Package: pdb2pqr / 2.1.1+dfsg-7

Metadata

Package Version Patches format
pdb2pqr 2.1.1+dfsg-7 3.0 (quilt)

Patch series

view the series file
Patch File delta Description
fix hashbangs.patch | (download)

pdb2pka/inputgen_pKa.py | 2 1 + 1 - 0 !
propka30/Source/corresponding_atoms.py | 2 1 + 1 - 0 !
propka30/Source/rotate.py | 2 1 + 1 - 0 !
propka30/propka.py | 2 1 + 1 - 0 !
4 files changed, 4 insertions(+), 4 deletions(-)

 fixes "broken" hashbangs
no_privacy_breach_logo.patch | (download)

doc/userguide.html | 2 1 + 1 - 0 !
examples/index.html | 2 1 + 1 - 0 !
html/master-index.html | 4 1 + 3 - 0 !
3 files changed, 3 insertions(+), 5 deletions(-)

 remove potential privacy breach logo


do_not_try_to_build_removed_js_target.patch | (download)

SConscript-main.py | 3 1 + 2 - 0 !
1 file changed, 1 insertion(+), 2 deletions(-)

 since some minimised js files without source were
 contained inside the upstream source which are not used in the
 resulting binary package these were removed from the source.
 This patch prevents the build system from accessing missing files.


fix_hardening_no_relro | (download)

SConscript-main.py | 3 3 + 0 - 0 !
1 file changed, 3 insertions(+)

 this fix prevents hardening-no-relro warning from appearing during
 lintian run
 

fix_no_debug_symbols_warning | (download)

build_config.py | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 this fix prevents debug-file-with-no-debug-symbols warning from 
appearing during lintian run


spelling.patch | (download)

pdb2pka/substruct/Algorithms.cpp | 4 2 + 2 - 0 !
1 file changed, 2 insertions(+), 2 deletions(-)

 fix spelling
python3_PR516.patch | (download)

apbs_cgi.py | 2 1 + 1 - 0 !
conf_avg/Ensemble_phimap.py | 1 0 + 1 - 0 !
extensions/__init__.py | 8 4 + 4 - 0 !
extensions/newresinter.py | 12 6 + 6 - 0 !
extensions/resinter.py | 8 4 + 4 - 0 !
extensions/salt.py | 2 1 + 1 - 0 !
main.py | 26 13 + 13 - 0 !
main_cgi.py | 12 6 + 6 - 0 !
pdb2pka/pKa_utility_functions_compat.py | 2 1 + 1 - 0 !
pdb2pka/pka_old.py | 1 0 + 1 - 0 !
pdb2pka/pka_routines.py | 4 2 + 2 - 0 !
pdb2pqr.py.in | 2 1 + 1 - 0 !
pka.py | 1 0 + 1 - 0 !
querystatus.py | 2 1 + 1 - 0 !
src/aa.py | 4 2 + 2 - 0 !
src/definitions.py | 12 6 + 6 - 0 !
src/forcefield.py | 10 5 + 5 - 0 !
src/hydrogens.py | 24 12 + 12 - 0 !
src/inputgen.py | 33 20 + 13 - 0 !
src/na.py | 2 1 + 1 - 0 !
src/pdb.py | 906 453 + 453 - 0 !
src/protein.py | 16 8 + 8 - 0 !
src/psize.py | 18 9 + 9 - 0 !
src/quatfit.py | 2 1 + 1 - 0 !
src/routines.py | 54 29 + 25 - 0 !
src/server.py | 2 1 + 1 - 0 !
src/server.py.in | 2 1 + 1 - 0 !
src/structures.py | 44 22 + 22 - 0 !
src/topology.py | 22 11 + 11 - 0 !
src/utilities.py | 10 7 + 3 - 0 !
30 files changed, 628 insertions(+), 616 deletions(-)

---
python3_scons.patch | (download)

SConscript-error.py | 10 5 + 5 - 0 !
SConscript-install.py | 2 1 + 1 - 0 !
SConscript-main.py | 102 51 + 51 - 0 !
fabfile.py | 28 14 + 14 - 0 !
scons/scons-time.py | 44 22 + 22 - 0 !
scons/scons.py | 4 2 + 2 - 0 !
scons/sconsign.py | 42 21 + 21 - 0 !
site_scons/site_init.py | 32 16 + 16 - 0 !
site_scons/test_tools.py | 22 11 + 11 - 0 !
tests/complete-test/SConscript | 4 2 + 2 - 0 !
10 files changed, 145 insertions(+), 145 deletions(-)

 use 2to3 to port from python2 to python3
Bug-Debian: https://bugs.debian.org/937262
python3_sundry.patch | (download)

