* add flipping of spiro rings as a way to solve clashes
* remove extra function
* add test file
* update coordgen parameters to allow for bond flipping
* fix failing tests
* Update Code/GraphMol/Depictor/EmbeddedFrag.h
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/Depictor/EmbeddedFrag.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/Depictor/EmbeddedFrag.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/Depictor/EmbeddedFrag.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* [bot] Update molecular templates header (#9234)
Co-authored-by: github-actions[bot] <github-actions[bot]@noreply.github.com>
* Add some std::ranges support (#9218)
* initial ranges support for Atom/Bond iterators.
needs more testing
* support random access
test sort
more testing please
* compiles on windows
* fix size()
more testing
add some benchmarking
* disable benchmarking code by default
* do not allow modifying the graph through the iterators
---------
Co-authored-by: = <=>
* mention AI tools in the contrib guidelines (#9224)
* mention AI tools in the contrib guidelines
* response to review
---------
Co-authored-by: = <=>
* Add getSGroupDataLabels() to MolDraw2D_detail namespace (#9189)
Adds a new function MolDraw2D_detail::getSGroupDataLabels() that returns
the text and molecule-coordinate positions of DAT SGroup labels, using
the same placement logic as the drawing code. This allows external
renderers to display SGroup labels consistently with RDKit's placement.
Refactors DrawMol::extractSGroupData() to call getSGroupDataLabels()
internally, eliminating the duplicate FIELDDISP parsing and position
computation logic.
Closes#7829
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
* MolDraw2D: configurable legend position and vertical side legends (Issue #9023) (#9183)
* Configurable legend position (Top/Left/Right/Bottom) and vertical text (GitHub #9023)
- Add LegendPosition enum and legendPosition, legendVerticalText to MolDrawOptions
- Support legend at Top, Left, Right, Bottom; vertical text for Left/Right
- Python: MolDrawOptions.legendPosition, .legendVerticalText; LegendPosition enum
- Python: MolToSVG() wrapper with legend/drawOptions; doc updates for MolToImage
- JSON: legendPosition (string), legendVerticalText (bool) in draw options
- C++ and Python tests; release note and Cartridge.md docs
* MolDraw2D: legend gutter for horizontal side legends; vertical side height fit
- Reserve horizontal gap between molecule and left/right horizontal legends
(scale mol to molWidth-gutter, align toward legend strip).
- Position horizontal side legend by measured text width from partition edge.
- Vertical side legends: iterative scale so n*max_h+(n-1)*gap fits panel.
- Catch: long vertical side legend section.
* Update legend-position tests and review-driven cleanup
Use enum/default wording for legendPosition docs, move the lightweight Python test to Wrap, add regex-based placement checks (including horizontal side and vertical stacking), and refactor extractLegend helpers per style guidance.
* Fix MolDraw2D legend edge cases
* MolDraw2D: review follow-up (legend tests, bounds, DRY Top/Bottom)
* Update no-FT legend test coords
* Address PR review: document constants, remove release-note text, and simplify extra-padding logic
* make sorting more consistent (#9239)
* Cleanup/get atoms and bonds (#9243)
* Fix bug in inversion term for UFF, add finite difference checker. (#9228)
* Fix copyright
* Address review comments
Removed finite diff from RDKit headers
Used explicit coordinates
* If templates match, skip ring number check (#9217)
* remove ring mathcing for templates
* remove extra code
* remove empty lines
* fix build error
* Tautomer insensitive hash v2, E/Z and stereocenter-preservation (#9128)
* Tautomer insensitive hash v2, E/Z and stereocenter-preservation
* Preserve E/Z stereochemistry and stereocenters in TautomerHashv2
Simplify extension logic to better protect stereocenters connected via
single bonds to aromatic systems. Preserve E/Z stereo on exocyclic
double bonds to distinguish geometric isomers (e.g., E/Z hydrazones).
