[med-svn] [pdb2pqr] 01/01: updated README.test + README.Debian

[Tatiana Malygina]

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latticetower-guest pushed a commit to branch master
in repository pdb2pqr.

commit 68cb0a3cf33af690bd47c565fc468e9e8fbc77cc
Author: latticetower-guest <merlettaia at gmail.com>
Date:   Mon Jul 4 19:02:34 2016 +0300

    updated README.test + README.Debian
---
 debian/README.Debian |  9 +++++++++
 debian/README.test   | 55 +++++++++++++++++++++++++++++++++++++++++++++++++---
 debian/changelog     |  1 +
 3 files changed, 62 insertions(+), 3 deletions(-)

diff --git a/debian/README.Debian b/debian/README.Debian
index f79bf8f..4a29e0b 100644
--- a/debian/README.Debian
+++ b/debian/README.Debian
@@ -1,3 +1,12 @@
+PDB2PKA
+=======
+
+For now PDB2PQR doesn't produce any results with PDB2PKA, since it requires 
+specific versions of `apbs` package. It works only if `apbs` installed and command  
+`python -c "from apbslib import *"` doesn't produce error.
+
+ -- Tatiana Malygina  Mon, 4 Jul 2016 18:49:01 +0300
+ 
 PROPKA
 ======
 
diff --git a/debian/README.test b/debian/README.test
index 2872bbb..0f7efe5 100644
--- a/debian/README.test
+++ b/debian/README.test
@@ -11,7 +11,6 @@ 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
@@ -30,10 +29,60 @@ 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.
+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/
diff --git a/debian/changelog b/debian/changelog
index 30908b3..bc4be93 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -14,6 +14,7 @@ pdb2pqr (2.1.1+dfsg-2) unstable; urgency=medium
   * add networkx to d/control and test dependencies, mention in README.test
   * fix order of commands in debian/rules - override_dh_auto_configure:
     scons is now called after several files are regenerated with swig.
+  * updated README.test + README.Debian
 
   [ Andreas Tille ]
   * Drop unused lintian overrides

-- 
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