":
for f in functions:
output.append(f)
for f in assignments:
output.append(f)
for x in odeterms:
if fmt == "ODE":
line = str(x)+"' = "+str(odeterms[x])
elif fmt == "DICT":
continue
elif fmt == "JACOBIAN":
continue
elif fmt == "STEADYSTATE":
continue
elif fmt in ["CODE", "PYTHON"]:
line = " yp["+str(k)+"] = " + str(odeterms[x])
k+=1
elif fmt == "LATEX":
line =x+"' &= "+latex(odeterms[x])[1:-1]+"\\\\"
else:
print "Error: interpret: invalid format requested: " + str(format)
raise SystemExit("Resubmit job with correct value for keyword.")
output.append(line)
if fmt =="ODE":
output = "\n".join(output)
elif fmt == "LATEX":
output.append("\\end{align*}")
output.append("\\end{document}")
output = "\n".join(output)
elif fmt in ["CODE", "PYTHON"]:
output.append(" return (yp)")
output = "\n".join(output)
outfile=ofile
if ("-out" in sys.argv):
i = (sys.argv).index("-out")+1
if i<len(sys.argv):
outfile=sys.argv[i]
else:
print("Error: interpret: expecting filename after -out option.")
outfile="interpreted-equations.out"
if len(outfile)>0:
outputfile = outfile
(left,right)=outfile.split(".")
j=1
while os.path.isfile(outputfile):
outputfile=left+str(j)+"."+right
j+=1
f=open(outputfile,"w")
if fmt == "DICT":
output = str(output)
f.write(output)
else:
f.write(output)
# output = map(lambda x:x+"\n",output)
# f.writelines(output)
f.close()
if "-time" in sys.argv:
print "(interpret time): %20.10f" %(clock() - start)
return os.path.abspath(outputfile)
if "-time" in sys.argv:
print "(interpret time): %20.10f" %(clock() - start)
return(output)
def generatePythonFunction(reactions, rates, ics, frozenvars, functions,
assignments, holdrates=[], substituteRates=False):
"""
input: reactions - list of reactions in cellerator text form
inputrates - list of rate constants in dictionary form
output: writes a function to file tmp.py that is solver-compatible
return values: (y, y0)
y: list of string names of variables ["y1", "y2",...]
y0: list of values of variables at initial time
"""
#print "solver:assignments:",assignments
#print "solver:frozenvars:",frozenvars
d=datetime.datetime.now().strftime("%Y-%m-%d %H:%M:%S")
codefile=utils.uniqueFileName("tmp.py")
f=open(codefile,"w")
f.write("from math import *\n")
if len(functions)>0:
f.write("\n")
for funct in functions: f.write(funct+"\n")
f.write("\n")
f.write("def ode_function_rhs(y,t):\n")
f.write(" # \n")
f.write(" # this odeint(..) compatible function was \n")
f.write(" # automatically generated by Cellerator "+d+" \n")
ver = sys.version.replace("\n"," ")
f.write(" # " + ver + "\n")
f.write(" # " + sys.platform + "\n")
f.write(" # \n")
f.write(" # =============================================================\n")
f.write(" # Model: \n #\n")
#
# there may be a whole boatload of reactions to print
# define a generator
def printable_reaction(k):
for j in xrange(k):
reaction=reactions[j]
yield " # " + reaction.strip() + "\n"
for r in printable_reaction(len(reactions)):
f.write(r)
#for reaction in reactions:
# f.write(" # " + reaction.strip() + "\n")
#
# write a whole shitload of comments with the rate constants, unless
# the rate constants are themselves written out
#
if substituteRates:
f.write(" #\n # Parameter values used: \n #\n")
for r in rates:
f.write(" # " + r + "=" + str(rates[r]) + "\n")
if len(holdrates)>0:
f.write(" global "+holdrates[0]+"\n")
if len(frozenvars) >0:
f.write(" #\n # Frozen Variables (species with fixed derivatives):\n #\n")
for v in frozenvars: f.write(" # "+str(v)+ "\n")
f.write(" # =============================================================\n")
results = interpreter.invokeParser(reactions, dump=False)
results = expand(results)
s=interpreter.makeSymbolDictionary(results, rates, ics)
odeterms = interpreter.makeODETerms(results, s, frozen=frozenvars)
if substituteRates:
newterms = substituteRateConstants(odeterms, rates, s, holdrates)
na = []
# rate constants also appear in assignment rules
for a in assignments:
value,assignment = a.split("=")
assignment = sympify(assignment)
newassignment = value+"="+str(applyReplacementRules(assignment, rates, s))
na.append(newassignment)
assignments = na
else: # better this way because applyReplacementRules grows superquadratically
newterms = odeterms
ks=rates.keys()
ks.sort()
f.write(" # rate constants\n")
for k in ks:
if k in holdrates:
continue
v=rates[k]
nextline=" "+k+" = " + str(v)+"\n"
f.write(nextline)
(y, yprime, ics) = makeODEfunc(newterms, s, ics)
y = map(str, y)
yprime = map(str,yprime)
f.write("# pick up values from previous iteration\n")
n = len(y)
for i in range(n):
nextline = " "+y[i]+" = "+"max(0, y["+str(i)+"])\n"
#
nextline = nextline.replace("{","[").replace("}","]")
#
f.write(nextline)
if (len(assignments)>0):
f.write("# apply boundary conditions / assignment rules \n")
for a in assignments:
f.write(" "+a+"\n")
f.write("# calculate derivatives of all variables\n")
f.write(" yp=[0 for i in range("+str(n)+")]\n")
for i in range(n):
nextline = " yp["+str(i)+"] = " + yprime[i]+"\n"
#
#
#
nextline = nextline.replace("{","[").replace("}","]")
#
#
f.write(nextline)
#print "solver:",nextline
f.write(" return yp\n")
f.close()
#sys.exit()
return (y, ics, codefile)