* add a test
* change stereo bond canonicalization
* update canonicalization watch test with fixed cases
* make canonicalization test stricter (compare CIP codes)
* add reverse symmetry condition
* rewrite double bond canonicalization code
* update tests
* fix multiline comment
* update java tests
* update python test
* nix switchBondDir (unused)
* fix and rename flipBondDir
* refactor comment
* fix shadowed var name, casting
* fix neighbor sorting
* make seen_bonds a vector
* abstract setDirectionFromNeighboringBond
* handle both sides of the bond have directions
* move getNeighboringStereoBond
* check seen_bonds after popping connectedBondsQ
* use references for arguments
* add release note
* add example required by Dan
* add example requested by Dan
* atropisomer handling added
* fixed non-used variables, linking directives
* BOOST LIB start/stop fixes, linking fix
* Fixes for RDKIT CI errors
* minimalLib fix
* changed vector<enum> for java builds
* check for extra chars in CIP labeling
* removed wrong deprecated message
* fix ostrstream output error?
* restored _ChiralAtomRank to lowercase first letter
* changes for merged master
* Fixed catch label for new Catch package
* update expected psql results
* get swig wrappers building
* restore MolFileStereochem to FileParsers
* fix java wrapper for reapplyMolBlockWedging
* some suggestions
* move a couple functions out of Bond
* Merge branch 'master' into pr/atropisomers2
* merged master
* Renamed setStereoanyFromSquiggleBond
* atropisomers in cdxml, rationalize atrop wedging, stereoGroups in drawMol
* fix for CI build
* attempt to fix java build in CI
* attempt to fix java build in CI #2
* New routine to remove non-explicit 3D-geneated chirality
* changed to use pair for atrop atoms and related bonds
* Changes as per PR reviews
* PR review respnses
* PR review reponse - more
* Fix merge from master
* fixing java ci after merge
* Updated the help doc for atripisomers
* update the atropisomer docs
* improve the images
* add the source CXSMILES
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* fix a crashing bug in SubstructLibrary
* fix a bunch of other potential seg faults
These are all places where the result from pyObjectToVect(),
which can legitimately return a nullptr, is not checked before
being dereferenced.
* document behavior
clear the result vector for the other pythonObjectToVect() overload
* change error message
in response to review
* 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 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>
* change minimal cmake version to a consistent 3.5
* progress towards a cleanup
* get the basic python deps working
* two more libs
* another round of changes
all tests pass at this point
* next round of changes
all tests pass at this point
* close to done
all tests pass
* very close
* almost done
* shift the RDBoost dependencies around a bit
* remove an extraneous python linkage
this is trying to get the mac builds working again
* Only link to python if it was built shared (#3091)
* change in response to review
Co-Authored-By: Ric <ricrogz@users.noreply.github.com>
* move that suppression of the maybe-uninitialized warning to BoostStartInclude.h
Co-authored-by: Brian Kelley <fustigator@gmail.com>
Co-authored-by: Ric <ricrogz@users.noreply.github.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
* Fixes#2437
getting the canonical atom ranking no longer results in molecules have a
RingInfo structure that's been initialized but contains nothing.
* update expected results for the MMPA tests
* remove all of the "from __future__" imports
* remove the first batch of rdkit.six imports/uses
* next step of rdkit.six removal
* removing xrange, range, and some maps
* next round of removals
* next round of cleanups
* fix inchi test
* last bits of "from rdkit.six" are gone
* and the last of the six stuff is gone
* strange importlib problem
* 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
* Adds canonicalization of atom maps
* Removes debugging statments and commented out code
* Fixed bad mapping of mmps with no cores (1-cut), remove sanitization
* Adds FragmentMol with minCuts specified
* Adds ability to cut by bond indices as opposed to smarts patterns
* Fixed API (remove maxBondCuts when bonds are sent in)
* Adds bond api test
* Fixes docs
* Small doc change
* Removes cstdint
* Adds ValueError minor bond retrieval optimization
* Removes fragMolHelper4
* Tests ValueError
* py3 fix
* - added -DBOOST_SYSTEM_NO_DEPRECATED to definitions for MINGW builds
- modified a few #ifdef's to discriminate better between MINGW and MSVC
- added a ios::binary to Code/GraphMol/FileParsers/testMolSupplier.cpp
(I already had to add some of those in the past to avoid the CR+LF issues on Windows)
- modified Code/GraphMol/FMCS/MaximumCommonSubgraph.cpp and
Code/GraphMol/FMCS/FMCS.h because checking the function pointer does not
work with DLLs as the function pointer changes upon different calls
- builds under MinGW with -DRDK_USE_BOOST_SERIALIZATION=OFF and
RDK_BUILD_THREADSAFE_SSS=OFF
* - added the possibility to define MSVC_RUNTIME_DLL to point to the
absolute path of an appropriate MSVC runtime DLL to enable
multi-threaded builds with MinGW
- modified C++ and Python tests of the multi-threaded conformation
embedder as under 32-bit MinGW lower numeric precision introduces minimal
coordinate differences with result in ~1-kcal energy difference.
Therefore the energy criterion has been made more lenient, and a
coordinate MSD criterion has been introduce to compare substantial
identity of conformations
* - reverted Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py and Code/GraphMol/DistGeomHelpers/testDgeomHelpers.cpp
to the upstream/master version
