* Fixes#1990
makes sure we don't destroy a double bond's StereoAtoms just because a bond connected to one of its atoms is removed
* change in response to review
The curl file download fallback option was not saving files as
the correct filename. Instead, it used the -O option, which
saved the files using the remote's name for the file! This
was problematic for files downloaded using specification of git
sha.
* spelling
* Allow types.h to be included in applications that set _USE_MATH_DEFINES
Our application defines _USE_MATH_DEFINES on the visual studio
compiler command line, so every compilation includes the macro
definition. Including types.h (or anything other RDKit header,
basically) causes compilation to fail with a "doubly defined
macro" error message.
This commit defines the macro locally and only if it is not already
defined
* Fixes#1454; still needs a bit more thinking though
* forgot the necessary version bump
* review related cleanup and a fix to allow the SWIG wrappers to be built
* remove a bunch of MSVC compiler warnings
* remove a compiler warning
* try running tests in appveyor
* typo
* investigation
* is the problem the os item?
* investigation
* output on test errors
* if only I could type
* suppress some warnings on windows (and remove a bogus attempt at doing so)
* build without serialization
* this should have been noticed for #1767
* Fixes#1810
There's still a problem with stereo atoms (see the commented out test),
but this takes care of the basics and that's up next.
* clean up that last problematic bit.
Still needs all tests to run
* this seems to be a necessary workaround for problems with VS2017.
It's a bit ugly, but shouldn't have any performance impact, so I'm not
going to get too worked up.
* This set of changes alters what we get for some of the InChI test cases.
Adjust for that.
* apply (manually) #1807 from @bp-kelley to modern_cxx branch and fix (hopefully) a windows problem
* another windows problem
* another windows problem
* windows now builds locally
* update link targets
* expose addRing to python
* backup commit
* basics of atom and bond loading
* basics of atom and bond loading
* do bond stereo too
* Loads of cleanups
Read conformers and molecule properties
Better tests
update one of the test values so that we aren't always testing ccw
* enable auto-download of rapidjson distrib
* reader now mostly done (still missing atomic/bond properties)
* a bit of optimization
* a bit of cleanup
* a bit more optimization
* backup
* test zero-order bonds
* prep work for writer (not done)
* add isotope support
* backup
* getting there with the writing
* progress on writing; still need to do the RDKit part though
* can now roundtrip, including chirality.
double bond stereo needs to wait for backend fixes
* add a timing test for benchmarking
* add a timing test for benchmarking
* add another template
* add parse params; optionally set bond types to aromatic; add python wrapper
* disable benchmark run by default
* write conformers
* refactoring
* docs
* port to commonchem
* switch representation
* start reading and writing properties
* fix a memory problem
* set a common_property for gasteiger charges
* parse partial charges
* add partial charge writing
* reformatting
* add support for disabling parts of the parsing
* remove the "name" property from files
* editing
* more post-review changes
* make the molinterchange build optional
* make them really optional
* This makes assignStereochemistry cleanIt=True not remove CIS/TRANS
bond stereo chemistry that was manually added as described in issue #1614.
Incorrect CIS/TRANS stereochemistry will still be removed by
'cleanIt=true' if symmetry is detected. However, this symmetry
detection doesn't work in more complex pseudo-stereo chemistry cases:
bond stereo that depends on other bond stereo to break symmetry; and
bond stereo that depends on other atom stereo centers to break
symmetry. Test cases for these cases have been added ifdef'd in based
on USE_NEW_STEREOCHEMISTRY.
However, getting USE_NEW_STEREOCHEMISTRY to work in a copacetic way is
not trivial, I tried a little bit here to no avail. I'm leaving the
test cases checked in as they should be useful when we decide to make
the plunge into using Canon::chiralRankMolAtoms for symmetry detection
instead of the CIP ranks.
So this fixes at least the glaring issue of STEREOCIS and STEREOTRANS
being incorrectly removed by 'cleanIt=true' when it is indeed valid
stereo. The checks made for symmetry are rudimentary, but don't feel
complete.
* add another test; make what's being tested explicit
* test smiles generation and function when Hs have been added
* add a test that fails
* I think that it's ok to remove this
* backup
* At this point all tests pass.
Bond wedging is now handled even if sanitization is turned off when mol files are read
* adjust to code changes
* fix a couple problems caused by rebase
* update docs
* Fix for issue #1730
setAromaticity() now works even if there are aromatic atoms present and the relevat test case is added
* Removed setaromaticity flag
* trying to add shape tversky
* alpha and beta no defaults, added more tverskyIndex tests to testGrid
* corrections to GridUtils.h and ShapeUtils.cpp
* corrections to GridUtils.h
