- Added Run Reactants and added JS Tests

Thank you so much for the suggested changes!

* fix hybridization for atoms with outgoing dative bonds

* expose and wrap C++ numPiElectrons

* deprecate AtomPairs.Utils.NumPiElectrons

* add & update tests

* fix draw2d test

* update expected hash

* add hybridization test

* move numPiElectrons to Atom.h

* take reference instead of ptr

* changed string_view to string in catch test

* fix bug in atrop wedge determination

* reverted changes from string_view to string

* clean up of python and c++ for-loops

* readd assignement

* Remove misleading walrus operators (rdkit#7323)

* Run installed tests if applicable (rdkit#7325)

* simpler check for equality

* Revert "simpler check for equality"

py assert does not work pointwise on lists on all platforms,
we need to iterate through all elements

This reverts commit 03cc0ad.

* fix ambiguity on truth value of np arrays

* compare list elementwise

---------

Co-authored-by: Matt Swain <m.swain@me.com>

* add tests

* fix

* Dotnet core build and test for RDKit

* Cmake dot net build and ctest working on windows

* Remove old Linux mono build

* Update to net8 and create RDK_BUILD_DOTNET_CSHARP_TESTS flag

* switch to range-based for loops

* Update Code/GraphMol/testChirality.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* fix a leak in the new DCLV code (rdkit#7279)

* fixes rdkit#7295 (rdkit#7303)

* tag 2024.03 release (rdkit#7308)

* tag release

* attempt to solve constant MD5 problems

* switch to getting the ComicNeue font from github instead of as a zip

* open new release cycle (rdkit#7314)

* restrict the application of 1,3- 1,5- conjugated cation normalization (rdkit#7287)

* propagate yaehmop build status (rdkit#7316)

* Fixes rdkit#7299 (rdkit#7304)

* clean up of python and c++ for-loops

* clang formatted testChirality

* fix test file

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
Co-authored-by: Riccardo Vianello <riccardo.vianello@gmail.com>

* fix 1,3- 1,5- conjugated cation normalizer transforms

* small refactoring

* add some test cases related to the normalization of conjugated cations

… away (rdkit#7291)

* Include macrocycles in atropisomer calculation

Previously, atropisomeric bonds were sanitized away if they were part of a "ring bond", which happens in macrocyclic systems.
None of the existing test cases fail if that sanitization check is removed.
The sanitization step is removed to support biaryls that are part of a larger macrocyclic system.
A set of test cases is included that cover potential macrocyclic atropisomeric systems

* Remove unmentioned files

* Keep ring check, and narrow it to when bond is in as many rings as atoms

* exclude atropisomer bonds if in rings < 8 atoms

Co-authored-by: tadhurst-cdd <112502803+tadhurst-cdd@users.noreply.github.com>

* Clarify macrocycle behavior in RDKit book

* fix typo

---------

Co-authored-by: tadhurst-cdd <112502803+tadhurst-cdd@users.noreply.github.com>

* add a test

* fix issue

…ee (rdkit#7344)

* Add exactConnectionsMatch option.

* Better python test.

* Better C++ test.

---------

Co-authored-by: David Cosgrove <david@cozchemix.co.uk>

* Extend double bond far enough.

* Oops.

---------

Co-authored-by: David Cosgrove <david@cozchemix.co.uk>

…t#7255)

* Correct unbranched alkane SMARTS to match the description: must restrict to only carbon and allow for terminal alkanes

* Add backwards incompatible change notes

* move and edit incompatible changes note

---------

Co-authored-by: Daniel Levine <levineds@meta.com>
Co-authored-by: levineds-meta <159849019+levineds-meta@users.noreply.github.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>

…rdkit#7194)

