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
* - 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
There seems to be a problem in some travis builds where some java wrapper files aren't finished writing before the next step of the build happens. This is an attempt to resolve that.
* refactored Bfp indexing and similarity search
* update CMakeLists.txt
* catch (and fix) inconsistent options around building static libs
* differentiate the data structures in inner and leaf pages
* code cleanup and some additional comments
* version bump
* fix renaming of cache function
* minor cleanup
* add -DUSE_BUILTIN_POPCOUNT to ${POPCOUNTFLAGS}