* add helper function to remove duplicated code
* Fix ring info and bond aromaticity handling in MolHash
- Add fastFindRings check in TautomerHashv2 before ring queries
- Set isAromatic consistent with bond type (true for AROMATIC bonds)
- Fix inverted condition in RegioisomerHash
* more consistent hashes regardless of stereo annotation
* Ensure that StereoGroups don't have duplicate atoms or bonds (#9258)
* check for duplicate atoms/bonds in StereoGroups
* explicit handling of duplicate stereogroup atoms in CTAB and CXSMILES parsers
---------
Co-authored-by: = <=>
* Add Getter functions to MMFF property python interface (#9254)
* Support using iterators with MolSuppliers (#9230)
* iterators for random-access MolSuppliers
add optional caching to SDMolSupplier
* add support to SmilesMolSupplier too
There is a lot of duplicate code between the random-access suppliers that would be worth trying to remove
but at the moment it looks like it would require multiple inheritance, and I think we want to avoid that
* add input iterators for ForwardSDMolSupplier()
* throw when calling begin() on a used supplier
* switch to use the spaceship operator
* init() should reset the mol cache
* Make SDMolSupplier and SmilesMolSupplier safe for multi-threaded reads
* add benchmarking
* add TDTMolSupplier support
improved testing
add benchmarks for parallel iteration
optional TBB support
* better const handling, add reverse iterators
doesn't look like const_iterator is possible since getting data from the underlyng supplier object is non-const
* improve docs
more usings
add reverse iterator to TDTMolSupplier
* tests only try execution::par when it is there
* fix typo
* more testing/demo
* remove accidentally added files
* review changes
* add default ctors
* disable a false-positive compiler warning
it is stupid to have to do this
---------
Co-authored-by: = <=>
* Pandastools improvements (#9251)
* Added automatic parsing functionality
* Added documentation
* Slightly changed check for gzip extension
* Apply suggestions from code review
Added small changes for readability
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Add optional default_val parameter to GetProp() (#9242)
* SHARED-12256: Add test and change function.
* SHARED-12256: Update to only wrapping changes.
* SHARED-12256: Parameterize tests.
* SHARED-12256: GetPropIfPresent changes.
* Revert "SHARED-12256: GetPropIfPresent changes."
This reverts commit f598f8c161.
* SHARED-12256: Make default the keyword in the boost wrappings.
* SHARED-12256: Overload function instead of using a sentinel.
* SHARED-12256: Extend GetProp changes.
* SHARED-12256: Add entry point for tests and fix tests.
* Extended fix for #9101 (#9255)
* fix extended boundary issue (3 mols)
* clang pass
* no change. retrigger CI for failed java test
there's a failing java test that seems to be failing by chance rather than by changes, as it depends on rng. this is just to retrigger the CI pipeline to confirm this
* no change. retrigger the CI (yet again)
* raw strings and removed garbage collector
* CIP labeller performance: Don't calculate auxiliary descriptors unnecessarily (#9171)
* CIP labeller: Don't calculate auxiliary descriptors unnecessarily
The first 3 rules (the constitutional rules) are pretty easy
to understand. After rule 3, we need to calculate auxiliary
stereo descriptors to break ties.
However, we _were actually_ calculating auxiliary stereodescriptors
for all centers! We should only need to calculate auxiliary
stereocenters for sites that are needed to break ties.
This cost time - it also caused errors if the auxiliary descriptors
needed a graph expansion, because bonds in the digraph might be
pointed in the wrong direction.
Example case PDB ID 4AXM
Before this commit, errored with "Could not calculate parity! Carrier mismatch"
after 14s. After this commit, completes successfully in 0.036s.
Labelled centers all match (for the centers that had labels in
the failure case).
Includes a test that I can imagine breaking with this optimization.
The reference labels are from before this change
* Ensure all "arms" of stereo bonds and atropisomer bonds are expanded
For tetrahedral centers, ranking using the constitutional rules
always expands as far as is needed (but no further). For SP2bond
and atropisomers, if the first side is not resolvable, the
second side is never visited.
If the constitutional rules don't resolve a side, we need to
label the auxiliary centers. It's important to label all
auxiliary centers that _will_ be visited, so we need to know
what centers will be visited.
This commit updates the label() call in SP2 and Atropisomer
bonds to always attempt to label both sides if using the
constitutional rule set.
The constitutional rules are cheap, and if they fail, we
always go on to the full rule set. It is not a savings to skip
the search on the second side if we're going to keep going
anyway!
