* 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>
Made the following changes
* removed RDK_USE_BOOST_REGEX cmake option and its references
* removed usage of RDKIT_USE_BOOST_REGEX macro
* removed install instructions related to boost regex
* wip
* user my fork for rdkit-js temporarily
* clean up obsolete files and refactor readme for it to make sense with new rdkit-js repository
* fix dockerfile
* fix URLs and cleanup documentation hierarchy
* further replacement of rdkit-js references where it makes sense
* add link to 2021 UGM in readme
* External/INCHI-API: drop unnecessary mutex
A mutex was introduced in 6cfd34 from 2012 around all InChI library
calls, and InChI v1.05 release notes from 2017 announce that they fixed
race conditions to support multithreading.
We find that the InChI library mutex is no longer necessary with v1.05
and this patch removes it, which enables rdkit users to concurrently
call InChI-related methods.
This patch also updates the InChI multithreading tests to cover
`MolBlockToInchi`, so we have test coverage of concurrently making all
InChI calls.
I ran `testInchi` under asan 200x and all runs passed cleanly. I was
unable to configure the build toolchain with msan or tsan, so it is
unclear to me if those sanitizers would flag any issues.
* External/INCHI-API: add second multithreading test
This test covers case where immediate concurrent usage of the InChI
library leads to memory corruption.
* remove ASAN workaround (not needed for InChI 1.06)
clang-format run
update inchi version to 1.06 in docs
Co-authored-by: Jin Pan <jinxp1@gmail.com>
* update version of japanese docs
* Remove external labels from cores
* Fix syntax errors
* Add better autodetection of labels, add dummyatom label, don't fall back to indexes when onlyMatchAtRgroups are set
* Add better autodetection of labels, add dummyatom label, don't fall back to indexes when onlyMatchAtRgroups are set
* Move autodetection before alignment, fix final core labelling
* Fix stupid bit twiddling mistake
* None of the original mol's should actually match the cores with onlyMatchAtRgroups
* Convert PRECONDITION to CHECK_INVARIANT
* Run clang-format
* use nullptr instead of 0 for pointers
* Handle cases where molecules don't have anything for an R-group properly.
Here's the python demo of the bug:
```
In [14]: scaffold2 = Chem.MolFromSmiles('c1c([*:1])cncn1')
In [15]: scaffold = Chem.MolFromSmiles('c1c([*:1])cccn1')
In [19]: mols2 = [Chem.MolFromSmiles(smi) for smi in 'c1c(F)cc(O)cn1 c1c(F)cncn1 c1c(Cl)cc(O)cn1'.split()]
In [20]: print(rdRGroupDecomposition.RGroupDecompose([scaffold,scaffold2],mols2,asSmiles=True,asRows=False))
({'Core': ['c1ncc([*:2])cc1[*:1]', 'c1ncc([*:1])cn1', 'c1ncc([*:2])cc1[*:1]'], 'R1': ['F[*:1]', 'F[*:1]', 'Cl[*:1]'], 'R2': ['[H]O[*:2]', '[H]O[*:2]', '']}, [])
```
* Fixes#2471
* add documents translated into Japanese
* add conf.py
* change links to images
* change Translation_into Japanese to Translation_into_Japanese
* move japanese translation to Book_jp
* update image paths
* makefile and config
* remove Book/Translation_into_Japanese
