Notes on how this package can be tested.
────────────────────────────────────────

This package can be tested by executing

    sh installation-test

in order to confirm its integrity.

If you have both pdb2pqr and pdb2pqr-doc packages installed, you can test their
installation by executing

    sh ligands-test

During data processing, pdb2pqr can write multiple warning messages to stderr. 
This output means that PDB file contains erranous data, which could be repaired
by pdb2pqr. In `installation-test` and other test scripts these messages should 
appear. For this to be processed in autopkgtest testsuite, `allow-stderr` restriction 
is set.

To test manually, run `pdb2pqr` like this (program output will be saved to 
`output.txt` in current directory):

```
pdb2pqr --ff=amber <valid PDB ID> output.txt
```

Possible PDB IDs can be found in RCSB PDB database [1] and other sources.

To see other options, call `pdb2pqr` without parameters or with `-h` key.

Notes on PDB2PKA-test
───────────────────────

For now this test is turned off:

    sh pdb2pka-test

It requires `apbs` package with python support to see any sensible results.
For now current version of `apbs` package doesn't seem to install apbs with 
corresponding headers. 

When --ph-calc-method=pdb2pka is used during `pdb2pqr` run, package requires 
python `networkx` library to be installed. Test `pdb2pka-test` passes only if 
this library is installed, otherwise it fails with corresponding error message. 

It doesn't fail because of `apbs` installation, but it also doesn't produce any
sensible results. When `pdb2pqr` is run like this:

    pdb2pqr --with-ph=7.0 --ph-calc-method=pdb2pka --ff=parse --verbose 1a1p 1a1p.pqr

- tail of program's output look like this:

    Missing libraries for interfacing with APBS
    You need to build APBS with Python support using the CMake variable 
    -DENABLE_PYTHON=ON.

- even if `apbs` is compiled and installed with -DENABLE_PYTHON flag. 
This output message indicates that command 

    python -c "from apbslib import *" 

- raised python's ImportError.

How to use APBS with PDB2PQR anyway
───────────────────────────────────

1. Call pdb2pqr with --apbs-input flag (since pdb2pka doesn't work, 
--ph-calc-method=propka must be used, other arguments can vary) [2]:

    pdb2pqr.py --ff=parse --apbs-input --ph-calc-method=propka 1FAS 1FAS.pqr
    
- this example call produces file `1FAS.in`, which contains valid input data 
for `apbs`. Then call [3]:

  apbs 1FAS.in

The result of this call is valid, but probably differs from `pdb2pqr` call with
pdb2pka method.

References:

[1]: RCSB PDB database (one of the possible sources of .pdb files)
    http://www.rcsb.org/pdb/home/home.do
[2]: PDB2PQR options 
    http://www.poissonboltzmann.org/docs/pdb2pqr-usage/
[3]: Examples of apbs usage:
    http://www.poissonboltzmann.org/docs/apbs-invocation/
