* Try not to make wedged bonds double in the kekulization code
This is a first pass implementation and definitely needs more testing of the new feature.
Probably looking at optimizing the code would also not be terrible.
All tests pass with this commit
* Some changes to the kekulization in presence of wedged bonds and additional testing
* additional kekulization test case
* start the kekulization in rings with wedged bonds
add some bulk tests
all tests now passing for me
* changes from review
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Co-authored-by: Riccardo Vianello <riccardo.vianello@gmail.com>
* check for ringinfo levels instead of init
* check for ring info in kekulizefragment
* add a test
* update tests
* update doctests
* revert ringinfo level checks
* Fixes#5505
* Switch to using hasBondTypeQuery()
* update the docs
* ensure we still fail with non-ring aromatic atoms
* changes in response to review
* fixes#4721
* - store in RingInfo the index of the ring(s) each atom and bond belongs to rather tham just their size
- expand the RingInfo API with a few useful methods
- identify rings that are certainly aliphatic upfront
- avoid unnecessary copying atomRings when RingInfo is already initialized
* - code modernization and cleanup
- better handling of dummies in aromatic rings
- exposed atomMembers() and bondMembers()
- added several tests
* - avoid order dependency on rings
- added test for the above
* changes in response to review
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* preliminary
* all tests pass
* cleanup
* more testing!
* we do still want to raise errors for aromatic atoms not in rings
fix one missed change for mol blocks
* update expected results for psql test
* minor preparatory refactor
* add test
* add reaction literals
* tests for the new literals
* add runReactant
first steps to making things work
* remove works
* backup
* all current tests passing except bond-order changes
some atom-property copying fixed
* bond changes now work
* handle atomic stereo
* some cleanup and more tests
* docs
* not-working
* add KekulizeIfPossible()
* return a value from KekulizeIfPossible
* Revert "not-working"
This reverts commit 2ebd8a5519.
* add in-place reactions to python wrapper
* simplify deprotection wrapper code
* support in-place deprotection
* changes in response to review
* forgotten change
* remove include from headers
* update implementation files
* completely remove BOOST_FOREACH (#7)
* convert those changes to use auto
* get rid of all usage of BOOST_FOREACH
Co-authored-by: Greg Landrum <greg.landrum@gmail.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
* add AtomValenceException
* refactor a bit and add KekulizeException
* add copy ctor and copy() method
* add detectChemistryProblems
* add getType() method
want to be able to get the type of the exception without requiring doing a bunch of dynamic casts
* first pass at exception inheritance/translation
needs some cleanup and expansion, but this does pass all tests.
* cleanup and finish the python wrappers for the new exceptions
* make sure things are truly polymorphic
* wrap shared_ptrs of the new exception types
* expose DetectChemistryProblems()
* get the java wrappers building again
* transfer those changes to the c# wrapper
* add detectChemistryProblems()
and deal with the fun fun exception inheritance things that ensue
* response to review
* first round of cleanups based on PVS-studio suggestions
* a couple more
* a few more cleanups
* another round of cleanups
* undo one of those cleanups
we want the integer rounding behavior here
* add a comment to make that clear
* Fix for filter catalog PRECONDITION redundancy
* 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
instead of using the property map interface.
A nice side-effect is that the wart of having to use property maps to loop over bonds or atom neighbors
is now gone.
This potentially breaks lots of client C++ code.
http://sourceforge.net/tracker/index.php?func=detail&aid=1942657&group_id=160139&atid=814650
This was handled by adding error/consistency checking to Atom.calcExplicitValence()
This includes another pretty big scale modification:
the allowed valence list for atoms (in atomic_data.cpp) can now contain a -1 at the end. If this is the case, the atom will tolerate valences above the ones listed.
This is done to allow "flexible" atoms (i.e. transition metals and the like) to accept arbitrary coordination numbers without generating errors.
