[med-svn] [pdb2pqr] branch master updated (b5c8aa5 -> 613e62e)
Andreas Tille
tille at debian.org
Thu Dec 31 07:52:15 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository pdb2pqr.
from b5c8aa5 Moved to Git
new 4cd2a48 Imported Upstream version 2.1.0+dfsg
new ba8d6d7 Merge tag 'upstream/2.1.0+dfsg'
new 3288c12 New upstream version
new 613e62e Add lintian overrides for false positives source-is-missing
The 4 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
3dmol/css/foundation.css | 6202 +
3dmol/css/pdb2pqr_3dmol.css | 542 +
3dmol/css/pure-min.css | 11 +
3dmol/css/toggles.css | 145 +
3dmol/css/ui_css.css | 10 +
3dmol/files/1fas.cube | 203213 ++++++++++++++++++
3dmol/images/rgb.png | Bin 0 -> 7523 bytes
3dmol/images/rwb.png | Bin 0 -> 6985 bytes
3dmol/js/3dmol.js.in | 420 +
3dmol/js/foundation.min.js | 6081 +
3dmol/js/foundation/foundation.abide.js | 340 +
3dmol/js/foundation/foundation.accordion.js | 67 +
3dmol/js/foundation/foundation.alert.js | 43 +
3dmol/js/foundation/foundation.clearing.js | 556 +
3dmol/js/foundation/foundation.dropdown.js | 448 +
3dmol/js/foundation/foundation.equalizer.js | 77 +
3dmol/js/foundation/foundation.interchange.js | 354 +
3dmol/js/foundation/foundation.joyride.js | 932 +
3dmol/js/foundation/foundation.js | 703 +
3dmol/js/foundation/foundation.magellan.js | 203 +
3dmol/js/foundation/foundation.offcanvas.js | 152 +
3dmol/js/foundation/foundation.orbit.js | 476 +
3dmol/js/foundation/foundation.reveal.js | 471 +
3dmol/js/foundation/foundation.slider.js | 263 +
3dmol/js/foundation/foundation.tab.js | 237 +
3dmol/js/foundation/foundation.tooltip.js | 307 +
3dmol/js/foundation/foundation.topbar.js | 452 +
3dmol/js/pitt_3Dmol.js | 31446 +++
3dmol/js/vendor/fastclick.js | 8 +
3dmol/js/vendor/jquery.cookie.js | 8 +
3dmol/js/vendor/jquery.js | 26 +
3dmol/js/vendor/modernizr.js | 8 +
3dmol/js/vendor/placeholder.js | 2 +
3dmol/js/visualize_html.js | 111 +
ChangeLog.md | 45 +-
INSTALL.md | 45 +-
README.md | 2 +-
SConscript-install.py | 2 +-
SConscript-main.py | 131 +-
ServerNotes.md | 72 +
apbs_cgi.py | 172 +-
build_config.py | 18 +-
debian/changelog | 7 +-
debian/source/lintian-overrides | 4 +
doc/PDB2PQR Release SOP.md | 39 +-
doc/flowchart.dot | 239 +
doc/pydoc/copy.html | 17 +-
doc/pydoc/getopt.html | 10 +-
doc/pydoc/index.html | 2 +
doc/pydoc/math.html | 75 +-
doc/pydoc/os.html | 59 +-
doc/pydoc/pdb2pqr.html | 23 +-
doc/pydoc/re.html | 28 +-
doc/pydoc/src.aa.html | 94 +-
doc/pydoc/src.definitions.html | 22 +-
doc/pydoc/src.forcefield.html | 7 +-
doc/pydoc/src.hydrogens.html | 14 +-
doc/pydoc/src.inputgen.html | 17 +-
doc/pydoc/src.na.html | 722 +-
doc/pydoc/src.pdb.html | 1667 +-
doc/pydoc/src.protein.html | 12 +-
doc/pydoc/src.psize.html | 13 +-
doc/pydoc/src.quatfit.html | 7 +-
doc/pydoc/src.routines.html | 83 +-
doc/pydoc/src.server.html | 19 +-
doc/pydoc/src.structures.html | 31 +-
doc/pydoc/src.topology.html | 7 +-
doc/pydoc/src.utilities.html | 10 +-
doc/pydoc/string.html | 29 +-
doc/pydoc/sys.html | 79 +-
doc/pydoc/time.html | 29 +-
doc/pydoc/xml.sax.html | 9 +-
dx2cube.py | 177 +
fabfile.py | 247 +
fabfile_settings.py | 26 +
html/server.html.in | 25 +-
js | 329 +
main.py | 298 +-
main_cgi.py | 4 +-
pdb2pka/apbs.py | 5 +-
pdb2pka/{ => graph_cut}/__init__.py | 0
pdb2pka/graph_cut/create_titration_output.py | 11 +
pdb2pka/graph_cut/graph.py | 113 +
pdb2pka/graph_cut/protein_complex.py | 756 +
pdb2pka/graph_cut/titration_curve.py | 227 +
pdb2pka/graph_cut/uncertainty.py | 101 +
pdb2pka/graph_cut/utils.py | 97 +
