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commit 2f96811d3a765076baf889cb1a0ba673985e8338 Author: latticetower-guest <[email protected]> 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 <[email protected]> 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 <[email protected]> -# 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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/pdb2pqr.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
