* Coulomb Mat v0.1 issue on linux
* use static 3D molecule instead of generating 3D conf for testing
* fix tokenize
* fix issue removeHs
* update test for sdf 3D molecule
* strip things back to just do the basic coulomb matrix
* add RDKIT_DESCRIPTORS_EXPORT
* fix 3 typos and a missing const
* Update rdMolDescriptors.cpp
Co-authored-by: greg landrum <greg.landrum@gmail.com>
Co-authored-by: Paolo Tosco <paolo.tosco.mail@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 pass at random smiles vector; c++ version
* add python wrappers for that
* Remove accidental change
* switch to using a cross-platform reproducible RNG
* First pass of fixing layout of OH/NH type drawing.
* Fixed scale for N/S NH type groups.
* Fixed bond end points with new display of heteroatoms.
* Fixed case where it drew aromatic dashed bonds in wrong ring for morphine.
* Minor edit.
* Fixed non-drawing of chiral bonds.
* Removed use of boost for_each.
* Modern atom traversal.
* Put in fixed scale for drawings.
Made drawMolecule() take note of prepareMolsBeforeDrawing.
Updated more iterators to modern idiom.
* Added fixed bond length for drawing.
* Fixed drawing of CH4, NH3 etc.
* Stash of working but ugly, prior to re-work.
* Better, simpler splitting of atom symbols.
* Took clang-tidy's advice about use of override.
* Tidied up drawing of text strings.
* Tweaked what is classed as vertical bond in drawing.
* fixedBondLength now down-scales if it would overflow the draw window.
* Some tidying.
* Tests for new parameters in JSON.
Fixed some existing tests where, for example, scale on picture is now different.
* Added option to rotate 2D draw coords before drawing.
* First pass at highlighting atoms in multiple colours. Circles only at the moment.
* Line width scales if big enough.
* Tweaked SVG text drawing.
* Added highlighting with more than 1 colour on an atom. C++ only.
* Fixed some issues with widths of highlights in a frustrating game of whackamole.
Updated some tests accordingly.
* Added Python wrapper for new drawing code.
* Removed debugging writes.
* Added C++ test for multi-coloured highlights.
* Added python test for multi-coloured highlights.
* Attempt to show radicals.
* Tidied up radicals in drawing, including a bullet instead of full stop in SVG.
* Fixed catch_tests.cpp for MolDraw2D.
* Fixed crash in Python wrappers on OSX.
* Fixed test5_2.svg bug (trailing </tspan>).
Made wavy line width scale as other lines do.
* Improved placing of charges.
* We're already in the future.
* Fixed a number of bugs that made drawMolecules not set the scales properly.
* Fixed Cairo wavy line width.
* Fixed non-closure of collision boxes.
* Added maximum font size for text, with tests.
* Addressed all Greg's first PR change requests.
* Fixed crash in extractAtomsymbols.
* stop using coordgen and adjust tests to reflect that
there's a bit of reformatting in here too
* Fixed layout of reactions.
* Fiddled with moldraw2DTest1 tests again.
* Fiddled with catch test.
* Fixed istope postion in W atom labels.
* Minor tweak to cairo,
* update expected results
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Fix a hang when trying to read mols from a directory not a file on linux
* thrown an exception at construction time
* clarify the readme
* update release notes
* Refactor the stream opening and checking code to a common method
Co-authored-by: Brian Kelley <bkelley@relaytx.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
Although these are probably nonsense, I've seen some pretty
big [r#] expressions in SMARTS expressions. In particular, for
SMARTS generated for toolkits that don't have the range
extension, people do this to mean "in rings bigger than 6" or
whatever:
[r7,r8,r9,r10
* backup
* rearrange the network to make it cleaner
- GenericBond scaffolds are now directly connected to the corresponding Generic scaffold
- Attachment points are no longer removed from Generic (or GenericBond) scaffolds
* remove dead code
* Add threaded pattern generator to help speed up library creation
* Add size to FPHolderBase
* Add more complete python wrapper, fix leak in doctest
* Add basic usage test for addPatterns, fix I/O leak
* Add basic test for trusted smiles
* Actually add the new code
* Export addPatterns on windows
* Try fixing the cartridge build
* Change pattern_factory to PatternFactory
* Change boost::ref to std::ref
* add reference input/output files for yaehmop
* orbital energies, overlap matrix, and hamiltonian on the C++ side
* add the python wrappers for the new functions
* [WIP] Add BCUT 2D descriptors
* Use the standard RDKit license
* Add Check for EIGEN3
* Add vector param, fix some formatting, remove debug print
* Add make_burden function, optimize symmetric eigenvalues
* Add some tests, finalize API
* Make the python API return tuples
* Updates docs
* Remove unused variable
* Fixed up C++ tests
* Remove std::pair wrapper, don't build BCUT when missing EIGEN
* Add bigger test case for BCUTs
* Accidentally removed the wrong code
* initial attempt to run doctests in CI
* add cairo support; disable other builds until we are done with this
* we don't actually need cairo
Adds cleanup code to cookbook
* be explicit about SVG
it does not seem like this should be necessary, but...
