* refactor the code to determine whether or not an atom is in brackets
* move the definition of isMetal to QueryOps
* atoms bound to metals in SMILES should always be in square brackets
Implementation and some test updates
needs confirmation that all of tests run
* basic tests pass
* java tests pass
* update js tests
* doc updates
* Update Code/GraphMol/catch_graphmol.cpp
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
* Update Code/GraphMol/SmilesParse/test.cpp
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
* finish fixing tests
* bump yaehmop version to allow compilation to work
---------
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
* Expand on Explicit Valence Error - Partial Sanitization recipe, including adding molecular structures for the unsanitized and partially-sanitized iterations
* Format `argument=value`
* Fix typo in formatting
* Update label to *Original* Source
* Correct rdqueries import, and formatting of testoutput blocks
* Print out hybridization create doctests
* doc updates
* add rdShapeAlign to the docs
* fix shape docs
* let's not add too much here, revert deprecation
* cleanup the python book
* more book cleanups
* bring in sphinx.napoleon so that we can use the numpy docstrings
* fix a typo
* Update rdkit.ML.rst
* Add "Include a Bond Index" recipe and image
* Add testoutput so doctest passes
* Use addBondIndices. Follow template of recipe "Include an Atom Index".
* update cookbook, draw molecule atomic indices
By default, RDKit 2023.09.3 does not explicitly displays atom index 0.
* describe absence of atom index zero in the formula
* backup
* does not work
* backup
* passes all tests
send more tests!
* backup
* seems to mostly work
needs cleanup still
* more tests + python wrappers
* more testing
* some cleanup
* fix problem with newer boost
* be more expansive about unsaturation
* be symmetric in choosing the starting bond
fix a test error
* passes all tests;
passes ChEMBL regression test
* docs
* update cookbook
* expose the new hash function to the cartridge too
* support v2 hash in the registration hash
* better testing
* alternate, simpler approach for that
* remove vestigial docs
* include info about query rendering
* Fixes#3897
* update images
* better documentation for the conformer generator
* conformer not conformation
* switch to using context managers and make sure we add hs before generating conformers
* yay more docs
* Finishing #3917
* more documentation of backwards-incompatible changes
* 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
* Added Cookbook_v2 title to toctree index.rst file
* Add Cookbook_v2 PNG images
* Add RDKit Cookbook_v2.rst document
* Added all corrections and suggestions from reviewer round 1
* Added note about reverse mapping.
* suggested changes
* rename step1
* replace old cookbook with the new one
* replace old cookbook with the new one
* replace old cookbook with the new one
* Minor corrections added requested in greg review
* Removed old markdown Cookbook and renamed new document Cookbook.rst
* fixed a note typo
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
