* Fixes#2311
at least I hope it does
* Stop using deprecated boost functionality
* allow the Murtagh module to import even if the code isn't built
update the associated tests
* update release notes
* typo
* fix integer division
* modify the uncharger to be use a canonical atom ordering
* add doCanonical cleanup parameter
make canonical ordering the default
document the change
* Add neutralization of additonal negative groups (not just acids).
This may not be the right thing to do.
* expose the new parameter to python
* changes in response to review
* remove all of the "from __future__" imports
* remove the first batch of rdkit.six imports/uses
* next step of rdkit.six removal
* removing xrange, range, and some maps
* next round of removals
* next round of cleanups
* fix inchi test
* last bits of "from rdkit.six" are gone
* and the last of the six stuff is gone
* strange importlib problem
* Add more options to GetAtomSmiles() to control output.
The most important one here is that you can now directly control whether or not isomeric SMILES is generated.
Expand the python interface so that we have more control over Atom.GetSmarts()
* make the use of isomeric atomic smiles explicit (since we can)
* start release notes for 2018.09.1
* python formatting
* this is a rough first pass, needs to be finished and is a strong argument for changing the names of some of the #defines that are currently used
* rationalize the rest of the #defines
add something to the release notes about this
* first pass, does not yet actually work
* pass2, same problems
* pass2, same problems
* another test
* new tests; bugfix
* move the code out to a header
* add a double bond example
* enable auto-downloads of the code
* move the function to its own namespace
* first pass at a basic python wrapper
* change coordgen commit used
* try supporting bond stereo; does not currently work
* cis/trans seems to now work.
* first pass at templates; needs testing
* use the fixed flag too
* need mol align
* expand test
* initial pass at python wrapper for template
* simplify tests
* add an option to directly use a substructure match for alignment
* scaling
* add #define
* Define a cache setting for RDK_COORDGEN_LIBS to allow these to be used in other packages
* return the conformer id from addCoords
* Make CoordGen the default when it’s available.
This is a backup commit… the tests don’t even come close to passing.
* add some debugging options for a bit
* add alignment step to testing when using non-fixed coords
* Add global to allow use of CoordGen to be disabled
get the basic depictor tests working
* make coordgen the default when it is available
* make sure things continue to work when coordgen is disabled
* get windows builds working
* mods to get this building on windows.
something is screwy with the fileParsersTest1
* no need to generate coords for the 1K C string
* fix java wrappers
* works on linux
* update the (stupid) way dependencies were handled on windows.
this allows a lot of cleanup of cmake files (still more to do)
the linux build is unlikely to work due to the way _statics aren't handled
* docs
* extend forceRDKit applicability
* switch coordgen version
* try using templates
* try to get the template dir finding reasonably robust w.r.t. conda install
* continuing to iterate on the way the template file is installed
* fix a problem caused by the merge
* remove test that should never have been checked in
* update expected results for cartridge tests
* switch back to using the RDKit as the default coordinate generator
* auto generate coords in mol block writer if includeChirality = True
* default to include chirality when writing mol blocks/files
* make isomeric smiles the default; note that not all tests are passing at the moment
* update a reaction test
* update expected cartridge search results
at this point all python, c++, and cartridge tests pass
* docs
* update incompatibility docs
* update doctests
* these now build
* minor example update
* update expected c++
* typo
* make allowCXSMILES=true the default
* add auto perception of chirality when reading 3D structures from mol blocks
* explain changes in release notes
* further doc update
* Fixes exceptions to use correct functionName
* Deprecates ChemDrawAdjustParams name sciquest integration/eln searching
doesn’t map to this behavior. renamed MatchOnlyAtRgroupAdjustParams
* Python wrapper for deprecated API
* fixHs now is more intelligent about merging hs.
The only cases where hs can’t be merged is if they are mapped
to a non hydrogen in the product.
* Updates deprecated ChemDrawAdjustParams