Includes a test that reproduces Ricardo's example.
This has no measurable effect on performance relative to the
original solution
* If any parts of the center have been seen, label it.
I couldn't make an example hit this, but Ric is totally
theoretically right
* Greg's ranges suggestion #2
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* any_of for container search
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* CIPLabeler performance: Store vector of bonds (#9250)
* CIPLabeler performance: Store vector of bonds
CIPLabelling refers to bonds by index over and over again. This
causes a measurable hit in performance in findConfigs() because
we iterate over a bitset of "allowed" bonds. For very large
molecules with many bonds, this can be a rate-limiting step!
This affects many PDB-sized structures.
2J3N goes from 0.7s to 0.25s with this change.
I had another example for which the findBondWithIdx() call was
taking 500ms of a 700ms call (after the performance update
in #9171 was implemented)
* yikes, XXL reserve
thanks, greg
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Address PR #9204 review feedback
Implemented performance improvements suggested by @greglandrum:
1. Move cheap degree check to start of isSpiroCenter()
- Early bailout eliminates ~95% of candidates immediately
2. Replace std::set with boost::dynamic_bitset<>
- Faster set operations for ring membership tests
- More efficient intersection using bitwise AND
3. Remove expensive PRECONDITION in flipAboutSpiroCenter()
- Caller already validates spiro center, no need to check again
All tests pass (testDepictor: 7.85s).
* Use boost::dynamic_bitset in removeCollisionsBondAndSpiroFlip
Replaced std::set<unsigned int> with boost::dynamic_bitset<> for
spiro center caching in collision resolution:
- Changed spiroCenters from std::set to boost::dynamic_bitset
- Updated tryResolvingCollisionWithSpiroFlip() signature
- Replaced set.find() with bitset.test() for membership checks
- Replaced set.insert() with bitset.set() for marking spiro centers
Benefits:
- Faster membership tests (O(1) bit test vs O(log n) tree lookup)
- Better cache locality (contiguous bit array vs scattered nodes)
- Simpler code (no iterator comparisons)
All tests pass (testDepictor: 2.64s).
* remove unnecessary reformatting
* more unneeded formatting
* even more unecessary formatting
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <github-actions[bot]@noreply.github.com>
Co-authored-by: Chris Von Bargen <christopher.vonbargen@schrodinger.com>
Co-authored-by: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-authored-by: Brandon Novy <142041993+Brandon-Cole@users.noreply.github.com>
Co-authored-by: Ricardo Rodriguez <ricrogz@users.noreply.github.com>
Co-authored-by: Kevin Boyd <kboyd@nvidia.com>
Co-authored-by: Eloy Félix <eloyfelix@gmail.com>
Co-authored-by: Marco Ballarotto <marco.ballarotto@icr.ac.uk>
Co-authored-by: Emily Rhodes <70823163+emilyrrhodes@users.noreply.github.com>
Co-authored-by: Raul Sofia <67133355+RaulSofia@users.noreply.github.com>
Co-authored-by: Dan Nealschneider <dan.nealschneider@schrodinger.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: = <=>
* remove no-op macros and dead code (pt 2)
* test failures due to whitespace changes?
* actually run the testFeatures tests
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Revert "Revert "Removed some code duplication between Depictor.cpp and common.h (#6368)" (#6797)"
This reverts commit 824616c5b9.
* security blanket: add back tests of the current usage pattern
* - fixed bug in get_sss_json() (#6806)
- added unit test for the above
Co-authored-by: ptosco <paolo.tosco@novartis.com>
---------
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* - implemented alignOnly mode into RDDepict::generateDepictionMatching2DStructure()
- the allowRGroups option now also supports potentially missing R groups (i.e., R groups that do not match any atom, such as those connected to generic aromatic atoms)
- added the adjustMolBlockWedging parameter (which defaults to true) to invert/clear molblock wedging information as appropriate
- added unit tests for the above new features
- added RDDepict::generateDepictionMatching2DStructure() overloads taking RDDepict::ConstrainedDepictionParams parameter for convenience
- removed some redundant RDDepict:: namespace specifications
* Fix chirality handling when the chiral atom is the first one in a SMARTS (#6730)
* Set _SmilesStart when parsing SMARTS.