* turn the other tests back on now that the doctests work
* try enabling the doc tests for mac and win too
* remove mac tests again, fix problem with windows
* trying to get tests working on windows
* stop requesting PNGs in the cookbook
* skip calls to molstogridimage too
* remove vestigial doctest directive
* backup
* backup
* backup
* getting close to v0.1
* switch to using node indices
* add pruning and flattening
* support multiple mols
* example notebook
* backup
* initial commit
Just includes the basic API and flatten
* add the pruning step
* add removeAttachmentPoints()
* add makeScaffoldGeneric()
* improve compilation speed by adding catch_main.cpp
* add getMolFragments()
* doc cleanup
* actually add the network building code
* first pass at python wrapper
* allow edges to be nicely converted to strings
* get node counts working
* backup python notebook
* switch example notebook to use wrapped C++ code
* add BRICS fragmentation option
* fix a bug with removing attachment points to aromatic heteroatoms
* add provisional attachment point merger to notebook
* fix a bug with includeScaffoldsWithAttachments=false
* backup of efforts to get this working on windows
* backup of efforts to get this working on windows
* does not work. backup
* Fix a substructure crash on Windows
* re-enable tests
* adjust to the new BRICS form
* in-code documentation
* more doc updates
* reformat
* change the string output format for edges
* remove old python implementation
* remove obsolete test
* include a generic scaffold for the pruned structure too
* default to keepOnlyFirstFragment=false with BRICS params
* bug in removal of attachment points from generic scaffolds
* more testing
* support working from std::shared_ptr as well as boost::shared_ptr
* more testing
* disable debug printing
* use memo-ization in getMolFragments() to avoid duplicate work
* add SWIG wrapper and basic testing
* add define for RDK_USE_BOOST_SERIALIZATION
* add serialization at the C++ level
* add a string ctor for a scaffold networks
* add pickle support on the python side
* formatting
* remove old notebook
* move the fantastically useful iterable_convertor to RDBoost/Wrap.h
* expose parameter constructor with std::vector<std::string>
* add scaffoldnetwork to documentation
* add overrides for what()
* translation fot KeyErrorException; update tests
* Switch all exceptions to `const char *` as a return type from message() (#4)
* switch return type of message() from std::string to const char *
* adjust one test to the new return type from message()
remove unnecessary verbosity from some tests
* fix cartridge build: update call to message().c_str()
* rebase agains master; fix another issue in cartridge build
* add deprecation note for message() and getMessage()
* amend Release notes
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* backup, does not work
* working on the C++ side
* backup
* fix the API
* document the new functionality
* improve that example
* final bit of cleanup
* switch to std::function
* get fileparsers catch tests building faster
should use this same approach across all of the catch2 tests
* Fixes#2916
* support parsing of STBOX for atoms and bonds in v3K mol files
add molStereoCare to common_properties
STBOX is translated to the molStereoCare property
* add stereocare support to adjustQueryProperties
make building the catch2 tests faster for the GraphMol package
* copy in AdjustQueryParameters JSON parsing from adapter.cpp
(That still needs to be ported to use the new code)
* get the cartridge using the new parsing code
* update test to reflect new parser behavior
* add a v2000 test
* changes in response to review