pdb2pka/pKa_base.py | 13 +-
pdb2pka/pMC_mult.cpp | 20 +
pdb2pka/pka_help.py | 58 +-
pdb2pka/pka_routines.py | 693 +-
pdb2pqr.spec | 21 +-
pdb2pqr_config.xml | 69 +-
pka.py | 70 +-
propka30/Source/determinants.py | 15 +-
querystatus.py | 467 +-
site_scons/defaults.py | 2 +-
site_scons/site_init.py | 17 +-
site_scons/test_tools.py | 156 +-
src/aa.py | 151 +-
src/pdb.py | 655 +-
src/routines.py | 233 +-
tests/SConscript | 29 +-
tests/pdb2pka-test/{ => 1a1p}/1a1p.pdb | 0
.../titration_curves/ARG_A_11.csv | 201 +
.../titration_curves/ASP_A_6.csv | 201 +
.../titration_curves/CTR_A_13.csv | 201 +
.../titration_curves/HIS_A_10.csv | 201 +
.../titration_curves/HIS_A_9.csv | 201 +
.../titration_curves/NTR_A_1.csv | 201 +
tests/pdb2pka-test/1a1p/test-output-correct.pqr | 233 +
tests/pdb2pka-test/1etm/1etm.pdb | 1006 +
.../titration_curves/CTR_A_17.csv | 201 +
.../titration_curves/GLU_A_7.csv | 201 +
.../titration_curves/NTR_A_6.csv | 201 +
tests/pdb2pka-test/1etm/test-output-correct.pqr | 220 +
tests/pdb2pka-test/2m0w/2m0w.pdb | 6793 +
.../titration_curves/ASP_A_1.csv | 201 +
.../titration_curves/CTR_A_23.csv | 201 +
.../titration_curves/LYS_A_23.csv | 201 +
.../titration_curves/NTR_A_1.csv | 201 +
.../titration_curves/TYR_A_11.csv | 201 +
tests/pdb2pka-test/2m0w/test-output-correct.pqr | 341 +
tests/pdb2pka-test/2m8f/2m8f.pdb | 7087 +
.../titration_curves/ASP_A_17.csv | 201 +
.../titration_curves/ASP_A_24.csv | 201 +
.../titration_curves/ASP_A_9.csv | 201 +
.../titration_curves/CTR_A_24.csv | 201 +
.../titration_curves/HIS_A_19.csv | 201 +
.../titration_curves/NTR_A_1.csv | 201 +
.../titration_curves/TYR_A_15.csv | 201 +
tests/pdb2pka-test/2m8f/test-output-correct.pqr | 359 +
tests/pdb2pka-test/SConscript | 25 +
tests/pdb2pka-test/test-output-correct.pqr | 235 -
visualize.py | 64 +-
visualize.py => visualize2.py | 21 +-
136 files changed, 280982 insertions(+), 2883 deletions(-)
create mode 100644 3dmol/css/foundation.css
create mode 100644 3dmol/css/pdb2pqr_3dmol.css
create mode 100644 3dmol/css/pure-min.css
create mode 100644 3dmol/css/toggles.css
create mode 100644 3dmol/css/ui_css.css
create mode 100644 3dmol/files/1fas.cube
create mode 100644 3dmol/images/rgb.png
create mode 100644 3dmol/images/rwb.png
create mode 100644 3dmol/js/3dmol.js.in
create mode 100644 3dmol/js/foundation.min.js
create mode 100644 3dmol/js/foundation/foundation.abide.js
create mode 100644 3dmol/js/foundation/foundation.accordion.js
create mode 100644 3dmol/js/foundation/foundation.alert.js
create mode 100644 3dmol/js/foundation/foundation.clearing.js
create mode 100644 3dmol/js/foundation/foundation.dropdown.js
create mode 100644 3dmol/js/foundation/foundation.equalizer.js
create mode 100644 3dmol/js/foundation/foundation.interchange.js
create mode 100644 3dmol/js/foundation/foundation.joyride.js
create mode 100644 3dmol/js/foundation/foundation.js
create mode 100644 3dmol/js/foundation/foundation.magellan.js
create mode 100644 3dmol/js/foundation/foundation.offcanvas.js
create mode 100644 3dmol/js/foundation/foundation.orbit.js
create mode 100644 3dmol/js/foundation/foundation.reveal.js
create mode 100644 3dmol/js/foundation/foundation.slider.js
create mode 100644 3dmol/js/foundation/foundation.tab.js
create mode 100644 3dmol/js/foundation/foundation.tooltip.js
create mode 100644 3dmol/js/foundation/foundation.topbar.js
create mode 100644 3dmol/js/pitt_3Dmol.js
create mode 100644 3dmol/js/vendor/fastclick.js
create mode 100644 3dmol/js/vendor/jquery.cookie.js
