[med-svn] [pdb2pqr] 01/02: pdb2pka-test fixed

[Tatiana Malygina]

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

commit 2f96811d3a765076baf889cb1a0ba673985e8338
Author: latticetower-guest <merlettaia at gmail.com>
Date:   Wed Jun 15 02:09:50 2016 +0300

    pdb2pka-test fixed
    
    1. fixed "ImportError: no module named pka", appearing in pdb2pka-test
    2. added pdb2pka/graph_cut/* files to corresponding dir in d/pdb2pqr.install
---
 debian/changelog          |  1 +
 debian/pdb2pqr.install    |  2 ++
 debian/tests/pdb2pka-test | 17 +++--------------
 3 files changed, 6 insertions(+), 14 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 0ae0d03..72b7a10 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -8,6 +8,7 @@ pdb2pqr (2.1.1+dfsg-2) UNRELEASED; urgency=medium
     without it
   * found parameter set when error raised (described in `pdb2pka-test` 
     in testsuite), updated d/docs
+  * fixed `pdb2pqr-test` - now should work ok (haven't checked with apbs yet)
 
  -- Tatiana Malygina <merlettaia at gmail.com>  Mon, 13 Jun 2016 15:31:19 +0000
 
diff --git a/debian/pdb2pqr.install b/debian/pdb2pqr.install
index b9099c8..e03c590 100644
--- a/debian/pdb2pqr.install
+++ b/debian/pdb2pqr.install
@@ -1,5 +1,6 @@
 pdb2pqr.py			usr/share/pdb2pqr/
 main.py				usr/share/pdb2pqr/
+pka.py				usr/share/pdb2pqr/
 main_cgi.py			usr/share/pdb2pqr/
 dat/*				usr/share/pdb2pqr/dat/
 extensions/*			usr/share/pdb2pqr/extensions/
@@ -7,6 +8,7 @@ src/*				usr/share/pdb2pqr/src/
 pdb2pka/*.py			usr/share/pdb2pqr/pdb2pka
 pdb2pka/ligandclean/*.py	usr/share/pdb2pqr/pdb2pka/ligandclean
 pdb2pka/substruct/*.py		usr/share/pdb2pqr/pdb2pka/substruct
+pdb2pka/graph_cut/*.py		usr/share/pdb2pqr/pdb2pka/graph_cut
 propka30/*			usr/share/pdb2pqr/propka30/
 # Binary parts
 pdb2pka/_pMC_mult.so		usr/lib/pdb2pqr/pdb2pka
diff --git a/debian/tests/pdb2pka-test b/debian/tests/pdb2pka-test
index 25e001d..f6859d3 100644
--- a/debian/tests/pdb2pka-test
+++ b/debian/tests/pdb2pka-test
@@ -1,7 +1,6 @@
 #!/bin/sh
 # autopkgtest check: build and run with default test data
 # Author: Tatiana Malygina <merlettaia at gmail.com>
-# this test is turned off now - currently raises error, explained in comments.
 
 set -e
 
@@ -24,17 +23,7 @@ done
 
 echo "Run pdb2pqr..."
 
-## following fails (this call also present in fabfile.py):
 pdb2pqr --with-ph=7.0 --ph-calc-method=pdb2pka --ff=parse --verbose 1a1p 1a1p.pqr
-## Traceback:
-## Running PDB2PKA and applying at pH 7.00... 
-## Traceback (most recent call last):
-##  File "/usr/bin/pdb2pqr", line 62, in <module>
-##    mainCommand(sys.argv)
-##  File "/usr/share/pdb2pqr/main.py", line 740, in mainCommand
-##    include_old_header = options.include_header)
-##  File "/usr/share/pdb2pqr/main.py", line 341, in runPDB2PQR
-##    myRoutines.runPDB2PKA(ph, ff, pdblist, ligand, verbose, ph_calc_options)
-##  File "/usr/share/pdb2pqr/src/routines.py", line 1503, in runPDB2PKA
-##    import pka
-## ImportError: No module named pka
+# error messages fixed, at my VM this still appears:
+## Missing libraries for interfacing with APBS
+## You need to build APBS with Python support using the CMake variable -DENABLE_PYTHON=ON.

-- 
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