Allow charge generation to fail gracefully

[pgrinaway]

I was wondering if potentially we can allow (or have an option) to have this fail gracefully. Sometimes, a large number of molecules are passed in, some of which are malformed. We don't always want the entire function call to fail, especially after parameterizing a couple hundred molecules successfully. If it's ok, I could imagine a couple ways to handle this:

• The function can present a warning indicating the failing molecule
• The function can return a list of failures (or successes) to indicate to the caller what forcefield information has been generated.

We could also add a flag to the signature, default False, that would induce this behavior.

Is this reasonable, or might this break things? If it's reasonable, I'd be willing to do it.

[pgrinaway]

Maybe related to #201

[jchodera]

We could also add a flag to the signature, default False, that would induce this behavior.

Sounds great. How about we add ignoreFailures=False to the signature? The function can also return a list of failures in that case. Default behavior is to raise an exception.