* 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
* Add private functions for batch removal of atoms/bonds
* Reset the unique_ptr not the bitvector
* Remove unused variable
* Forgot to reset stero atoms
* Remove unecessary post batch edit check
* Set min_idx to the number of bonds, this makes it a sentinel
* Don't need rdcast
* Responses to review
* Removed unused variable
* Add missing braces
* Consolidate bond removal loops
---------
Co-authored-by: Brian Kelley <bkelley@relaytx.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
* 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
* Fixes atom documentation
* Fixes#1461
This is a complicated one. Basically URANGE_CHECK when
used on unsigned integers has a problem when the size of
the range it’s checking is 0. The standard operations is
to check
URANGE(num, size-1)
Which (for unsigned integers) obviously rolls over.
This fixes all usage cases to be
URANGE(num+1, size)
And fixes the bugs found. (addBond and the mmff tests)
* Fixes#1461 - Updates URANGE_CHECK to be 0<=x<hi
Conformer.cpp: make sure we don't ask for space for zero atoms.
Kekulize.cpp: don't complain about marked bonds if we aren't removing markers.
molopstest.cpp: bad smiles corrected in one test.exe
ROMol.cpp, RWMol.cpp: extra preconditions added (should have been there all along)
Wrap/MolOps.cpp: docs for replacesubstructs.
