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

This package can be tested by executing

    sh installation-test pdb2pka-test

in order to confirm its integrity.

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.

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

1. Call pdb2pqr with --apbs-input flag:

    pdb2pqr --ff PARSE --apbs-input 1FAS 1FAS.pqr
    
This example call produces file `1FAS.in`, which contains valid input data 
for `apbs`. Then call [2]:

  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]: Examples of apbs usage:
    http://www.poissonboltzmann.org/docs/apbs-invocation/
