* change to make the SWig builds work on windows
* add the wrapper. Still needs tests
* first rgd java wrapper test, does not pass
* get static builds working on windows
* unused vars in bison parser cleanup
* initialization order in TopologicalTorsionGenerator
* unused params in SLN bison
* sln flex unused params
* throwing destructor in TDTWriter
* signed comparison in substructmethods
* unused input param in smiles/smarts bison
* unused ms param in sln bison
* signed comparison in FingerprintGenerator
* store return of fscanf in StructCheckerOptions
* unreferenced var in catch
* uninitialized value in FileParserUtils
* avoid override overload warning in MolDraw2DSVG
* non-final overrides in Validate.h
* unused static var in Avalon
* unused vars in catch blocks
* make AvalonTools avalonSimilarityBits & avalonSSSBits const int
* assert fscanf result in StructCheckerOptions
* Allow Atoms to be copyied in Python.
The dunder copy method is the idiomatic way to support
making copies in Python. Includes a test to make sure that
copied atoms are usable.
* Use RWMol in Code/GraphMol/Wrap/rough_test.py
Co-Authored-By: d-b-w <dan.nealschneider@schrodinger.com>
* Allow access to an atom's copy constructor in Python
* Add writing of enhanced stereo to cxsmiles
* changes in response to review
* fix an interaction between the fragment and enhanced smiles bits
* fix a logic error
* 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
* first crude pass
* fix a deprecation
* change naming scheme, support bools
* add standalone function
* add a default value for missings
* support long lines
* stupid typo
* make operator[] work
* revisit missing value handling
* modify missing value handling
* switch to an alternate scheme for specifying missing values
* clang-format
* First pass at property list parser
still needs more tests
* add test for processMolPropertyLists
* get this working as part of the ForwardSDMolSupplier
* first pass at python wrappers and tests
* clang-format run
* add creation of property lists at the mol level
* wrap long lines on output
* remove PoC implementation
* fix python wrappers
* remove out-of-date reference to the Python PoC
* changes in response to review
* WIP - Substruct Library Serialization
* Add serialization to SubstructLibrary
* Add SubstructLibraryDefs
This holds the definition of whether the substruct
library is serializable
* Wrap serialization in python
* Remove .h file, add .h.in file
* Configure header file into source dir
* Use RDConfig.h to configure serialization
* Move serialization code to seperate header file
* Fixes for review comments
* Removes some code redundancy
* Make pickling mols less memory intensive
* Check if molholders come back as the right types
Since #2022, RDkit mols have had information about groups of atom
with defined relative stereochemistry (StereoGroup). This commit
allows EnumerateStereoisomers to generate stereoisomers defined
in a mol's stereo groups.
By default, this includes the stereo groups in the generated
stereoisomers. Also adds an option to constrain stereo expansion
to _only_ expand sites specified at a stereogroup. This allows
the resulting set of molecules to (optionally) retain any
ambiguity in assignment in the original mol.
* don't use a ctab as input for the computation of 2D coordinates
Fix GitHub issue 1062.
* make sure that the output 2D coordinates are ordered correctly
* very basics of writing as PoC: atom labels end up in output
* further progress, does not currently work
* stop writing coordinate bonds;
we represent these in SMILES already
* add coords
* fix typo in dealing with atom properties
* get atom props working
* changes in response to PR
* Fixes#2277
* changes in response to review
the big one is to move the PXA parser into the normal mol file parsing
* move the PXA changes to the writer as well
* SCN actually only needs 7 characters
* add test
* fixes in response to review
* handle blanks (instead of zeros) in the counts line.
The ctfile.pdf doc says we should do this
* Make the SGroup reader more robust w.r.t. bad data
The current behavior leads to uncaught exceptions when a line is too short.
This should clear that up so that we always throw the usual FileParseException
* make error messages a bit easier to read
* not quite done yet
* Fixes#2244
* Fixes#2148
This fixes a few of the knock-on effects of the actual fix.
* Test that we still write SMILES properly
* Fixes#2266 (#2269)
* Fixes#2268 (#2270)
* Improve interactivity of output SVG (#2253)
* Add clickable atoms when tagAtoms() is called
* add python tests
* add class tags for atoms and bonds
* add marker to allow easy insertion of extra text
* Add clickable atoms when tagAtoms() is called
* add python tests
* add class tags for atoms and bonds
* add marker to allow easy insertion of extra text
