* simple modernization
* more
* done with RWMol for this pass
* the ROMol.cpp variant
* Atom
* minor change to bond
* simplify Conformer
* monomerinfo, queryatom, querybond
queryatom and querybond cpp files still need to be done
* typos
* revert a dumb change
* suggestion from review
* some initial work...
Still some real questions here about what should be done with dp_mol data members
* add some tests for move semantics of Dict and Props
remove extraneous clear()
* more in-depth testing of the molecule results
* test refactoring
* improve the molecule move test
* fix some leaks found by valgrind
the new tests are now all clean in valgrind
* additional classes
QueryAtom, QueryBond, RingInfo, Conformer
* get swig working again.
Not sure why this is necessary, but SWIG is a mysterious beast
* fixes in response to review
* updates in response to review
* a bit of simple refactoring
* Fixes#4311
- adds getValenceContrib() to QueryBond
- adds hasBondTypeQuery() and hasComplexBondTypeQuery() to QueryOps namespace
- atoms with complex bond type queries now have explict and implicit valences of 0
- adds tests for the above
* add a test
* start refactor query pickling
* further query pickling refactoring
* bit of modernization
* partial implementation of query writing
* serialize recursive queries
* new tests
* support QueryAtom and QueryBond with null queries
* more query cleanup
* tests pass
* switch from std::variant to boost::variant
* update clang version for CI
* explicit instantiation of templates
* get dll builds working on windows
* optionally skip h counts on parsing; more query tests
* change in response to review
* changes in response to review
* 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>
* Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers
* Actually delete atoms and bonds...
* RWMol::clear now calls destroy to handle atom/bond deletion
* Changes broken Atom lookup for windows/gcc
* Adds tests for running with valgrind
* Adds test designed for valgrind and molecule deletions
* Removes RNG, actually tests bond deletions
* update swig wrappers
* deal with most recent changes on the main branch
