* added new attributes for scsr template as per BIOVIA doc 2003
* changed to allow any attributes for an SCSR Template def
* removed unneeded defs for TEMPLATE attribute names
* Throw error when V2000 coords are out of range
* Update Code/GraphMol/FileParsers/MolFileWriter.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Response to review. Fixes Max/Min, force v3000 when out of bounds
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* remove no-op macros and dead code (pt 2)
* test failures due to whitespace changes?
* actually run the testFeatures tests
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Fixes#7306
Do not cross bonds which were previously aromatic
* revert one of the test changes
* change in response to review
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Co-authored-by: Riccardo Vianello <riccardo.vianello@gmail.com>
* add MolToV2KMolBlock()
small refactoring in the mol block writing
* throw an exception for more than 999 atoms, bonds, or SGroups
update docs for that
changes in response to review
- isotopic labelling should not depend on the presence of a query atom feature, but rather on the presence of common_properties::_MolFileRLabel
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* insert line breaks in stereo groups
* Add a test
* simplify the approach
* fix test issue
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* 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>
* Fixes for canonicalization, and stereochemistry
* chnages from code review
* test that was omitted for canon correction
* PR review changes
* changes as per PR review
* missed file checkint to make PR tests compile
* PR conflict resolution
* change to fix PR buld errors (hopefully)
* line delete to force re-running of tests
* changes as per PR review
* resolve merge conflicts with master
* some suggestions
* revert chirality modifications when sanitization isn't being done
* addl changes: no stereo percept when no sanitize
* missing test expected files added
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* add test
* fix the issue
* make imines w/ implicit H unspecified, but allow unknown
* improve test in 6527
* do not mark double bonds as EITHERDOUBLE if no neighbors
* first pass at writing v3K rxns
* python wrapper
* test other C++ call
* cleanup
* Fixes Windows DLL build issue
* changes in response to review
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* backup commit
This is mabye heading in the right direction and at least passes the basic tests which are there.
* some progress
* more tests and refactoring
* additional aliases
add carboaryl
* add CYC and ACY
* add ABC
* add AHC
* CBC and AOX
* add CHC and HAR
* add CXX
* cleanup: remove a bunch of nullptrs
* initial tagging support
* remove atom labels/sgroups after using them
* docs
* start handing writing
NOTE: this does not currently work: the generic code needs to move out of SubstructSearch
* move the generic groups to their own library
Signed-off-by: greg landrum <greg.landrum@gmail.com>
* make sure the generic groups end up in ctabs
* add forgotten CMakeLists.txt
* fix includes
* expose this stuff to Python
* CYC needs to initialize rings
* renaming
* add docs
* change 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>
* Fix ROMol->RWMol static casts
* Fix accessing of end-iterator.
* Fix some test build issues I saw while compiling with Clang.
* Add build settings for sanitizers.
* Revert "Add build settings for sanitizers."
This reverts commit 5dc84374f0.
* 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
* make sure LINKNODE is saved from v3k mol files
v2k still needs work since the format is different
* write v3k linknodes
* support reading V2000 mol blocks too
* 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>
* Add convenience functions for generating v3K mol blocks and mol files
* first pass at parsing/writing the remaining atom properties from the CTAB spec
* handle SUBST
* write out the bond props that were being read but not written
* add an additional test
* fix a couple of problems caught in review
* first cleanup
* next round of changes. all tests pass
* Fixes#2909
* Fixes#2910
* further cleanup
* some cleanup/refactoring of the Dict class
* remove now extraneous calls to hasProp() before clearProp()
* minor refactoring of RDProps.h
* Switch from using our own version of round() to std::round()
* replace some boost::math stuff with the equivalents from std::
* cleanups in SmartsWrite
* refactor out a bunch of duplicated code
* fix an instance of undefined behavior
* changes in response to review
* 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 a molblock writing problem
with undervalent atoms from the organic subset
* Fixes#2649
Also ensures that allenes are not written as crossed bonds
(which does not make sense at the moment anyway)
* clang-format run
* 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
