* - fixes MinGW build
- make sure that supplier istream is opened in binary mode or istream::tellg() will
report wrong offsets on MinGW builds (MSVC will make no difference)
- avoid that in MSVC conda DLL builds the libboost_*.lib static
libraries are picked by cmake instead of the boost_*.lib import libraries
by defining BOOST_ALL_DYN_LINK
* - make sure that C# wrappers build with MinGW compilers
- make sure that static builds work under Windows with both MSVC and
MinGW
* - disable building static libraries on Windows also when using MinGW compilers
- fix the C# wrapper build on Windows under both MSVC and MinGW
* reverted -DSWIGWORDSIZE64 as it was originally
* reverted -DSWIGWORDSIZE64 definition
Co-authored-by: Paolo Tosco <paolo.tosco@novartis.com>
* support read-only access to cstates from python
* expose GetBrackets
* expose getAttachPoints too
remove vestigial SubstanceGroupCState_VECT
* backup
* backup
* basics working
* backup
* add label_mol_abbreviations
* fix a bug in the chirality handling
* add linkers, needs more testing
* add another peptide test
* sanitize results by default
* just need rings
* getting started with the C++ form of abbreviations
* a bit of error handling
* add findApplicableMatches
* actually apply the abbreviations
* make the getDefault functions more efficient
* add labeling (creating s groups)
* docs
* basic python wrappers (maybe this is enough?)
* add _displayLabel and _displayLabelW support to MolDraw2D
update the docs for that
* use displayLabel props
* add more default abbrevs
* change default linker defns
add parseLinkers convenience function
* make sure attachment point atoms aren't aromatic
* change the color of dummies to be darker gray
* remove python implementation
* support abbreviations in the java wrappers
* add abbreviations to the csharp wrappers
* add abbreviations to the js wrappers
* add molParity to the list of atom props not written to CXSMILES
* support condensing SUP substance groups
* add that to the python wrappers
* Update testAbbreviations.py
* clear ring info if we added it
* document that the molecules with abbreviations removed have not been sanitized
* Deprecation: planned removal of .message() and .getMessage() methods
* Deprecation: planned removal of old MolHash code
* document deprecations
* output the diffs when the psql tests fail
* remove .message() from SWIG wrappers
note that the KeyError doesn't work properly. We should clean up the the exceptions here anyway
* typo
* add AtomValenceException
* refactor a bit and add KekulizeException
* add copy ctor and copy() method
* add detectChemistryProblems
* add getType() method
want to be able to get the type of the exception without requiring doing a bunch of dynamic casts
* first pass at exception inheritance/translation
needs some cleanup and expansion, but this does pass all tests.
* cleanup and finish the python wrappers for the new exceptions
* make sure things are truly polymorphic
* wrap shared_ptrs of the new exception types
* expose DetectChemistryProblems()
* get the java wrappers building again
* transfer those changes to the c# wrapper
* add detectChemistryProblems()
and deal with the fun fun exception inheritance things that ensue
* response to review
* add linux_java build
* trigger azure pipelines builds on dev/ branches
* make sure boost::iostreams gets linked in the SWIG wrappers
* updates to get static boost builds working on mac
* update linux a bit and add mac build
* forgot to save the mac file
* install version of boost with -fPIC
* try to force use of the boost installed in /usr
* typo
* add library hint
* diagnosing a failing build
* be explicit about CXX version
* try to force use of the system compilers
instead of the ones from conda
* stop using conda
* typp
* re-enable full build
* disable the appveyor builds
* Move RDBoostStreams to RDStreams
* RDBoostStreams->RDStreams
* RDBoostStreams->RDStreams
* Wrap SWIG (with Java test)
* Fix missing declaration
* Use the file that already exists
* Revert to original version
* Revert to CXSMiles version
* Update boost version
* Remove redundant code
* Add zlib
* check for win32
* FileParsers now builds static on windows
* add a couple test files
* backup
* first pass at some theory documentatin
* it's a draft
* Update enhanced stereochemistry documentation
Adds initial target use case and caveats about the tentative
nature of the current implementation.
* Support read/write of molfile enhanced stereochemistry
This includes reading and writing of enhanced stereochemistry
from v3000 molfiles (sdf). Enhanced stereochemistry encodes
the relative configuration of stereocenters, allowing
representation of racemic mixtures and compounds with
unknown absolute stereochemistry.
It does not include:
* Python wrapping
* invalidation of the enhanced stereochemistry
* use of enhanced stereochemistry in search
* depiction of enhanced stereochemistry.
* Update to reflect changes from #1971
* change names of enum elements to allow compilation in VS2017
I think it's also clearer to do things this way
* Addressed most review comments.
* Run missed test "testEnhancedStereoChemistry"
* In tests, added size checks to group equality checks
* Updated copyright statements
* Deleted mol created for a test
* Use perfect forwarding in RWMol::setStereoGroups()
* use references for stereo groups that are checked in write and pickle
* Updated stereogroup.h in hopes of fixing compilation on Windows.
* clang-format
* try allowing a switch to boost regex and requiring it for g++-4.8
* do a better job of that
* typo
* Code review comments. Updated Copyright notice.
* When an atom is deleted, delete stereo groups containing it.
Also updates StereoGroup toUse accessors instead of
constant member attributes. This allows move of StereoGroups.
* RDKit style guide
* Add header required on Windows.
* get the SWIG wrappers to build
* this is a rough first pass, needs to be finished and is a strong argument for changing the names of some of the #defines that are currently used
* rationalize the rest of the #defines
add something to the release notes about this
* Fixes csharp build for 64 bit systems
* Need to support make and make install stages
* switch to an alternate strategy and get it working for the java wrappers too
this now builds for me on 64bit win10 with MSVC14
* add missing files from that last commit
* Hopefully fixes unix and osx builds while maintaining msvc builds
* Fixes mono builds, removes python check