* SmartsWriter should also invert first atoms, like SMILES.
* Update test cases now these SMILES match themselves as SMARTS.
* rerun bison
* cleanup a possible repeated define
* When an atom moves from the first to second position winding should flip in SMARTS (i.e. same as SMILES).
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Some small cleanups from the UGM Hackathon (#6744)
* move definition of a couple global constants from a .h to a .cpp
* careful removal of some redundant atom PRECONDITIONS
* careful remove of some redundant ROMol PRECONDITIONS
a bit of additional cleanup
* optimization masquerading as modernization
* some more tidying
* a bit more atom cleanup
* change in response to review
* Fixes#6756 (#6780)
* update release notes and cmakelists for beta (#6788)
* move problematic functions to Chirality namespace
* - implemented alignOnly mode into RDDepict::generateDepictionMatching2DStructure()
- the allowRGroups option now also supports potentially missing R groups (i.e., R groups that do not match any atom, such as those connected to generic aromatic atoms)
- added the adjustMolBlockWedging parameter (which defaults to true) to invert/clear molblock wedging information as appropriate
- added unit tests for the above new features
- added RDDepict::generateDepictionMatching2DStructure() overloads taking RDDepict::ConstrainedDepictionParams parameter for convenience
- removed some redundant RDDepict:: namespace specifications
* move problematic functions to Chirality namespace
* added missing dependency
* let's check what is going wrong
* CoordGen tests should not run if CoordGen support is not available in the build
---------
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
Co-authored-by: John Mayfield <john@nextmovesoftware.com>
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* straightenDepiction should not consider 0-degree rotations as multiples of 60
* improved JS straightenDepiction test which was a bit silly
* changes in response to review
---------
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* change default behavior so that dative bonds are not included in ring finding
* make sure that generating 2D coords does not lose the rings
* cleanup some leftover problems
* update AvalonTools to version 2.0.1
* Improvements to 2D depiction and alignment/RMSD calculation
- Refactored the straightenDepiction code which is now much simpler and more readable and supports a minimizeRotation parameter
- added C++, Python and JS tests for the new minimizeRotation parameter
- refactored tests to use CalcRMS rather than an internal implementation to compute RMS deviations
- Removed duplicated code in CalcRMS() and getBestRMS() and made their APIs consistent with respect to supported parameters
IMPORTANT NOTE: for backwards compatibility I set the CalcRMS() default for the new symmetrizeConjugatedTerminalGroups
to false as this parameter was not originally supported. @greg: I would be very much in favor of setting this to true instead
if you agree, even though it might change results for existing scripts, as I think it is a much more sensible default.
- Improved documentation to clarify the difference between CalcRMS() and getBestRMS()
- Added unit tests for CalcRMS() as there was none previously
- Added tests for the additional CalcRMS() and getBestRMS() parameters
- Added a new getBestAlignmentTransform() function
- The CFFI function set_2d_coords_aligned() now returns the matching atoms similarly to the C++, Python and JS counterparts
IMPORTANT NOTE: this required an API change for the additional char ** parameter used to return the match.
Existing code using set_2d_coords_aligned() will fail to compile and will require a last NULL parameter to be added to compile again
- Removed duplicated code between CFFI set_2d_coords_aligned() and JS generate_aligned_coords()
- Added has_2d_coords() to the CFFI library
- generate_aligned_coords() now supports JSON parameters and the previous versions are deprecated
- set_2d_coords_aligned() and generate_aligned_coords() both support an alignOnly parameter (which defaults to false).
