class CompoundT(MoleculeT):
## @brief constructor for class CompoundT
# @param molec_set A MolecSet Object
def __init__(self, molec_set):
self._C = MolecSet(molec_set.to_seq())
## @brief return the molecules in the compound
# @return a Set containing the molecules in the compound
def get_molec_set(self):
return self._C
## @brief count the number of atoms of a element in the compound
# @param e the element to check for in the compound
# @return integer indicating the number of atoms of element e in the compound
def num_atoms(self, e):
temp_seq = self._C.to_seq()
count = 0
for molecule in temp_seq:
count += molecule.num_atoms(e)
return count
## @brief return an ElmSet of the elements in the molecules that are in the compound
# @return ElmSet containing the elements
def constit_elems(self):
molecs = self._C.to_seq()
elems = []
for molecule in molecs:
elems.append(molecule.get_elm())
return ElmSet(elems)
## @brief check if two compounds are equals
# @param d the object to compare against
# @return boolean indicating if they are equal
def equals(self, d):
return self.get_molec_set().equals(d.get_molec_set())
def test_equals(self):
O = MoleculeT(1, ElementT.O)
H2 = MoleculeT(2, ElementT.H)
H2O = CompoundT(MolecSet([H2, O]))
o = MoleculeT(1, ElementT.O)
h2 = MoleculeT(2, ElementT.H)
h2o = CompoundT(MolecSet([h2, o]))
assert H2O.equals(H2O)
assert not H2O.equals(h2o)
def test_rhs_coeff(self):
H2 = MoleculeT(2, ElementT.H)
O2 = MoleculeT(2, ElementT.O)
O = MoleculeT(1, ElementT.O)
H2O = CompoundT(MolecSet([H2, O]))
H2 = CompoundT(MolecSet([H2]))
O2 = CompoundT(MolecSet([O2]))
L = [H2, O2]
R = [H2O]
reaction = ReactionT(L, R)
cR = reaction.get_rhs_coeff()
assert cR[0] == 2
def test_get_lhs(self):
H2 = MoleculeT(2, ElementT.H)
O2 = MoleculeT(2, ElementT.O)
O = MoleculeT(1, ElementT.O)
H2O = CompoundT(MolecSet([H2, O]))
H2 = CompoundT(MolecSet([H2]))
O2 = CompoundT(MolecSet([O2]))
L = [H2, O2]
R = [H2O]
reaction = ReactionT(L, R)
l = reaction.get_lhs()
l = l[0].get_molec_set().s
l = l[0]
assert l.get_elm() == ElementT.H
assert l.get_num() == 2
def test_num_atoms(self):
oxy = MoleculeT(1, ElementT.O)
h2 = MoleculeT(2, ElementT.H)
h2o = CompoundT(MolecSet([h2, oxy]))
h_num = h2o.num_atoms(ElementT.H)
o_num = h2o.num_atoms(ElementT.O)
assert h_num == 2
assert o_num == 1
def test_get_molec_set(self):
oxy = MoleculeT(1, ElementT.O)
h2 = MoleculeT(2, ElementT.H)
h2o = CompoundT(MolecSet([h2, oxy]))
s = h2o.get_molec_set().to_seq()
assert s[0].get_elm() == ElementT.H
assert s[0].get_num() == 2
assert s[1].get_elm() == ElementT.O
assert s[1].get_num() == 1
def test_get_rhs(self):
H2 = MoleculeT(2, ElementT.H)
O2 = MoleculeT(2, ElementT.O)
O = MoleculeT(1, ElementT.O)
H2O = CompoundT(MolecSet([H2, O]))
H2 = CompoundT(MolecSet([H2]))
O2 = CompoundT(MolecSet([O2]))
L = [H2, O2]
R = [H2O]
reaction = ReactionT(L, R)
r = reaction.get_rhs()
r = r[0].get_molec_set().s
r1 = r[0]
r2 = r[1]
assert r1.get_elm() == ElementT.H
assert r1.get_num() == 2
assert r2.get_elm() == ElementT.O
assert r2.get_num() == 1
def setup_method(self, method):
self.s1 = Set([3, -6, 4, 0, 12, 9])
self.e1 = ElmSet([ElementT.H, ElementT.O])
self.m1 = MoleculeT(2, ElementT.H)
self.m2 = MoleculeT(7, ElementT.O)
self.m3 = MoleculeT(2, ElementT.H)
self.m4 = MoleculeT(2, ElementT.O)
self.m5 = MoleculeT(1, ElementT.O)
self.c1 = CompoundT(MolecSet([self.m1, self.m2]))
