* Fix vulnerabilities found by fuzzer.
* Fix Typo in RWMol.cpp
* Update RWMol.cpp
This is an attempt to double check where the test failure is coming from.
* Update RWMol.cpp
Re-adding changes to test tests.
* - fixed a crash in Avalon occurring when an atom idx in the bond table is out of bounds
- removed 0-padding ahead of parsing bond line as it is unnecessary and potentially harmful
- forked Avalon so it can be patched more conveniently
* updated the Avalon pre-relase number and updated the checksum
* updated pre-release number and checksum
* moved the Avalon fork under RDKit organization
updated checksum and release
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Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* get the config of the windows DLL builds to match the main windows builds
* bump boost version
* Update vs_build_dll.yml
* sigh...
* disable python on that build
* add back cairo
* Minimal update to fix hang in the legacy stereo checker
* a small amount of cleanup and some refactoring
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Co-authored-by: Brian Kelley <bkelley@relaytx.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
- Use the nodejs version bundled with emscripten to run tests since the one in Ubuntu is ancient and does not support recent wasm features
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* - Fix a couple of docstrings that were confusing boost::python
- Python keywords should not be used as parameter names
* changes in response to review
* removed two leftover BOOST_PYTHON_FUNCTION_OVERLOADS
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Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
The docstring claimed that it returned the new number of atoms. It actually returns the index of the new atom.
I think it makes more sense to change the documentation than the behavior, because callers are definitely out there using the current behavior.
* Scale bonds, make the Wedge detection cleaner, add more tests
* Readd comment
* Use document bond length
* Adds roundtrip test through a molblock
* a bit of cleanup
* change expected results for a bogus structure
add a non-ambiguous version of it
* fixes#6462
* document incompatibility
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Co-authored-by: Brian Kelley <bkelley@relaytx.com>
* Fixes#6395: Move string index appropriately with molfiles
This code gives a fix to issue #6395, where properties lines in molfiles might not be processed correctly when dealing with pairs of values.
* Update tests to reflect molblock parsing changes
* straightenDepiction should not consider 0-degree rotations as multiples of 60
* improved JS straightenDepiction test which was a bit silly
* changes in response to review
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Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