* - renamed getParamsFromJSON() to updateSmilesWriteParamsFromJSON() and moved it from the anonymous namespace to the RDKit namespace such that it is publicly available
- implemented updateCXSmilesFieldsAndRestoreBondDirOptionFromJSON()
- added CFFI and JS tests
- get_smiles(), get_smarts(), get_cxsmiles() and get_cxsmarts() are now available in MinimalLib in both CFFI and JS layers and they can be passed JSON parameters
- CFFI get_qmol() now returns NULL if it fails to generate a RWMol rather than returning the "Error!" const char[] string, for consistency with what get_mol() and get_rxn() do. This was documented in release notes

* suggestions

---------

Co-authored-by: ptosco <paolo.tosco@novartis.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>

* removed string_view in favor of string for catch test

* add parsing and generation of atropisomers when coords not present

* changed string_view to string in catch test

* more docs

* reformulation of the docs

* make an error message a little bit more useful

* small optimization
clang-format

* add `BondWedgingParameters` to new function

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

…" (rdkit#7370)

This reverts commit 2159594.

* Fixes rdkit#7331

Essentially this modifies the code to use the isolobal analogy

Also improves error reporting a bit.

* generalize that a bit

* more testing

* for-loop modernization

* declaration and initialization together

* switch statements, min&max from std

* switch statement

* use of std min&max

* fixed unsigned int to int comparison

* implement switch statement

* fix unsigned int to int comparison

* revert previous mistake

* Update Code/DataStructs/DiscreteValueVect.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* implemented suggestions

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* fixes bug with overly large count_bounds

bug found and submitted by Andrew Dalke

* add another test

…ged sites (rdkit#7382)

* Add mono build back into C# build

* Add mono build back into C# build

* Add mono build back into C# build

* Don't do mono build on Linux if dotnet is used

* CSharp dotnet build always on windows. Enable dotnet testing in vs_build_swit

* Fix typos

…less the bond type (rdkit#7386)

* Allow reapplyMolBlockWedging to restore the original wedging regardless the bond type

* update python wrapper for Chirality::reapplyMolBlockWedging

* changes in response to review

* update the API documentation

…kit#7388)

Co-authored-by: ptosco <paolo.tosco@novartis.com>

* use references, skip batch remove if nothing to remove

* fix commitBatchEdit

* reword comment

PostgreSQL 16 got stricter wrt proper Pointer and Datum handling.

Signed-off-by: Michael Cho <michael@michaelcho.dev>

This reverts commit 7a050b4.

Co-authored-by: ptosco <paolo.tosco@novartis.com>

… output (rdkit#7395)

* Allow any bond (smiles ~) recognition in CDXML

* Move anybond.cdxml to the right place

* a bit of simplification

---------

Co-authored-by: Brian Kelley <bkelley@relaytx.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

…oxime oxygen (rdkit#7403)

* changed string_view to string in catch test

* fix bug in atrop wedge determination

* reverted changes from string_view to string

* changed to make build work

* removed changes made to allow build

* backup

* remove default valence for Tl

* Added Wrapper Files

* Addd interface file

* Edited interface file

* Rascal SWIG wrapper finished

* Remove from Java wrapper

* add java wrappers too

* Update GraphMolCSharp.i

* Update Code/JavaWrappers/RascalMCES.i

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

* Update Code/JavaWrappers/RascalMCES.i

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

* deprecations for the 2024.09 release

* update doctests

* Fixes rdkit#7402

* get tests passing when the cairo build is not there

* fix a problem in the tests

* Expose QueryOpts::replaceAtomWithQueryAtom.

* Indentation error.

* Response to review.

* Update docstrings in response to review.

---------

Co-authored-by: David Cosgrove <david@cozchemix.co.uk>

…dering (rdkit#7418)

* removed string_view in favor of string for catch test

* add parsing and generation of atropisomers when coords not present

* changed string_view to string in catch test

* more docs

* reformulation of the docs

* make an error message a little bit more useful

* small optimization
clang-format

* add `BondWedgingParameters` to new function

* changes for CIP test errors

* Updated internal doc to match what it does

* changes per PR review

* removed cout statements in tests

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* prefer wedging ring bonds for atropisomers

