* 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>
* allow CXSMILES generic query atoms to be parsed from mol;
need more tests here
* remove vestigial directory
* Add d_queryType to Query
This opens up additional flexibility with customizing the way queries are handled
Also includes some assorted cleanups in the Query directory
* remove the MolFileSymbol hack added in #3235
We don't need it anymore
* Add support for additional ChemAxon extensions and document them
Signed-off-by: greg landrum <greg.landrum@gmail.com>
* bump pickle version
* add an additional test
* Fixes#3153
Added logic to handle cases where there is C+ aromatic atom by adding an explicit hydrogen to it
* Improved tests by adding checks if the scaffold network is created correctly
* Replaced implemented linear search by pre-implemented STL find function
* 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>
* 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
* a round of cleanups courtesy of PVS studio
* add a test to make sure that a warning is a false alarm
* bug fix
* Fix a UFF bug
* more PVS studio cleanups
* next round of PVS studio cleanups
* completely remove the chances for that bug
* changes in response to review
* add an additional test
+ a bit of reformatting that snuck in
* do not use new on loggers
* del pointers in testDistGeom
* Update Dict hasNonPOD status on bulk update
* delete new Dicts in memtest1.cpp
* fixes in MolSuppliers and testFMCS
* PeriodicTable singleton as unique_ptr
* fix EEM_arrays leak
* fix leaks in testPBF
* fix ParamCollection leak in test UFF
* fix leaks in MMFF
* clear prop dict before read in in pickler
* fix leaks in testFreeSASA
* fix leaks in test3D
* modernize Dict.h & SmilesParse.cpp
* fix leaks in testQuery
* fix leaks in testCrystalFF
* fix leaks in cxsmilesTest
* fix leaks in Catalog & mol cat test
* fix leaks in ShapeUtils & tests
* fix leaks in testSubgraphs1
* fix leaks testFingerprintGenerators
* fix leaks in Catalog/FilterCatalog
* fix leaks in graphmolqueryTest
* these changes reduce bison parse leaks
* fixed leaks in testChirality.cpp
* fix leaks + 2 tests in testMolWriter
* fix 4m leaks in substructLibraryTest
* small improvements to molTautomerTest; still leaks
* fix leaks in testRGroupDecomp
* fix leaks in test; parser still leaks
* fix leaks in itertest
* fix 4m leaks in testDepictor
* fixes in smatest; still leaking due to parser
* fixes in testSLNParse; still leaking due to parser
* flex/bison: always add atoms with ownership; smarts error cleanup
* fix leaks in testReaction
* fix leaks in testSubstructMatch
* fix leaks in resMolSupplierTest
* fix leaks in testChemTransforms + bug in ChemTransforms
* fix leaks in testPickler
* fix leaks in testMolTransform
* fix leaks in testFragCatalog
* fix leak in testSLNParse. Still leaks due to Smiles
* fixed most leaks in testMolSupplier
* pre bison fix
* fix some atom & bond parse problems; others still fail
* bison smiles & smarts, atoms & bonds more or less fixed
* fix leaks in molopstest.cpp
* fix leaks in testFingerprints, MACCS.cpp & AtomPairs.cpp
* fix leaks in moldraw2Dtest1
* fix leaks in testDescriptors
* fix leaks in testInchi
* fix leaks in testUFFForceFieldHelpers
* fix leaks in hanoiTest & new_canon.h
* fix leaks in testMMFFForceField
* fix leaks in graphmolTest1
* fix leaks in testMMFFForceFieldHelpers
* fix leaks in testDistGeomHelpers
* fix leaks in testMolAlign
* initialize occupancy & temp facto with default values
* fix leak in TautomerTransform
* updated suppressions
* fix testStructChecker
* fix logging & py tests
* fix TautomerTransform class/struct issue
* remove misplaced delete in testSLNParse
* deinit in testAvalonLib1
* fix Avalon-triggered(?) bug in StructChecker/Pattern.cpp
* fix random testMolWriter/Supplier fails
- diversify output file names to avoid clashing.
- unify Writers close/destruct behavior.
- flushing/closing in tests.
* use reset in FFs Params.cpp
* comments on testMMFFForceField
* unrequired 'if's added to mol suppliers
* correct cast in FilterCatalog.h
* use unique_ptr in MACCS Patterns
* remove unrequred if in new_canon
* update & move suppressions
* 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
* add a SmilesParserParams object to prepare for this
* add a SmilesParserParams object to prepare for this
* add tests for the SmilesParseParmas
* support name parsing, should it be the default?
* rename CXNSmiles to CXSmiles;
add a spirit parser for CXSmiles coordinate that is at least syntax correct
* abandon boost::spirit for now; crude atom token parser
* support params in smiles parser (not tested, may not build)
* can read coords and atom labels along with mol names; crude, but works
* read coordinate bonds
* remove some compiler warnings with VS2015
* remove a bunch of compiler warnings on windows
* remove more warnings on windows
* remove more warnings on windows
* backup commit: first pass at parsing query features
* radical spec parsing
* handle attachment points using atom mapping
* switch to a named property for atom labels
* fix handling of the "A" atom query
* add functions to construct A and Q queries (needs more work)
* fix a problem created while cleaning up warnings earlier
* add some additional convenience functions for making generic atoms.
Still need M and to recognize these while writing CXSMILES
* add M queries; update some tests
* fix a linux compile problem
* get the cxsmiles stuff working in python; basic testing
* support "M" in CXSMILES
* Adds replaceCore function that takes a matchVect
* Fixes error reporting, adds tests
* Switches PRECONDITION to ValueError exceptions
* Fixes MatchVectType annoyance in swig. Don't know why this is necessary.
* Silences warnings
* Adds working doctests and better explanations.
* Adds useChirality to replaceCore, fixes atom ordering
n.b. when replaceDummies==False and labelByIndex==True
the indices used are the indices of the dummy atom,
previously they were the atoms the dummy was connected
to.
* Adds useChirality to the remaining functions in ChemTransforms
* Adds a mess o tests
* Fixes labelByIndex=false ordering for dummies
* Removes debugging statements
o rdkit gains a RDKit::common_properties namespace that contains common string value properties
o Dict.h and below gain getPropIfPresent that attempts to retrieve a property and returns
true/false on success or failure. This is used to optimize access.
o rdkit learns how to pass property keys by reference, not value.
A new namespace has been added to RDKit, common_properties
that contains the std::string values for commonly used
properties. This helps to avoid typos in string values
but also avoids a creation of std::strings from character
values. All accessors (has/get/clear and getPropIfPresent) now pass
the key by reference.
Additionally, getPropIfPresent removes the double lookup
of hasProp/getProp which can be a significant speedup
in the smiles and smarts parsers (10-20%)