self.c2 = CompoundT(MolecSet([self.m3]))
self.c3 = CompoundT(MolecSet([self.m4]))
self.c4 = CompoundT(MolecSet([self.m3, self.m5]))
# 2 H2 + O2 --> 2 H2O
self.r1 = ReactionT([self.c2, self.c3], [self.c4])
# 2 N --> N2
self.m8 = MoleculeT(1, ElementT.N)
self.m9 = MoleculeT(2, ElementT.N)
self.c8 = CompoundT(MolecSet([self.m8]))
self.c9 = CompoundT(MolecSet([self.m9]))
self.r2 = ReactionT([self.c8], [self.c9])
def test_constit_elems(self):
O = MoleculeT(1, ElementT.O)
H2 = MoleculeT(2, ElementT.H)
H2O = CompoundT(MolecSet([H2, O]))
s = H2O.constit_elems()
assert s.s == [ElementT.H, ElementT.O]
R = Set([12, -6, 0, 1, 5])
print(S.equals(R))
print(S == R)
print(str(R.to_seq()))
for i in R.s:
print(i)
# ElmSet Examples
E = ElmSet([ElementT.H, ElementT.O])
E.add(ElementT.C)
print(E == ElmSet([ElementT.H, ElementT.C, ElementT.O]))
# MoleculeT Examples
M1 = MoleculeT(2, ElementT.H)
M2 = MoleculeT(7, ElementT.O)
print(M1.num_atoms(ElementT.C))
print(M1.constit_elems() == ElmSet([ElementT.H]))
print(M1.equals(M2))
print(M1 == M2)
# CompoundT Examples
C1 = CompoundT(MolecSet([M1, M2]))
print(C1.num_atoms(ElementT.H))
e = C1.constit_elems()
print(e.equals(ElmSet([ElementT.H, ElementT.O])))
print(C1.equals(CompoundT(MolecSet([M1]))))
# ElmSet Examples E = ElmSet([ElementT.H, ElementT.O]) E.add(ElementT.C) print(E == ElmSet([ElementT.H, ElementT.C, ElementT.O])) # MoleculeT Examples M1 = MoleculeT(2, ElementT.H) M2 = MoleculeT(7, ElementT.O) print(M1.num_atoms(ElementT.C)) print(M1.constit_elems() == ElmSet([ElementT.H])) print(M1.constit_elems().to_seq()) print(M1.equals(M2)) print(M1 == M2) # CompoundT Examples C1 = CompoundT(MolecSet([M1, M2])) print(C1.num_atoms(ElementT.H)) e = C1.constit_elems() print(e.to_seq()) print(e.equals(ElmSet([ElementT.H, ElementT.O]))) print(C1.equals(CompoundT(MolecSet([M1])))) # ReactionT Examples # H2 + O2 --> H2O M3 = MoleculeT(2, ElementT.H) M4 = MoleculeT(2, ElementT.O) C2 = CompoundT(MolecSet([M3])) C3 = CompoundT(MolecSet([M4])) M4 = MoleculeT(1, ElementT.O) C4 = CompoundT(MolecSet([M3, M4]))
def test_CompoundT_get_molec_set(self):
assert self.c1.get_molec_set() == MolecSet([self.m1, self.m2])
def test_equals_cmp():
assert iron_oxide.equals(CompoundT(MolecSet([iron2, oxygen3])))
assert not iron_oxide.equals(
CompoundT(MolecSet([MoleculeT(2, ElementT.H), oxygen3])))
def test_get_molec_set():
assert iron_oxide.get_molec_set() == MolecSet([iron2, oxygen3])
assert iron_oxide.get_molec_set() != MolecSet([ElementT.H, ElementT.Tc])
from MoleculeT import *
from CompoundT import *
from ReactionT import *
# Global varibale declarations
test_set = Set([1, 2, 3, 4, 5])
oxygen3 = MoleculeT(3, ElementT.O)
iron1 = MoleculeT(1, ElementT.Fe)
carbon1 = MoleculeT(1, ElementT.C)
iron2 = MoleculeT(2, ElementT.Fe)
oxygen2 = MoleculeT(2, ElementT.O)
oxygen1 = MoleculeT(1, ElementT.O)
hydrogen2 = MoleculeT(2, ElementT.H)
iron_oxide = CompoundT(MolecSet([iron2, oxygen3]))
carbon = CompoundT(MolecSet([carbon1]))
iron = CompoundT(MolecSet([iron1]))
carbon_oxide = CompoundT(MolecSet([carbon1, oxygen2]))
hydrogendioxide = CompoundT(MolecSet([hydrogen2, oxygen1]))
reaction1 = ReactionT([iron_oxide, carbon], [iron, carbon_oxide])
reaction2 = ReactionT([hydrogen2, oxygen2], [hydrogendioxide])
# testing Set
def test_add():
test_set.add(6)
assert test_set == Set([1, 2, 3, 4, 5, 6])
def __init__(self, molec_set):
self._C = MolecSet(molec_set.to_seq())