* - Fixed a bug which prevented FMCS to work correctly on Windows when
linking to DLLs
* - removed spurious debugging info
- fixed function name
* - correct fix for the pyFMCS issue
* - the already existing macro RDKIT_WRAP_DECL is used in lieu of
RDFMCS_DLLIMPORT
* - this should fix the problem with "Inchi" being hardcoded into PostgreSQL
* - moved the InChI check code out of the main CMakeLists.txt
into FindInchi.cmake
* - calcImplicitValence() and setNumExplicitHs() are now called after
all aromaticity flags have been set
* - ChemicalForceFields.MMFFHasAllMoleculeParams() now operates on a copy of the molecule
such that atom and bond aromaticity are not altered by the check
- test11 was added to GraphMol/ForceFieldHelpers/Wrap/testHelpers.py to check
for the two bugs fixed by this PR
* - modified the prototype of MMFFHasAllMoleculeParams() to take a const ROMol&
and make a copy of that within the function body
- removed unnecessary imports from testHelpers.py
- replaced EmbedMolecule() with a quicker test
* - WIP
* - now the issue seems to be properly fixed, as the implicit valence
made explicit does not sum up anymore to the already explicit valence
* Fixes#982
also changes bond-wedging algorithm to favor lighter non-ring bonds
* prefer wedging bonds to lower-degree atoms
* Fixes#983
* small fixes
- Fix a problem where a chiral atom is selected to draw a wedge to instead of a ring atom
- Fix a problem where two calls to PrepareMolForDrawing() led to two wedged bonds from an atom.
* Fixes#985
This isn't the most satisfying solution (the wedged bonds are sometimes a bit too large), but it gives reasonable results on the test cases I've tried.
In Fedora land, format-security GCC warnings are treated as errors
so the build would fail like this:
In file included from /usr/include/pgsql/server/postgres.h:48:0,
from rdkit.h:40,
from mol_op.c:33:
mol_op.c:339:19: error: format not a string literal and no format arguments [-Werror=format-security]
elog(WARNING, t);
^
* A big step towards solving #910
1) Rank atoms by inverse atomic number (ensures Hs go last)
2) Use heavy-atom degree when doing layout (ensures Hs do not change gross geometry)
* basic testing
* take degree into account with ranks too
* further improvements of relative ranking.
definitely need some cleanup of this now
* some cleanup
* add an explicit test
* download junit.jar automatically when it is needed
* do not need to download junit anymore
* doc update
* try a different maven url to see if that solves the MD5 problems
* Fixes#852
The test added is the usual thing for the drawing code: produce some files for visual inspection.
* limit the number of lines in a short wedge
