* Make sure that added R-groups have non-zero coordinates
* - renamed setHydrogenCoords to setTerminalAtomCoords (and parameters accordingly)
- switched from ROMol* to RoMol& to remove a PRECONDITION
- documented the newly exposed C++ function
- added a Python wrapper
- added C++ and Python tests
* fixed conflicts and added a test
* Update Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/RGroupDecomposition/testRGroupDecomp.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/MolOps.h
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/Wrap/MolOps.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* changes in response to review
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* backup
* simple first pass, passes all tests
* cleanup a bunch of existing uses
* ensure that we can safely add atoms/bonds while in edit mode
* add context manager on python side
* handle exceptions properly in those
* changes in response to review
* RGD modifications for any atom and index labels
* Continued development
* All tests working
* Added comment
* CR changes suggested by PTosco
* Fix catch_rgd for autocrlf
* Core dummy matches on output. RGroups on heavy atom. Dummy atoms User rgroups only when they are degree 1.
* Start work on test fixes
* testRGroupDecomp test working
* CPP and Python tests working
* Removed options for matching core query atoms on sidechains
* Windows build fix
* R groups off ring. User group matches single heavy substituent. Remove extraneous hydrogens
* Updated fingerprint variance score and tie selection
* Refactor fingerprint variance score functions to class
* Removed fingerprint distance score
* Boost::trim fix
* Updated RGD test notebook
* Fixed AddHs.cpp
* - fixes the kekulization issue
- avoids that empty R-group labels are included in cores
- makes sure that SMILES cores are always canonical
- adds a few missing const declarations and avoids unintentional copying
* Support for allowNonTerminalRGroups parameter. Remove R groups that contain H or Nothing. Ignore R group labels on non-dummy atoms
* Fixed tests for Paolo's changes. Rebuilt test notebook. Increased weighting of rgroup penalty in fingerprint variance score
* remove some debug output
Co-authored-by: Brian Kelley <fustigator@gmail.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
- switched to using std::vector<int> instead of std::list<int> for _ErGAtomTypes property
- added RegisterListConverter<std::vector<unsigned int>>
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
* add "needsHs()" query
* add warning for embedding without Hs
* add H checks to UFF and MMFF as well;
a small amount of cleanup in the MMFF atom typing
* 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>
* Add better support for isotopic Hs to removeHs() and addHs()
* simplify the new code to add Hs back
* Changes in response to review
* revert FindCairo.cmake that I pushed by mistake (grrr)
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* 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>
* Progress on #3168
* Fixes#3167
* Fixes#3169
* deal with CBONDS too
* test PATOMS
* Fixes#3175
* a bit of code simplification and test updates
still needs more testing
* more testing
* handle s-group hierarchy
also a couple of other changes in response to the review
* add forgotten test file
* changes in response to review
* Fixes#3150
Fixes removeHs removing Hydrides by adding a removeHydrides flag to RemoveHsParameters.
If removeHydrides is false, Hydrogen atoms with formal charge -1 and degree less than or equal to 1 are kept
removeHydrides is kept true by default
* Made suggested changes
Removed extraneous comments and redundant code
Added tests for both ```removeHydrides = true``` and ```removeHydrides = false```
Added tests that ```removeAllHs()``` also removes hydrides
Exposed ```removeHydrides``` parameter to python
* Explicity Added removeHydrides=true in removeAllHs
Corrected typo for removeHydrides
* make formatting consistent
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* do not throw in desctructor
* remove unused var; reserve
* provide operator= for DiscreteValueVect
* provide operator= for SparseIntVect
* remove unknown 'omp' #pragmas; refactor loop
* remove unused var
* remove unused variables
* give EmbeddedAtom a default constructor & early exit on self assignç
* handle unused vars/args
* catch exception by ref
* address unused args
* fix signed type comparison; refactor extra checks
* remove unused variable
* suppress switch fallthtough warning
* handle signed type comparison
* handle signed type comparison
* potentially uninitialized vars
* fix abs() of bool
* unused vars in catch statements
* remove unused variables
* python::list returns will be copied
* give ValidationMethod constructor & virtual destructor
* remove extra semicolon
* 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
* backup commit; won't even compile
* backup commit
* Fixes#2848
* A few changes
- add a bunch of tests
- some fixes
- add ROMol version to API
* add python wrapper and associated tests
* add RemoveAllHs()
* changes in response to review
- add removedMapped option
- add docstrings for options
* changes in 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
* Modify removeHs so that it does not remove degree 0 atoms
Update the docs at the same time.
* include a warning when not removing some Hs
* clear up a problem with the warning log
* Fixes#1810
There's still a problem with stereo atoms (see the commented out test),
but this takes care of the basics and that's up next.
* clean up that last problematic bit.
Still needs all tests to run
* this seems to be a necessary workaround for problems with VS2017.
It's a bit ugly, but shouldn't have any performance impact, so I'm not
going to get too worked up.
* This set of changes alters what we get for some of the InChI test cases.
Adjust for that.
* Add AtomPDBResidueInfo during molops::addhs
* Test addhs and AtomPDBResidueInfo
* Little cleanup
* Fix serial
* Refactor code, add unique Hs labels
* Move code to separate function + bugfix.
* Make function optional (AddHs residueInfo param)
* Rename argument
* 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
This changes the CIPCode and CIPRank atom properties to no longer be computed properties.
Note: under linux I was unable to actually get the bug to manifest (converting the uint property to an int didn't cause problems), but that doesn't mean it shouldn't still be fixed.
