File: README.test

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pdb2pqr 2.1.1%2Bdfsg-2
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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
    sh pdb2pka-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.

When --ph-calc-method=pdb2pka is used, package requires python networkx library
to be installed. Test `pdb2pka-test` passes only if this library is installed.

References:

[1]: RCSB PDB database (one of the possible sources of .pdb files)
    http://www.rcsb.org/pdb/home/home.do