main_cgi.py | 114 57 + 57 - 0 !
pdb2pka/NEWligand_topology.py | 68 34 + 34 - 0 !
pdb2pka/apbs.py | 14 7 + 7 - 0 !
pdb2pka/charge_mon.py | 10 5 + 5 - 0 !
pdb2pka/example.py | 20 10 + 10 - 0 !
pdb2pka/graph_cut/create_titration_output.py | 2 1 + 1 - 0 !
pdb2pka/graph_cut/graph.py | 6 3 + 3 - 0 !
pdb2pka/graph_cut/protein_complex.py | 52 26 + 26 - 0 !
pdb2pka/graph_cut/titration_curve.py | 18 9 + 9 - 0 !
pdb2pka/graph_cut/uncertainty.py | 2 1 + 1 - 0 !
pdb2pka/graph_cut/utils.py | 8 4 + 4 - 0 !
pdb2pka/inputgen_pKa.py | 10 5 + 5 - 0 !
pdb2pka/ligand_topology.py | 86 43 + 43 - 0 !
pdb2pka/ligandclean/ligff.py | 36 18 + 18 - 0 !
pdb2pka/ligandclean/peoe_PDB2PQR.py | 8 4 + 4 - 0 !
pdb2pka/pKaIO_compat.py | 114 57 + 57 - 0 !
pdb2pka/pKa_utility_functions_compat.py | 2 1 + 1 - 0 !
pdb2pka/pMC_mult.py | 6 3 + 3 - 0 !
pdb2pka/pka_help.py | 12 6 + 6 - 0 !
pdb2pka/pka_old.py | 70 35 + 35 - 0 !
pdb2pka/pka_routines.py | 156 78 + 78 - 0 !
pdb2pka/prepare_pKa_ligand.py | 84 42 + 42 - 0 !
pdb2pka/substruct/Algorithms.cpp | 20 17 + 3 - 0 !
pka.py | 56 28 + 28 - 0 !
propka30/Source/bonds.py | 10 5 + 5 - 0 !
propka30/Source/calculator.py | 8 4 + 4 - 0 !
propka30/Source/chain.py | 6 3 + 3 - 0 !
propka30/Source/compare.py | 10 5 + 5 - 0 !
propka30/Source/corresponding_atoms.py | 2 1 + 1 - 0 !
propka30/Source/coupled_residues.py | 2 1 + 1 - 0 !
propka30/Source/debug.py | 14 7 + 7 - 0 !
propka30/Source/determinants.py | 10 5 + 5 - 0 !
propka30/Source/iterative.py | 6 3 + 3 - 0 !
propka30/Source/lib.py | 8 4 + 4 - 0 !
propka30/Source/ligand.py | 10 5 + 5 - 0 !
propka30/Source/mutate.py | 68 34 + 34 - 0 !
propka30/Source/output.py | 8 4 + 4 - 0 !
propka30/Source/parameters.py | 12 6 + 6 - 0 !
propka30/Source/parameters_new.py | 4 2 + 2 - 0 !
propka30/Source/parameters_std.py | 4 2 + 2 - 0 !
propka30/Source/pdb.py | 14 7 + 7 - 0 !
propka30/Source/protein.py | 50 25 + 25 - 0 !
propka30/Source/protonate.py | 8 4 + 4 - 0 !
propka30/Source/protonator.py | 16 8 + 8 - 0 !
propka30/Source/residue.py | 14 7 + 7 - 0 !
propka30/Source/rotate.py | 10 5 + 5 - 0 !
propka30/Source/vector_algebra.py | 6 3 + 3 - 0 !
propka30/Source/version.py | 56 28 + 28 - 0 !
propka30/compare.py | 2 1 + 1 - 0 !
propka30/experiment.py | 4 2 + 2 - 0 !
propka30/propka.py | 6 3 + 3 - 0 !
propka30/propka_det.py | 10 5 + 5 - 0 !
propka30/propka_gui.py | 10 5 + 5 - 0 !
propka30/propka_mut.py | 12 6 + 6 - 0 !
propka30/propka_pdb.py | 6 3 + 3 - 0 !
querystatus.py | 166 83 + 83 - 0 !
56 files changed, 780 insertions(+), 766 deletions(-)

 use 2to3 to port from python2 to python3
Bug-Debian: https://bugs.debian.org/937262
python3_scriptbang.patch | (download)

src/psize.py | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

---
use_pkg config.patch | (download)

SConscript-main.py | 3 2 + 1 - 0 !
1 file changed, 2 insertions(+), 1 deletion(-)

 use pkg-config to correctly detect libpython3.7m
reproducible build.patch | (download)

src/aconf.py.in | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 make the build reproducible