* update expected results

* handle 3D as well

* prefer wedging to larger rings

wedging bonds in 5 rings make later attempts at improving kekulization very difficult

update expected results

* extend those changes to 3D

* update tests for those changes

* avoid wedging atropisomers if possible

response to review

* Fixes rdkit#7414
Fixes rdkit#7409

* skip that test if cairo is not enabled

* fix unsigned int to int comparison

* revert previous mistake

* declaration & init together, sinthetaSq in [0, 1]

* using std::swap

* use that sinThetaSq in [0,1]

* declare & init at same time

* use knowledge about target range

* use std::clamp

* use std::max

* numerically more stable trigonometrics

* numerically more stable trigonometrics

* numerically more stable trigonometrics

* range based for-loop

* actually do the assignement

* Update Code/ForceField/MMFF/Params.h

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* implemented suggested changes

* Revert "implemented suggested changes"

This reverts commit f56e8f0.

* auto typing

* remove old comment

* revert to numerically more stable expression

* now correctly formatted

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* check for ringinfo levels instead of init

* check for ring info in kekulizefragment

* add a test

* update tests

* update doctests

* revert ringinfo level checks

* make wedgeBondsFromAtropisomers get symm SSSR if not present

* add atropisomer wedging ring info test

* add a test

* update test

* ignore ct stereo status, enh stereo status, atom type on read

* do not prefix maestro properties

* add a test

* Query atom information in swig

* Atom query swig wrapping working

* SWIG wrapper for queries

* Add match to QueryAtom and QueryBond

* CShart test

* Added Java test

* Replace var with type for Java test

* Apply suggestions from code review

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

* Update Code/JavaWrappers/Queries.i

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

* Apply suggestions from code review

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>

* Get SWIG build working again

* Remove trailing whitespace from Queries.i

* Update Queries.i to use shared_ptr

* small simplification

* remove boost::make_iterator from ROMol.i

* further simplification

---------

Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
Co-authored-by: ptosco <paolo.tosco@novartis.com>

* support pickle params in SWIG wrappers
csharp tests need to be tested

* make that work with csharp too

* basic code to convert dative to single if we aren't outputting dative to the SMILES

add forms of GetAtomSmiles() and GetBondSmiles() that take SmilesWriteParams

* dative/coordinate bond support when writing CXSMILES

* expose all of that to Python

* remove usage of _doIsoSmiles property
add params to smarts writers

* allow disabling dative bonds in SMARTS

* typo

* add support to the reaction writers

* support params for SMARTS

…kit#7462)

* Allow the substruct library to be deleted when refcount goes to 0

* Remove whitespace changes

* Update Code/GraphMol/SubstructLibrary/Wrap/SubstructLibraryWrap.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

…roperty prefixing (rdkit#7454)

* update prefix to _rdkit_, special treatment for group label prop

* update tests

This moves the function into the Chirality namespace.

* fix: Restrict lowercase atomic numbers

* fix: Add missing test for aromatic aluminum

* fix: Add independent test case for aromatic aluminum

* changed string_view to string in catch test

* fix bug in atrop wedge determination

* reverted changes from string_view to string

* changed to make build work

* removed changes made to allow build

- Added Run Reactants and added JS Tests

…rdkit#7194)

* - renamed getParamsFromJSON() to updateSmilesWriteParamsFromJSON() and moved it from the anonymous namespace to the RDKit namespace such that it is publicly available
- implemented updateCXSmilesFieldsAndRestoreBondDirOptionFromJSON()
- added CFFI and JS tests
- get_smiles(), get_smarts(), get_cxsmiles() and get_cxsmarts() are now available in MinimalLib in both CFFI and JS layers and they can be passed JSON parameters
- CFFI get_qmol() now returns NULL if it fails to generate a RWMol rather than returning the "Error!" const char[] string, for consistency with what get_mol() and get_rxn() do. This was documented in release notes

* suggestions

---------

Co-authored-by: ptosco <paolo.tosco@novartis.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>

* changed string_view to string in catch test

* fix bug in atrop wedge determination

* reverted changes from string_view to string

* changed to make build work

* removed changes made to allow build