If set to true, rather than re-generating a fresh 2D layout around templateMol, the existing coordinates (if any) are simply aligned
to the provided templateMol. If the molecule has no coordinates, a set of 2D coordinates is generated independently of templateMol
and then aligned to the provided templateMol
- avoid that when acceptFailure is false set_2d_coords_aligned() and generate_aligned_coords() overwrite existing coordinates
* - explicitly link testDepictor to MolAlign library
* - add MolAlign dependency to testDepictor (rather than to the catch test as in the previous commit)
- add a couple of tweaks
* suppress compiler warnings (1st pass)
* warnings: 2nd pass
* warnings: 3rd pass
* - alignOnly mode should also support allowRGroups
* - fixed C++ build
- added tests for allowRGroups+alignOnly combination
* changes in response to review
* added an entry to backward incompatible changes regarding set_2d_coords_aligned()
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* - adds normalizeDepiction() and Python wrappers
- adds straightenDepiction() and Python wrappers
- adds an early check for R-labels to be in the accepted range to avoid throwing an exception later on
- adds a kekulize flag to process_details() to enable depicting molecules which fail to kekulize from JavaScript
- adds JavaScript functions to get fingerprints as Uint8Array
- adds JavaScript function to generate pickled molecule as Uint8Array
- adds JavaScript function to restore molecule from Uint8Array pickled
- adds has_coords() JavaScript function
- adds set_new_coords() to set JSMol coordinates in-place
- adds get_mol_copy() to obtain a JSMol copy
* fix build failures
* changes in response to review
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* add test
* fix some of the horribly broken comment formatting
* a start at modernization
* more modernization
* more modernization
* more modernization
* add some actual regression testing
(such as it is)
* more modernization
* more modernization
* more modernization
* more modernization
* more modernization
* fixed, still some py failures to investigate
* fixed
* remove a bunch of debugging cruft
* changes in response to review
* Apply suggestions from code review
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* - generateDepictionMatching2DStructure can be used with referencePattern smaller than reference
to only use part of a scaffold
- adds generateDepictionMatching2DStructure overload to pass a matchVect instead of doing a substructure match
- adds allowRGroups parameter to enable using a scaffold bearing R groups as reference
* changes in response to review
* added comments
* fixes failing doctest
* - reverted change committed accidentally
- fixed get_sss_json for the case where R groups are not included in the match
- added tests for the return value of generate_aligned_coords
* Documented the value returned by GenerateDepictionMatching2DStructure (Python)
* changes in response to review
* - changes in response to review
- fixed sortMatchesByDegreeOfCoreSubstitution that was not working
- added Python wrappers for sortMatchesByDegreeOfCoreSubstitution and getMostSubstitutedCoreMatch
- added C++ and Pyhon unit tests for the above
* added missing variable initialization
Co-authored-by: Tosco, Paolo <paolo.tosco@novartis.com>
* do not use new on loggers
* del pointers in testDistGeom
* Update Dict hasNonPOD status on bulk update
* delete new Dicts in memtest1.cpp
* fixes in MolSuppliers and testFMCS
* PeriodicTable singleton as unique_ptr
* fix EEM_arrays leak
* fix leaks in testPBF
* fix ParamCollection leak in test UFF
* fix leaks in MMFF
* clear prop dict before read in in pickler
* fix leaks in testFreeSASA
* fix leaks in test3D
* modernize Dict.h & SmilesParse.cpp
* fix leaks in testQuery
* fix leaks in testCrystalFF
* fix leaks in cxsmilesTest
* fix leaks in Catalog & mol cat test
* fix leaks in ShapeUtils & tests
* fix leaks in testSubgraphs1
* fix leaks testFingerprintGenerators
* fix leaks in Catalog/FilterCatalog
* fix leaks in graphmolqueryTest
* these changes reduce bison parse leaks
* fixed leaks in testChirality.cpp
* fix leaks + 2 tests in testMolWriter
* fix 4m leaks in substructLibraryTest
* small improvements to molTautomerTest; still leaks
* fix leaks in testRGroupDecomp
* fix leaks in test; parser still leaks
* fix leaks in itertest
* fix 4m leaks in testDepictor
* fixes in smatest; still leaking due to parser
* fixes in testSLNParse; still leaking due to parser
* flex/bison: always add atoms with ownership; smarts error cleanup
* fix leaks in testReaction
* fix leaks in testSubstructMatch
* fix leaks in resMolSupplierTest
* fix leaks in testChemTransforms + bug in ChemTransforms
* fix leaks in testPickler
* fix leaks in testMolTransform
* fix leaks in testFragCatalog
* fix leak in testSLNParse. Still leaks due to Smiles
* fixed most leaks in testMolSupplier
* pre bison fix
* fix some atom & bond parse problems; others still fail
* bison smiles & smarts, atoms & bonds more or less fixed
* fix leaks in molopstest.cpp
* fix leaks in testFingerprints, MACCS.cpp & AtomPairs.cpp
* fix leaks in moldraw2Dtest1
* fix leaks in testDescriptors
* fix leaks in testInchi
* fix leaks in testUFFForceFieldHelpers
* fix leaks in hanoiTest & new_canon.h
* fix leaks in testMMFFForceField
* fix leaks in graphmolTest1
* fix leaks in testMMFFForceFieldHelpers
* fix leaks in testDistGeomHelpers
* fix leaks in testMolAlign
* initialize occupancy & temp facto with default values
* fix leak in TautomerTransform
* updated suppressions
* fix testStructChecker
* fix logging & py tests
* fix TautomerTransform class/struct issue
* remove misplaced delete in testSLNParse
* deinit in testAvalonLib1
* fix Avalon-triggered(?) bug in StructChecker/Pattern.cpp
* fix random testMolWriter/Supplier fails
- diversify output file names to avoid clashing.
