Most notably, added test cases for C++ and Python which just make sure
the code runs without crashing, no comparison of results with
existing test files.
* atoms: radical electrons and presence of a chiral tag
* bonds: presence of stereo
* add new atom queries to python wrapper
* add queries for missing atom chiral tags
* Fixes#1021, kind of.
The test for the bug passes, but there are other failures
* all tests except hanoi pass
* passes all tests
* remove some vestigial code
* remove debug-droppings
* minor documentation
* - 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
* Adds replaceCore function that takes a matchVect
* Fixes error reporting, adds tests
* Switches PRECONDITION to ValueError exceptions
* Fixes MatchVectType annoyance in swig. Don't know why this is necessary.
* Silences warnings
* Adds working doctests and better explanations.
* Add an initial version of wavy bonds
Used for attachment points and unknown stereochem
This is not a perfect implementation, but is a decent place to start
Currently only supports SVG and Cairo canvases.
* code review cleanup
* Adds Atom atom map and rlabel apis
* Moves RLabels to their own namespace, adds other properties.
* Removes namespaces, liberally adds Atom to function names.
* move detail::computedPropName to RDKit::detail::computedPropName
* Adds useChirality to replaceCore, fixes atom ordering
n.b. when replaceDummies==False and labelByIndex==True
the indices used are the indices of the dummy atom,
previously they were the atoms the dummy was connected
to.
* Adds useChirality to the remaining functions in ChemTransforms
* Adds a mess o tests
* Fixes labelByIndex=false ordering for dummies
* Removes debugging statements
* - 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.
* passes all tests, but is still not 100 percent there
* generalize _centerInVolume for possible future use
* better testing of tetrahedral centers
update tests
* only test ring atoms
* handle 4-coordinate n too
* add a volume check; not all tests pass
* turn off debug printing
* rearrange the order of tests.
if this is not done, we get a seg fault when the github55 test runs.
the whole thing needs to be run under valgrind to track this down
* clear up a memory leak
* a bit more documentation
add a constant for one of the threshold values
* get more permissive on the energy tests.
Only do the extra tetrahedral tests for atoms in at least two rings.
* add a DEBUG_EMBEDDING option to make tracking down failures easier
* enable better debugging when the flag is set
* remove a FIX
* remove some debug printing from the tests
