Python Porting about apbs

[sobolevnrm]

The overall approach outlined here looks great to me.

[ashermancinelli]

Closing for now in favor of interfacing C code with python and gradually porting as needed. We can reopen when this is again relevent.

[ashermancinelli]

Note also that the propka repo has an implementation of an Atom class (and other common utilities), though they are quite different from what we see in this repo. Perhaps when we have enough tests in place, we can use propka as a dependency and write implementations for the higher level algorithms in this repo using the classes in propka.

[ashermancinelli]

As per my conversation with @intendo offline, he and Arron Phillips will work on test cases which require a bit more domain knowledge, such as the methods atom_surface and accessable_outside_inflated_venderwalls_rad of the class AtomComplexCalc (formerly method ivdwAccExclus of class Vacc).

CC @sobolevnrm

[sobolevnrm]

Note also that the propka repo has an implementation of an Atom class (and other common utilities), though they are quite different from what we see in this repo. Perhaps when we have enough tests in place, we can use propka as a dependency and write implementations for the higher level algorithms in this repo using the classes in propka.

It would be outstanding if we could figure out how to expand the PROPKA Atom class to include the functionality we need in PDB2PQR.

[ashermancinelli]

It almost feels like we have the opposite situation with the PROPKA atom class - it seems to have an immense amount of data/behavior associated with it, and not much overlap with what we have here. But we can still investigate this 😄