- unify Writers close/destruct behavior.
- flushing/closing in tests.
* use reset in FFs Params.cpp
* comments on testMMFFForceField
* unrequired 'if's added to mol suppliers
* correct cast in FilterCatalog.h
* use unique_ptr in MACCS Patterns
* remove unrequred if in new_canon
* update & move suppressions
* this is a rough first pass, needs to be finished and is a strong argument for changing the names of some of the #defines that are currently used
* rationalize the rest of the #defines
add something to the release notes about this
* first pass, does not yet actually work
* pass2, same problems
* pass2, same problems
* another test
* new tests; bugfix
* move the code out to a header
* add a double bond example
* enable auto-downloads of the code
* move the function to its own namespace
* first pass at a basic python wrapper
* change coordgen commit used
* try supporting bond stereo; does not currently work
* cis/trans seems to now work.
* first pass at templates; needs testing
* use the fixed flag too
* need mol align
* expand test
* initial pass at python wrapper for template
* simplify tests
* add an option to directly use a substructure match for alignment
* scaling
* add #define
* Define a cache setting for RDK_COORDGEN_LIBS to allow these to be used in other packages
* return the conformer id from addCoords
* Make CoordGen the default when it’s available.
This is a backup commit… the tests don’t even come close to passing.
* add some debugging options for a bit
* add alignment step to testing when using non-fixed coords
* Add global to allow use of CoordGen to be disabled
get the basic depictor tests working
* make coordgen the default when it is available
* make sure things continue to work when coordgen is disabled
* get windows builds working
* mods to get this building on windows.
something is screwy with the fileParsersTest1
* no need to generate coords for the 1K C string
* fix java wrappers
* works on linux
* update the (stupid) way dependencies were handled on windows.
this allows a lot of cleanup of cmake files (still more to do)
the linux build is unlikely to work due to the way _statics aren't handled
* docs
* extend forceRDKit applicability
* switch coordgen version
* try using templates
* try to get the template dir finding reasonably robust w.r.t. conda install
* continuing to iterate on the way the template file is installed
* fix a problem caused by the merge
* remove test that should never have been checked in
* update expected results for cartridge tests
* switch back to using the RDKit as the default coordinate generator
* clean up the header a bit
clang-format
* clang-format
* add test for #1286
* backup
* fixes the specific failure, but needs more looking
* add an additional test
* update the inchi code to explicitly include queue
* fix a typo identified during the review
Most notably, added test cases for C++ and Python which just make sure
the code runs without crashing, no comparison of results with
existing test files.
* A big step towards solving #910
1) Rank atoms by inverse atomic number (ensures Hs go last)
2) Use heavy-atom degree when doing layout (ensures Hs do not change gross geometry)
* basic testing
* take degree into account with ranks too
* further improvements of relative ranking.
definitely need some cleanup of this now
* some cleanup
* add an explicit test
This does not address the non-canonical rendering piece -- that will
be considerably more work -- but it does take care of the
epoxides being rendered inside the ring.
