Surprising result from formula()

[bjodah]

I would expect this to output 4, not 3:

>>> periodictable.formula('NH3 + H{+}').atoms[periodictable.H]
3

Py 2.7, periodictable 1.4.1

[bjodah]

So there is a distinction between ions and elements, I wrote a small utility function to get the elements of a formula:

from collections import defaultdict
def elements(formula):                                                                                        
    d = defaultdict(int)
    for atm, n in formula.atoms.items():
        try:
            d[atm.element] += n
        except AttributeError:
            d[atm] += n
    return d

Would it be of interest to have such a method in formulas.Formula? (I could open a PR)

[pkienzle]

The H+ is indexed as an ion:

>>> f = periodictable.formula('NH3 + H{+}')
>>> f.atoms
{H: 3, N: 1, H.ion[1]: 1}
>>> f.hill
formula('H3H{+}N')

It was easy enough to have ions treated as elements as far as counting is concerned:

>>> f = periodictable.formula('NH3 + D{+}')
>>> f.atoms
{H: 4, N: 1}
>>> f.isotopes
{H: 3, N: 1, H[2]: 1}
>>> f.ions
{H: 3, N: 1, H[2].ion[1]: 1}
>>> f.hill
formula('H4N')
>>> f.charge
1

I haven't checked it in yet. Before doing so I need to cross check the rest of the code base for whether f.atoms should change to f.isotopes or f.ions.

[pkienzle]

Looking at your alternative, leaving f.atoms alone and adding f.elements and f.isotopes is another way to go. This has the advantage of not changing the existing interface, but with the disadvantage of a more confusing naming scheme.

[bjodah]

I understand your dilemma between backwards compatibility and API cleanliness, nobody likes getting code broken..

On an unrelated note (didn't know if it's worth adding an issue for it): periodictable.formula('H{-}') raises a ValueError claiming -1 is not a valid charge for H, even though this is the hydride anion. Other physically sound examples raises this exception, e.g. He{+}.

[pkienzle]

I didn't document my source of oxidation states. I'll add a ticket saying some are missing.

[pkienzle]

I added count_elements() to accumulate across isotopes/ions.