def fill(t, p):
"""Takes a flattened list of Atom objects and adds hydrogen atoms to them where appropriate.
t: list of Atom objects
p: Parser object"""
res = copy.copy(t)
for j in range(len(t)):
atom = t[j]
if isinstance(atom, Atom.Atom):
num_h = 4 - len(
atom.bonds
) #Since Atom objects cannot have more than 4 bonds, the only spaces that remain must belong to hydrogens.
# print num_h
if num_h > 0:
for n in range(
num_h
): #for every space that remains in atom.bonds, append a Hydrogen object to the bonds list.
hyd = Atom.Hydrogen('H' + str(p.i))
res.append(hyd)
final_atom = res[j]
final_atom.bonds.append(hyd)
p.i += 1
else:
fill(t[j], p)
return res
def fill_hydrogens(t):
"""Takes a flattened list of Atom objects (from the function flatten()) and fills in all the missing hydrogen Atoms such that each Atom object has four bonds.
t: list of Atom objects
Returns: list of Atom objects.
"""
i = 0
res = copy.copy(t)
#for debugging/testing purposes -- can delete later! This variable will keep count of the number of hydrogens added at a given point in time.
c = 0
for j in range(len(t)):
atom = t[j]
num_h = 4 - len(
atom.bonds
) #Since Atom objects cannot have more than 4 bonds, the only spaces that remain must belong to hydrogens.
# print num_h
if num_h > 0:
#Again, these two lines are for debugging purposes only. Delete them if you do not want extra output.
c += num_h
print c
for n in range(
num_h
): #for every space that remains in atom.bonds, append a Hydrogen object to the bonds list.
print('Adding a Hydrogen')
hyd = Atom.Hydrogen('H' + str(i))
res.append(hyd)
final_atom = res[j]
final_atom.bonds.append(hyd)
i += 1
return res
