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

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

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.

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

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

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

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

 fix spelling

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(-)

---

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

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/experiment.py | 2 1 + 1 - 0 !
propka30/propka.py | 4 2 + 2 - 0 !
propka30/propka_det.py | 6 3 + 3 - 0 !
propka30/propka_gui.py | 6 3 + 3 - 0 !
propka30/propka_mut.py | 8 4 + 4 - 0 !
propka30/propka_pdb.py | 4 2 + 2 - 0 !
querystatus.py | 166 83 + 83 - 0 !
55 files changed, 770 insertions(+), 756 deletions(-)

 use 2to3 to port from python2 to python3
Bug-Debian: https://bugs.debian.org/937262

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

---

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

 use pkg-config to correctly detect libpython3.7m

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

 make the build reproducible