* Create a function to extract some specified atoms from a ROMol as a new ROMol by creating new graph (#8742)
This adds a new api, `RDKit::MolOps::ExtractMolFragment`, to allow efficient
extractions of mol fragments from large mols. Compared to the approach where
we delete "unwanted" atoms/bonds from the input mol, this api is faster for
small mols (about 2x faster) and at least 3x faster for big mols
(was 10x faster for "CCC"*1000).
* clang-format
* review comments
* cleanup
* Consolidate copying subsets of molecules
* Readd missing tests
* Update comment to restart build
* Remove missing test
* Remove debugging comment, fix warnings
* Fix warnings on gcc11
* Add docs
* Make vector<bool> dynamic_bitset<>
* Update copyright
* Add swig wrappers
* Use new designated constructor API
* Fix windows builds
* Change enum values from unsigned int to integer
* Fix unsigned int variable
* Update Code/GraphMol/Wrap/test_subset.py
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/GraphMol/Subset.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Update Code/JavaWrappers/gmwrapper/src-test/org/RDKit/ChemTransformsTests.java
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Reponse to review
* Fix documentation
* Remove comments
* Remove unnecessary comments
* Fix one liners
* Change assertion to be clearer (and not one-liners)
* Run clang-format
---------
Co-authored-by: Your Name <you@example.com>
Co-authored-by: Hussein Faara <hussein.faara@schrodinger.com>
Co-authored-by: Brian Kelley <bkelley@glysade.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* try to reduce the number of valence combinations by checking neighbour valence and bonding
* fixed error message. Remove test that fails now because determineBondOrders finishes too quickly.
* cleanup
* adjust checking
* fix building
* add interrupt test back in but use a molecule that still takes a bit of time.
* improve error messaging
* change "test interrupt" to use xyz
* fix for atoms without valence information. and apply suggestions
* Update Code/GraphMol/DetermineBonds/DetermineBonds.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* first pass at allowing Hs to be ignored in getBestRMS()
* add support in getAllConformersBestRMS()
* do getBestAlignmentTransform()
* cleanup, error checking, and a fix
* this is more painful than it seems like it should be
* add python wrappers and tests
* response to review
* move test to catch2
* fix one broken test
* make some stuff constexpr
* refactor some checks involving exceptions
* replace CHECK_INVARIANT
* replace CHECK_INVARIANT
* clean up commented out debug logging
* initialize var
* remove redundant REQUIRE_MSG
* add function to convert embedParams to json
* add catch test
* add function to python wrapper
* test python function
* update copyright
* undo formatting and cleanup
* more cleanup
* remove the map flag and added round trip
* add bounds mat output
* run clang-format
* Enhance StereoisomerEnumerator to return original molecule when no flippers are available and add test for embedding behavior with input acceptance.
* Use std::make_unique for ROMol construction
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* First pass at port
Mostly auto-converted using claude sonnet 4
Things are a bit slower in this initial port. Here's some timing data for molecules from SMILES (no coords) and from SDF (with coords)
# MASTER
## smiles
read: 50000 mols.
9.260000s wall, 8.650000s user + 0.600000s system = 9.250000s CPU (99.9%)
serialize
3.060000s wall, 2.400000s user + 0.660000s system = 3.060000s CPU (100.0%)
deserialize
1.350000s wall, 1.250000s user + 0.090000s system = 1.340000s CPU (99.3%)
## SDF
read: 50000 mols.
9.340000s wall, 8.930000s user + 0.400000s system = 9.330000s CPU (99.9%)
serialize
6.630000s wall, 5.960000s user + 0.680000s system = 6.640000s CPU (100.2%)
deserialize
1.450000s wall, 1.450000s user + 0.000000s system = 1.450000s CPU (100.0%)
# Boost::JSON
## smiles
read: 50000 mols.
9.250000s wall, 8.830000s user + 0.420000s system = 9.250000s CPU (100.0%)
serialize
4.770000s wall, 4.410000s user + 0.350000s system = 4.760000s CPU (99.8%)
deserialize
2.320000s wall, 2.100000s user + 0.230000s system = 2.330000s CPU (100.4%)
## SDF
read: 50000 mols.
9.500000s wall, 9.100000s user + 0.400000s system = 9.500000s CPU (100.0%)
serialize
8.760000s wall, 8.330000s user + 0.420000s system = 8.750000s CPU (99.9%)
deserialize
2.540000s wall, 2.330000s user + 0.210000s system = 2.540000s CPU (100.0%)
* some json parser optimization
* around the edges
* optimizations for the writer
* hopefully get things compiling
* convert the MinimalLib stuff to use boost::json
Again, a lot of the lifting here was done using Claude Sonnet 4 in VS Code Copilot
* fix Windows DLL build
* response to review
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
* better not to blindly accept suggestions
* fix the problems in MinimalLib
---------
Co-authored-by: Paolo Tosco <paolo.tosco.mail@gmail.com>
Co-authored-by: = <=>
* Fixes a bug with chirality perception of T-shaped centers in very large rings
* remove those files from the chemdraw tests
should be added later once we figure out and fix what the problem on the chemdraw side is (it is not directly connected to this PR)
* be more systematic about the tolerance values
carry the same tolerances over into the bond wedging code
* re-enable those chemdraw tests
* typo
* Iterated interface to substructure search
* Add a test
* Add python unit test
* Expose the toTryChunkSize parameter to python
* Respect the maxHits parameter; sort the hitset
* Treat maxHits=-1 as infinite
* Add callback versions of fp and rascal search; conform to C++ style
* Add fp and rascal C++ tests
* maxHits=-1 tripped me up again
* Add fp and rascal python wrappers.
Changed the name of the callback-based method to have "Incremental"
in the name because the overloaded versions with default arguments
can't be reliably selected by the boost python runtime. Probably
better to have a different method name anyway since the return type
is None instead of a results object.
* Delete stray printf.
* Run clang-format
* Use std::int64_t instead of ssize_t for portability
* Make docstrings on callback-based methods more descriptive
* Stop incremental search if the callback returns true.
* Add an example of incremental synthon search to the getting started docs
* trivial commit to force CI rerun
* Reformat single line if statements.
* Make SearchResultsCallback take const ref input
* Fix another one-liner
* Oops - another one-liner
* Do not reset the ringInfo information when adding bonds
This call was inconsistent (for example, the version of addBond() in ROMol did not do it)
and is unnecessary since the standard assumption is molecules need
to be re-sanitized after adding atoms and bonds
* response to review
clear the property cache on atoms after adding a bond.
* add a property cache update to the reaction runner
* add something to the release notes
* add option to track atoms involved in each bit for morgan FP
Needs test still
* support similarity maps using fingerprint generators
* support RDKit, AP, and TT
still need tests
* add some testing
* response to review
* added new attributes for scsr template as per BIOVIA doc 2003
* changed to allow any attributes for an SCSR Template def
* removed unneeded defs for TEMPLATE attribute names
* merge ABS groups on setStereoGroups
* warn/fail on multiple ABS groups on strict parsing
* add a test for setStereoGroups
* add a test for multiple ABS groups in mol blocks
* Drop the warning
* Allow the same core to match more than once in a molecule.
* Update annotation.
* Changes after review.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* 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>
