def get_lifetime():
"""
Calculate the lifetime of species.
"""
rxns = []
lines = parse_rxn()
for i in lines:
a = Rxn(i)
rxns.append(a)
sim_time = rxns[-1].nstep
mols = []
lines = parse_molid()
for i in lines:
a = Mol(i)
mols.append(a)
for i in range(len(mols)):
id = mols[i].id
start = 0
end = sim_time
for j in range(len(rxns)):
#print id, rxns[j].proid
if id in rxns[j].proid:
start = rxns[j].nstep
if id in rxns[j].reacid:
end = rxns[j].nstep
mols[i].lifetime = end - start
output_molid_ext(mols)
def get_lifetime():
"""
Calculate the lifetime of species.
"""
sim_time = self.rxns[-1].nstep
mols = []
lines = parse_molid()
for i in lines:
a = Mol(i)
mols.append(a)
for i in range(len(mols)):
id = mols[i].id
start = 0
end = sim_time
for j in range(len(self.rxns)):
#print id, rxns[j].proid
if id in self.rxns[j].proid:
start = self.rxns[j].nstep
if id in self.rxns[j].reacid:
end = self.rxns[j].nstep
mols[i].lifetime = end - start
output_molid_ext(mols)
def get_initial_reactants(self, tag):
"""
Get all the possible initial reactants for any specified
reaction (tag)
"""
# get reaction mol id
nstep = int(tag.split("_")[0])
id = int(tag.split("_")[1])
for i in self.rxns:
if i.nstep == nstep and i.id == id:
reac = i.reacid
# reaction species
print "-" * 72
print "reaction species are: "
for i in reac:
print i
print "-" * 72
# read molid file
mols = []
lines = parse_molid()
for i in lines:
a = Mol(i)
mols.append(a)
# get atoms
atoms = []
reac_atoms = []
for i in reac:
for j in mols[i - 1].atoms:
atoms.append(j)
reac_atoms.append(j)
max_mol = max(reac)
# @note: need to be a parameter
n_inital = 24
print "reactions species from begining are: "
for i in range(n_inital):
n_match = 0
for j in reac_atoms:
if j in mols[i].atoms:
n_match += 1
m = n_match * 1.0 / mols[i].natom
if m > 0:
print mols[i].id, m
print "-" * 72
print "intermidate mol id involved are: "
for i in range(max_mol, n_inital, -1):
flag = 0
for j in reac_atoms:
if j in mols[i].atoms:
print i
break
print "-" * 72
for i in range(max_mol, n_inital, -1):
flag = 0
for j in atoms:
if j in mols[i].atoms:
flag = 1
break
if flag:
for k in mols[i].atoms:
if k not in atoms:
atoms.append(k)
print "All possible species involved from begining are: "
initial_mols = []
for i in range(n_inital):
n_match = 0
for j in atoms:
if j in mols[i].atoms:
n_match += 1
m = n_match * 1.0 / mols[i].natom
if m > 0:
print mols[i].id, m
def get_initial_reactants(self, tag):
"""
Get all the possible initial reactants for any specified
reaction (tag)
"""
# get reaction mol id
nstep = int(tag.split("_")[0])
id = int(tag.split("_")[1])
for i in self.rxns:
if i.nstep == nstep and i.id == id:
reac = i.reacid
# reaction species
print "-"*72
print "reaction species are: "
for i in reac:
print i
print "-"*72
# read molid file
mols = []
lines = parse_molid()
for i in lines:
a = Mol(i)
mols.append(a)
# get atoms
atoms = []
reac_atoms = []
for i in reac:
for j in mols[i-1].atoms:
atoms.append(j)
reac_atoms.append(j)
max_mol = max(reac)
# @note: need to be a parameter
n_inital = 24
print "reactions species from begining are: "
for i in range(n_inital):
n_match = 0
for j in reac_atoms:
if j in mols[i].atoms:
n_match += 1
m = n_match * 1.0 / mols[i].natom
if m > 0:
print mols[i].id, m
print "-"*72
print "intermidate mol id involved are: "
for i in range(max_mol, n_inital, -1):
flag = 0
for j in reac_atoms:
if j in mols[i].atoms:
print i
break
print "-"*72
for i in range(max_mol, n_inital, -1):
flag = 0
for j in atoms:
if j in mols[i].atoms:
flag = 1
break
if flag:
for k in mols[i].atoms:
if k not in atoms:
atoms.append(k)
print "All possible species involved from begining are: "
initial_mols = []
for i in range(n_inital):
n_match = 0
for j in atoms:
if j in mols[i].atoms:
n_match += 1
m = n_match * 1.0 / mols[i].natom
if m > 0:
print mols[i].id, m