* backup
* basic tests pass
* add JSON out to substruct match parameters
* serialize the substruct match parameters in reactions
* add that to the python wrapper
* more testing
* Fixes#6138
* If we aren't initialize, don't dump AllProps
* Save atom props for agents as well
---------
Co-authored-by: Brian Kelley <bkelley@relaytx.com>
* reader stub. Navigates the file successfullly
* works
* works
* read out all metadata, not just ours
* first pass at reading out molecules
* support mol blocks too
* add python wrapper for parser
* add direct writer
* get rid of multiple definitions in PNParser.h
* update from code review
* robustification
* handle reading compressed metadata
* support compressing metadata too
* reorder arguments to make this more consistent
* add writers to python wrappers
* forgotten file
* add pickle support
* explicit zlib dependency
* get windows builds working
at least with conda boost+zlib
* switch to using boost::iostreams to do the compression/decompression
* switch to using a vector of string pairs to store the metadata
need this so that we can contain "duplicate" keys
* add metadata output to MolDraw2DCairo
still need python test
* add a python test
* initial work at reading/writing reactions from PNGs
refactor the ReactionParser.h header a bit
* cleanup debug messages
* reaction PNG support -> python
* ReactionPickler no longer includes all ProductTemplate props
* handle metadata at the MolDraw2D level
Currently only supported by MolDraw2DCairo, it's worth extending this to SVG too
* support reading multiple molecules from a png
* support multiple molecules from files and in python
* stop duplicating tags with multiple molecules
* update to get windll builds working
this change should be propagated to more cmakelists.txt files
* make sure the metadata ends up in the notebook
* make sure PNGs in the notebook also have metadata
efficiency improvements for some notebook bits (i.e stop going PNG->Image->PNG)
* no need to pretend that we might be using PIL anymore
* documentation
* update docs to show new functionality
* not sure why the doctests failed on linux
* still trying to diagnose those failures
* protect doctests in case python interpreters are being re-used
* switch tags
* the wrapped functions to read png data from files weren't working
* <sigh>... windows dlls
* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke
* fix problem on windows
* initial pass at pickling reaction properties
* move more of the property handling functions to props.hpp
Wouldn't be bad to rename these at some point.
* add reaction properties to python wrappers
- Module to generate reaction fingerprints: structural FP for screening,
difference FP for similarity search
- Add some utility functions to simplify handling of reactions
- Add new functionality to include agents in the reactions, some adaptions
to parsers and writers had to be done
- Supports intra-bond breaks in products now
- Molecules with rxn role (atom property) can be parse as reaction now
