* support providing custom features
* expose that to python
* switch to tuples (on get) and objects (on set) for attributes
* allow aligning mols directly with ShapeInputOptions
* changes for review
* add warning
* Set explicit COST=100 for SQL functions
* Adjust COST to 100 in current databases and up the cartridge version
* Use CREATE OR REPLACE for consistency
* Update the version number in rdkit.control
Fixes github issue #8597.
* UFFGetMoleculeForceField was returning
PyForceField* before the class was registered via rdForceField,
which caused “No Python class registered” errors in Python when
using multiple conformers.
* This patch forces rdForceField to be
imported during rdForceFieldHelpers module init, ensuring the
class is always registered before helper functions are used.
* Add unit test
* Adds missing options docstring
* Always be cleaning
* Fix typos in RGroupDecomposition module
* Update documentation on configuring doxygen
* Was a step that I couldn't find reference to besides in the Makefile
* Undo american spelling of labelling
* British spelling appears more consistent
* Fix style of RGroupDecompositionParameters parameter
* Also fixes a typo
* Remove unintentional use of docstring
* Was assigning documentation about the parameters to the
RGroupDecomposition
* Remove empty string
* Apply suggestions from code review
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* backup
builds but no tests
* deprecate old form
* initial basic tests for bond property lists
* Tests pass
Fixes#8777
* add deprecations to release notes
* - avoid computing size of a constant at runtime
- replace multiple instances of a numeric constant with a literal constant
- avoid unnecessary copying of strings in iterations and function calls
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Changed linux build from source docs to use miniconda
- closer to the azure builds
- uses conda-forge
- consolidated all dependencies into one command
- removed two cmake flags causing warnings that were not in the azure builds
* readability
* Switch to miniforge installers
* - avoid code duplication through a templated function
- enable switching off boolean flags via JSON and not just on as before
* ran clang-format
* change in response to review
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
isascii() (which is the standard) or __isascii(), but it guesses wrong for
Emscripten builds (which I do during sketcher compilation). This change
passes -D__isascii=isascii when building InChi,
which means that the wrong guess will still wind up with the right
function name.
* add test
* potential fix
* whops\!
* support disabling ring stereo in rankMolAtoms
* pass atom ranks into the ring-stereo detection code
* all tests pass
* forgot a file
---------
Co-authored-by: Ric R. <ricrogz@gmail.com>
* Fist pass at CDX support
* Enable CDX support for reading (also) in the CDXMLParser API
* Add cdxml test files
* Update swig wrappers for CDXMLFormat and Parameters
* Add constructor to ChemDrawParserParams
* Add Java SWIG support for ChemDraw
* Add chemdraw define to rdconfig
* Add missing chemdraw deps
* Remove direct expat link
* Fix Java linkages for ChemDraw
* Remove bad merge code
* Remove bad merge code
* Fix csharp builds
* Add sniffer for the ChemDraw DataStream
* Include filesystem
* Fix test on windows
* Add more CDX tests
* Ensure streams are open in binary mode to support CDX on windows
* Fix text to show that a Block is the text input, not a file
* Fix CSharp test
* Disable CDX tests when not building chemdraw
* Turn back on chemdraw
* Response to review
* Turn off chemdraw support for the limited external test
---------
Co-authored-by: Brian Kelley <bkelley@glysade.com>
* Fixes a bug with bad H positions in output conformer
This would only trigger when the number of H atoms is equal
to the number of features, but it was terrible when it happened.
* spell that better
* docs
---------
Co-authored-by: = <=>
* Fix parse error messages for bad characters
This updates the SMILES and SMARTS parser error messages to include the token
position for "bad" characters.
* copy generated files
* add test
* Try tab-separated before space-separated when reading synthon lines.
Fix bug in looking up reactions by name.
amino_acid.txt had a mixture of tab-separated and space-separated lines which is no longer allowed.
* Typo
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* get SynthonSpace.cpp to build also when RDK_USE_BOOST_SERIALIZATION is
not defined
* test should not fail when RDK_USE_BOOST_SERIALIZATION is not defined
* - expose reading/writing PNG metadata to CFFI and MinimalLib
- add relevant CFFI and MinimalLib unit tests
- add RDK_USE_BOOST_PROGRAM_OPTIONS CMake option
- enable using standalone zlib in the absence of boost::iostreams for parsing PNG files
- enable linking against maeparser in the absence of boost::iostreams also on Windows
- enable building RDKit in the absence of boost::program_options
* add check for boost::program_options
* change size_t into std::uint64_t in SearchResults for consistency with doTheSearch() which uses std::uint64_t
* change size_t into std::uint64_t in SearchResults for consistency with
SynthonSpaceSearcher::doTheSearch()
* set CMake policy to allow YAeHMOP to require a version which is not
actually supported
* reverted External/YAeHMOP/CMakeLists.txt to master version
* check if Windows build will work
* fix build
* configure zlib install location
* build zlib dependency
* include zlib header directory
* explicitly set PropertyFlags.AllProps so the test does not fail on
static builds
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
