* change minimal cmake version to a consistent 3.5
* progress towards a cleanup
* get the basic python deps working
* two more libs
* another round of changes
all tests pass at this point
* next round of changes
all tests pass at this point
* close to done
all tests pass
* very close
* almost done
* shift the RDBoost dependencies around a bit
* remove an extraneous python linkage
this is trying to get the mac builds working again
* Only link to python if it was built shared (#3091)
* change in response to review
Co-Authored-By: Ric <ricrogz@users.noreply.github.com>
* move that suppression of the maybe-uninitialized warning to BoostStartInclude.h
Co-authored-by: Brian Kelley <fustigator@gmail.com>
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke
* fix problem on windows
* disable builds of the StructChecker code by default
* operator"" _smarts() doesn't need to catch sanitization errors
* remove unused function
* turn back on some tests that shouldn't have been disabled
* Remove unused code from SMARTS parser and simplify a bit
SmilesParseOps::AddFragToMol is now used only from the SMARTS parser, so we can simplify the API
* Removes obsolete special case code for SMARTS
This was relevant when organic atoms in SMARTS queries were stored as two-part queries.
* improve SMARTS testing
make sure we can generate SMARTS from all the examples and then parse that again.
* Fixes#2814
* Fixes#2815
* some additional smarts tests to improve coverage
* test copy ctor and getPos
* remove obsolete test_list files
* include tests for the morgan invariant generators
* more cleanups and coverage improvements
* remove files that were mistakenly added
* 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
* 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
Windows git client, which converts line terminators to CR+LF
- added a conditional compilation clause to Code/RDBoost/import_array.h
to avoid a compilation error on Windows with Python3
