* 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>
* parse templates as smarts
* accept ring templates in SMARTS format
* undo CLAUDE mistake
* rename files
* enable templating for macrocycles
* enable macrocycle templating
* Add test for macrocycle templating
Tests that ring system templates are used only for macrocycles (rings
with size > 8). The test verifies the exact threshold by generating
coordinates with and without templates for rings of size 4-14.
Addresses review feedback on PR #9203.
Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
---------
Co-authored-by: Claude Sonnet 4.5 <noreply@anthropic.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: = <=>
* CRDGEN-360
allow subset of rings to match templates
* also add a template check for the whole ring system
* wip
* fix build error
* fix test errors
* code review
* wip
* fix test
* avoid unnecessary calls to substructure search
* remove dead code
* backup
* further optimization
revert the accidentally committed changes to the tests
* comment cleanup
* some more optimization
* Update Code/GraphMol/Depictor/EmbeddedFrag.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* fix an out-of-bounds write
* Update Code/GraphMol/Depictor/EmbeddedFrag.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---------
Co-authored-by: greg landrum <greg.landrum@gmail.com>
* Add trans layout for double bonds in rings
If there is a trans double bond in a ring, it's important to
add a trans 2d depiction! This is important for visualization,
but it is also important for chemical accuracy. SDF uses the 2D
coordinates to discern bond stereochemistry, and some 3D embedding
techniques may start from 2D.
Without this commit, trans double bonds in rings invert on
roundtrip through SDF.
Here's a very simple assertion that fails before this commit
and passes after:
smi = "C1=C/CCCCCCCCCCCC/1"
assert smi == Chem.MolToSmiles(Chem.MolFromMolBlock(Chem.MolToMolBlock(Chem.MolFromSmiles(smi))))
* Fix "or" keyword to "||".
* Make sure that `embedRing()` signature is unchanged.
* un/signed comparisons in molops
* reference in loop in EmbeddedFrag.cpp
* un/signed comparison in filtercatalogtest.cpp
* un/signed comparison in Descriptors/catch_tests.cpp
* un/signed comparisons in DetermineBonds.cpp
* drop unused 'params' arg from static functions in MolInterchange/Writer.cpp
* un/signed comparisons in MolDraw2D/catch_tests.cpp
* unused var in SubgraphUtils.cpp
* 'move' preventing copy ellision in CDXMLParser.cpp
* fix infinite recursive call in SubstructLibraryWrap.cpp
* DRAFT: Use templates in RDKit coordinate generation
* added option in python
* Addressed some comments and added tests
* removed unused code
* A few updates to templating code
* Added params struct for compute2DCoords
* Added several tests for multiple templates and templates + coord maps
* Addressed a few other comments from reviews
* addressed another comment
* remove extra line
* Update Code/GraphMol/Depictor/Wrap/rdDepictor.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Some cr suggestions
* forgot to remove original .smi file
* Update Code/GraphMol/Depictor/Wrap/testDepictor.py
Removed test
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* the coordMap pointer can be to a const object
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* add ROMol::atomBonds() and ROMol::atomNeighbors() methods
* remove some warnings
* start using the new code
* add default for those template params
* some more applications
* get the SWIG builds working
* get rid of extraneous ref
* remove extraneous comments
* 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>
* remove include from headers
* update implementation files
* completely remove BOOST_FOREACH (#7)
* convert those changes to use auto
* get rid of all usage of BOOST_FOREACH
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* run clang-tidy with modernize-use-default-member-init
* results from modernize-use-emplace
* one uniform initialization per line
otherwise SWIG is unhappy
Co-authored-by: Brian Kelley <fustigator@gmail.com>
* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke
* fix problem on windows
* first round of cleanups based on PVS-studio suggestions
* a couple more
* a few more cleanups
* another round of cleanups
* undo one of those cleanups
we want the integer rounding behavior here
* add a comment to make that clear
* Fix for filter catalog PRECONDITION redundancy
* Removes ATOM/BOND_SPTR in boost::graph in favor of raw pointers
* Actually delete atoms and bonds...
* RWMol::clear now calls destroy to handle atom/bond deletion
* Changes broken Atom lookup for windows/gcc
* Adds tests for running with valgrind
* Adds test designed for valgrind and molecule deletions
* Removes RNG, actually tests bond deletions
* update swig wrappers
* deal with most recent changes on the main branch
* 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
* add cis and trans to bond stereo
* compiles, does not work
* tests all pass
* Whitespace cleanup to recent changes.
* C++ test case for Bond::setStereo using Bond::STEREOCIS and Bond::STEREOTRANS
* Adding a PRECONDITION to Bond::setStereo to make sure the stereo atoms
are already specified if CIS or TRANS is being specified.
E/Z is technically defined by the topology of the molecule so the
stereo atoms are redundant (easier to understand and use!), but
ultimately redundant with the graph. However, CIS and TRANS is _only_
defined in this usage as the orientation of the atoms in the
getStereoAtoms vector.
* Exposing Bond::setStereo to Python and adding test cases to make sure
it can be used to set CIS/TRANS stereochemistry.
* verify substructure matching works
* Adding Bond::setStereoAtoms to C++ Bond class.
This allows setting the atoms to be considered for CIS or TRANS
directly without a much more costly determination of ranking that E/Z
requires.
* Wrap Bond::SetStereoAtoms into python with a new type of test case.
* docs
* 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
- added #ifdef M_PI (...) #endif in all relevant places
- made length() and sqLength() method consistent
with respect to usage of pow(x, 2) vs x*x in
Code/Geometry/point.h
- removed gzip-related boost.iostreams dependency and
replaced with portable "cmake -E tar xzf" command
in Code/ForceField/MMFF/CMakeLists.txt
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.
instead of using the property map interface.
A nice side-effect is that the wart of having to use property maps to loop over bonds or atom neighbors
is now gone.
This potentially breaks lots of client C++ code.
