* do not remove hydrides by default
* add a minimal test
* add release note about behavior change
* require Hydrides to have degree 1
* also allow hydrides with degree 0 (ionic bond)
* suggested changes
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* backup
builds but no tests
* deprecate old form
* initial basic tests for bond property lists
* Tests pass
Fixes#8777
* add deprecations to release notes
* - avoid computing size of a constant at runtime
- replace multiple instances of a numeric constant with a literal constant
- avoid unnecessary copying of strings in iterations and function calls
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Fixes#8379
* check in some working tests
* test passes
* test passes
* test passes
* test passes
* test passes
* ensure that the invariants flush the streams on failure
* tests pass
* test passes
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* tests pass
* Fixes#8391
* tests pass
* fix a test with legacy
not clear why this was not causing problems before
* make a test work
* Fixes#8396
* gcc builds work
* fingerprint tests pass
* mention backwards incompatible change
* fix a problem with FindMolChiralCenters
* more testing details
* enable the test status output
* Fixes#8432
fix a bug in double-bond stereo handling for template matching
* all depictor tests pass
* use the new-stereo chiral ranks in the depiction code
* always assign new-stereo chiral ranks
* make _ChiralAtomRank a computed property
This is analogous to _CIPRank
* tweak to the way the atom ordering is computed for 2D coordinate generation
* update two expected results
* backup
* response to review
* tests pass
* tests pass
---------
Co-authored-by: = <=>
* 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>
* Remove GetUniqueCombinations, use instead GetUniqueCombinations_new for improved speed. Update related tests.
* Remove unused and uncalled parameter `which`
* Update tests for GetUniqueCombinations to be in numerical order. Remove unused variable `x`. "Alias" GetUniqueCombinations_new to GetUniqueCombinations for backwards compatibility. Add note about backwards incompatibility for GetUniqueCombinations to ReleaseNotes.md.
* Create _compareCombinationsOrderUnimportant and use for testGetUniqueCombinations for order-insensitive comparison
* Replace call to GetUniqueCombinations_new with GetUniqueCombinations in Gen2DFingerprint for consistency
* Properly cleanup Dict::Pair when serializing HasPropWithQueryValue
* Make sure pickling doesn't change original molecule
* Fix bad cut and paste
* Add PairHolder utility class for memory management of non Dict Dict::Pairs, fix mem leak in pickler
* Edit comment to force a rebuild
* Ignore PairHolder from Java/Swig builds
* Ignore PairHolder API from swig
* Reponses to review
* Add backward incompatible change
* Make release note a bullet point
* - moved SMILES and RGroupDecomp JSON parsers to their own translation units
- added missing DLL export decorators that had been previously forgotten
- changed the signatures of MolToCXSmiles and updateCXSmilesFieldsFromJSON
to replace enum parameters with the underlying types
- updated ReleaseNotes.md
* make sure cxSmilesFields is only updated if the JSON string contains keys
belonging to the CXSmilesFields enum
* added missing copyright notices
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* First try at using DistViolationContribs
only the most basic of testing has been done
also add ForceField::distance2 to allow some optimizations
* allow testing using old approach
* optimization
At this point testUFFForceFieldHelpers fails since the check for std::max_element
in the e_contribs vector at Embedder.cpp:513 is now doing something totally different
(instead of a bunch of small distance violation contribs, we have one big one).
We'll need to come up with something for this.
With the benchmarking set that I'm using - 500 DG conformers for ~465 COD molecules
using 10 threads - this runs in almost 10% less time than master.
* backup;
builds, tests do not pass
* all tests pass except the old failure
* more constification
* backup/debugging
* add fourthdim contribs the same way
* tests now pass
* deprecations
* remove unused vars and code
* changes in response to review
* change valence model to use isolobal analogy
Remove support for five-coordinate C+ and, by analogy, five-coordinate N+2
Removes support for charge states that take atoms past the end of the periodic table
i.e. [Lv-4] is no longer supported
* update the tests for that
* remove valence state of 6 for Al
* fix representation of phosphate in the mol2 parser
this is a correction of what was done during #5973
* cleanup the exceptions for P, S, As, and Se
* drop valence states:
Si 6, P 7, As 7
* a couple of additional changes from #7397
* update java tests
* fix an inconsistency: Rb now supports valence -1
* documentation
* - replace operator[] with at() for bounds check
- extract some code into a function to avoid duplication
- use TAB as separator throughout in the periodic table data for consistency
* removing the .at() usage
We know that these vectors aren't empty, so there's no need for the bounds check.
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* deprecations for the 2024.09 release
* update doctests
* Fixes#7402
* get tests passing when the cairo build is not there
* fix a problem in the tests
* - 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>
* 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>
* 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 (#7279)
* fixes#7295 (#7303)
* tag 2024.03 release (#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 (#7314)
* restrict the application of 1,3- 1,5- conjugated cation normalization (#7287)
* propagate yaehmop build status (#7316)
* Fixes#7299 (#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>
* expose symmetrizeTerminalAtoms() to the public API
* support symmetrizing terminal groups in RMS pruning in confgen
* add that to the python wrapper
* add backwards compatibility note
* allow JSON config of the new option
* backup
* backup
* backup
* new testing file
* reorder things in the SMILES and SMARTS parser
parameters to allow easier struct initialization
* add v2 of SmilesMolSupplier
v1 is not yet there
* add TDTMolSupplier
add some very basic tests for v1 suppliers
* more progress
* all tests passing
I think all the suppliers are now moved over
* check for maeparser before building the tests
* get SWIG builds working
* changes in response to review
* refactoring of MolStandardize validation module
* redefine MolStandardize::ValidationErrorInfo as an alias for std::string
* changes in response to review
* describe the backward incompatible changes to MolStandardize in the release notes
* Sanitize number of radical electrons in case of invalid value assigned by CXSMILES (#6370)
* static_cast<int> for integer comparison
* Add unittests for 0 explicit hydrogens
* Fix unittests of radical count in fileParsersTest1
* Fix testMolWriter
* Fix testMrvToMol
* Address Greg's comments
* fix a float comparison in a test
* make ETKDGv3 (i.e. v2 of the torsion parameters) the default.
This should have been done a long time ago.
* change default for onlyHeavyAtomsForRMS too
* release notes update
