* run clang-tidy with modernize-use-default-member-init
* results from modernize-use-emplace
* one uniform initialization per line
otherwise SWIG is unhappy
Co-authored-by: Brian Kelley <fustigator@gmail.com>
* clean up in testDatastructs
* avoid jump on unassigned mem in rxns
* set valgrind error exit code
* update suppressions
* clean up RDValue in testDict
* don't leak mol if parsing Maestro file fails
* don't leak mol if parsing PDB block fails
* cleanup leftover rxns in testReaction
* cleanup mol if CX extensions cannot be parsed
* cleanup leftover mols in smiTest1
* cleanup leftover mols in moldraw2DTest1
* cleanup leftover mols in testSubstructMatch
* make testEnumeration go easier on valgrind
* reduce R counts
* 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
* Adds C++ Enumeration Engine to the RDKit
* Adds Sanitization helpers, wrappers and tests
* Clang format
* Remove unused enumerationStateOnly flag
* Fixes docStrings to current API
* Adds doc strings
* Removes RGroupPosition, adds getPosition to EnumerationBase
* Fixes readability.
* Adds EnumerateLibraryBase::reset and getReaction
* Added getReagents method to EnumerateLibrary
* Make the tests have the same naming
* Need to save the initial state for resetting.
* Stupid case-insensitive file systems
* Moves ResetState to EnumerateLibraryBase
* Adds removeNonmatchingReagents helper
* Renames currentPosition to getPosition
* Adds Enumeration Toolkit tutorial
* Fixes Python3 serialization and enumerators
* Verified to run on python2 and 3
* Fixes integer issues on windows
* The number of enumeration should be unsigned.
* Adds deserialization constructor
* Moves boost_serialization to the end
* Deprecates Clone in favor of copy
* Update tests to use copy.copy not Clone
* Move RGROUPS and BBS into an EnumerationTypes namespace
* Make sure old pickles work
* Adds pickle for backwards compatibility
* Moves to uint64_t from size_t for public api
* Whups, accidentally used the binary archiver.
* Commits boost 1.55 serialization
* Makes serialization turnoffable Like Filter Catalog
* Fixes tests when serialization not available. Adds more enumeration strategy tests
* Fixes a syntax error on some versions of python
* Fixes sanitizeRxn to actually make proper RGroup atoms
* Updates SanitizeRXN python API
* Updates Enumeration API to a parameter class - fixes reagent removal
* Adds a mess of tests
* Change stats to return a string.
* Exposes EvenPairSamplingStrategy Stats to python
* Fixes a crash bug in SanitizeRxn
* Adds better testing of the even pair sampling
* Fixes namespace
* One more try to fix gcc
* Enum classes are c++11 and a microsoft extension.
* Fix typo
* Fixes np.median for python3
* Fixes atom iterators
* Adds virtual tags to derived virtual functions (for clarity)
* Fixes size comparison issues
* Adds doc string
* Small cleanup (has no effect since flags aren’t used)
* fixes crash bug on windows
* get the tests working on windows
* Updates tutorial
* Adds Glare implementation to Contrib