create mode 100644 3dmol/js/vendor/jquery.js
create mode 100644 3dmol/js/vendor/modernizr.js
create mode 100644 3dmol/js/vendor/placeholder.js
create mode 100644 3dmol/js/visualize_html.js
create mode 100644 ServerNotes.md
create mode 100644 debian/source/lintian-overrides
create mode 100644 doc/flowchart.dot
create mode 100644 dx2cube.py
create mode 100644 fabfile.py
create mode 100644 fabfile_settings.py
create mode 100644 js
copy pdb2pka/{ => graph_cut}/__init__.py (100%)
create mode 100644 pdb2pka/graph_cut/create_titration_output.py
create mode 100644 pdb2pka/graph_cut/graph.py
create mode 100644 pdb2pka/graph_cut/protein_complex.py
create mode 100644 pdb2pka/graph_cut/titration_curve.py
create mode 100644 pdb2pka/graph_cut/uncertainty.py
create mode 100644 pdb2pka/graph_cut/utils.py
rename tests/pdb2pka-test/{ => 1a1p}/1a1p.pdb (100%)
create mode 100644 tests/pdb2pka-test/1a1p/pdb2pka-output-correct/titration_curves/ARG_A_11.csv
create mode 100644 tests/pdb2pka-test/1a1p/pdb2pka-output-correct/titration_curves/ASP_A_6.csv
create mode 100644 tests/pdb2pka-test/1a1p/pdb2pka-output-correct/titration_curves/CTR_A_13.csv
create mode 100644 tests/pdb2pka-test/1a1p/pdb2pka-output-correct/titration_curves/HIS_A_10.csv
create mode 100644 tests/pdb2pka-test/1a1p/pdb2pka-output-correct/titration_curves/HIS_A_9.csv
create mode 100644 tests/pdb2pka-test/1a1p/pdb2pka-output-correct/titration_curves/NTR_A_1.csv
create mode 100644 tests/pdb2pka-test/1a1p/test-output-correct.pqr
create mode 100644 tests/pdb2pka-test/1etm/1etm.pdb
create mode 100644 tests/pdb2pka-test/1etm/pdb2pka-output-correct/titration_curves/CTR_A_17.csv
create mode 100644 tests/pdb2pka-test/1etm/pdb2pka-output-correct/titration_curves/GLU_A_7.csv
create mode 100644 tests/pdb2pka-test/1etm/pdb2pka-output-correct/titration_curves/NTR_A_6.csv
create mode 100644 tests/pdb2pka-test/1etm/test-output-correct.pqr
create mode 100644 tests/pdb2pka-test/2m0w/2m0w.pdb
create mode 100644 tests/pdb2pka-test/2m0w/pdb2pka-output-correct/titration_curves/ASP_A_1.csv
create mode 100644 tests/pdb2pka-test/2m0w/pdb2pka-output-correct/titration_curves/CTR_A_23.csv
create mode 100644 tests/pdb2pka-test/2m0w/pdb2pka-output-correct/titration_curves/LYS_A_23.csv
create mode 100644 tests/pdb2pka-test/2m0w/pdb2pka-output-correct/titration_curves/NTR_A_1.csv
create mode 100644 tests/pdb2pka-test/2m0w/pdb2pka-output-correct/titration_curves/TYR_A_11.csv
create mode 100644 tests/pdb2pka-test/2m0w/test-output-correct.pqr
create mode 100644 tests/pdb2pka-test/2m8f/2m8f.pdb
create mode 100644 tests/pdb2pka-test/2m8f/pdb2pka-output-correct/titration_curves/ASP_A_17.csv
create mode 100644 tests/pdb2pka-test/2m8f/pdb2pka-output-correct/titration_curves/ASP_A_24.csv
create mode 100644 tests/pdb2pka-test/2m8f/pdb2pka-output-correct/titration_curves/ASP_A_9.csv
create mode 100644 tests/pdb2pka-test/2m8f/pdb2pka-output-correct/titration_curves/CTR_A_24.csv
create mode 100644 tests/pdb2pka-test/2m8f/pdb2pka-output-correct/titration_curves/HIS_A_19.csv
create mode 100644 tests/pdb2pka-test/2m8f/pdb2pka-output-correct/titration_curves/NTR_A_1.csv
create mode 100644 tests/pdb2pka-test/2m8f/pdb2pka-output-correct/titration_curves/TYR_A_15.csv
create mode 100644 tests/pdb2pka-test/2m8f/test-output-correct.pqr
create mode 100644 tests/pdb2pka-test/SConscript
delete mode 100644 tests/pdb2pka-test/test-output-correct.pqr
copy visualize.py => visualize2.py (78%)
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