apbs/README.md

APBS - Adaptive Poisson-Boltzmann Solver

This repository contains the APBS software.

For more information about APBS, please see

• Home page: http://www.poissonboltzmann.org/
• Documentation: http://apbs.readthedocs.io

Python Package

Note: under heavy devlopment

Development dependencies:

• SWIG >4.0
• GCC capable of C++17 (recommended >=7.5.0)
• pip >=19

To install the python package, use the following:

$ python setup.py build
$ python setup.py install

To use the python module:

>>> import apbs
>>>
>>> # access bits of APBS already ported to python
>>> from apbs import (
>>>     chemistry,
>>>     geometry,
>>>     grid,
>>>     multigrid,
>>>     pqr,
>>>     )
>>>
>>> # To access swig bindings to the C code:
>>> from apbs.bindings.swig import *
>>>
>>> # To access pybind bindings to the C code:
>>> from apbs.bindings.pybind import *
>>>
>>> # To get path to binaries:
>>> apbs.bin.get_path()
>>>
>>> # To get path to libraries:
>>> apbs.lib.get_path()

Or, to run apbs binaries directly without having to change your path:

$ # run apbs on the input file `input.mol`, and 
$ python -m apbs apbs input.mol
$
$ # return the help message for the apbs binary.
$ python -m apbs apbs --help
$
$ # view available binaries
$ python -m apbs --list