* Vulnerability fixes
* Vulnerability fixes
* Move Iterator bounds check to a PRECONDITION for parse_data_sgroup_attr.
* Update MolFileParser.cpp
Remove ill-advised ASCII filter when parsing SDF V3000
* Update MolFileParser.cpp
Remove extra whitespace.
* Squashed commit of the following:
commit 1a1279c137afeca77d4fd68b287a7e36c6bf5c37
Merge: 7d0765c8b 3d2a43470
Author: James Thompson <thompj@google.com>
Date: Wed Dec 18 14:22:29 2024 +0000
Merge branch 'vuln_fix' of https://github.com/thomp-j/rdkit_vuln into vuln_fix
commit 7d0765c8ba2e0be54649613fce2f61545ad5d9d2
Author: James Thompson <thompj@google.com>
Date: Wed Dec 18 14:20:54 2024 +0000
Squashed commit of the following:
commit 5a5902a874109d42cc4a20de535bdca0855c429b
Merge: ec0ff4ee2 3d2a43470
Author: James Thompson <thompj@google.com>
Date: Wed Dec 18 14:18:02 2024 +0000
Remove whitespace
commit 3d2a43470f
Author: thomp-j <58603847+thomp-j@users.noreply.github.com>
Date: Wed Dec 18 09:08:57 2024 -0500
Update MolFileParser.cpp
Remove extra whitespace.
commit a8a718923c
Author: thomp-j <58603847+thomp-j@users.noreply.github.com>
Date: Wed Dec 18 09:08:09 2024 -0500
Update MolFileParser.cpp
Remove ill-advised ASCII filter when parsing SDF V3000
commit 270136d6c0
Author: thomp-j <58603847+thomp-j@users.noreply.github.com>
Date: Wed Dec 18 09:07:05 2024 -0500
Move Iterator bounds check to a PRECONDITION for parse_data_sgroup_attr.
commit ec0ff4ee29e9cca5bbd9591d30f8a96646484ec5
Merge: ca4ed2faa 2d257b119
Author: James Thompson <thompj@google.com>
Date: Wed Dec 18 14:04:30 2024 +0000
Merge branch 'vuln_fix' of https://github.com/thomp-j/rdkit_vuln into vuln_fix
commit ca4ed2faa4219abfd97628d529be3a1fd97048bf
Merge: c11caffbd63123278c
Author: James Thompson <thompj@google.com>
Date: Wed Dec 18 13:59:48 2024 +0000
Merge branch 'vuln_fix' of https://github.com/thomp-j/rdkit_vuln into vuln_fix
commit 2d257b1194
Merge: d4561233474fc77f95
Author: thomp-j <58603847+thomp-j@users.noreply.github.com>
Date: Wed Dec 18 09:03:06 2024 -0500
Merge branch 'rdkit:master' into vuln_fix
commit d456123344
Merge: c11caffbd63123278c
Author: James Thompson <thompj@google.com>
Date: Wed Dec 18 13:59:48 2024 +0000
Merge branch 'vuln_fix' of https://github.com/thomp-j/rdkit_vuln into vuln_fix
commit c11caffbd7
Author: James Thompson <thompj@google.com>
Date: Tue Dec 17 15:26:41 2024 +0000
Vulnerability fixes
commit 74fc77f959
Author: Paolo Tosco <paolo.tosco.mail@gmail.com>
Date: Wed Dec 18 13:40:57 2024 +0100
normalizeDepiction() should always center coordinates on the coordinate centroid, irrespective of the canonicalize parameter (#8107)
* normalizeDepiction() should always center coordinates on the coordinate centroid, irrespective of the canonicalize parameter
* Update Code/GraphMol/Depictor/catch_tests.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* fix catch test
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
commit e589f173fd
Author: David Cosgrove <davidacosgroveaz@gmail.com>
Date: Wed Dec 18 04:14:11 2024 +0000
Use endian-aware read/write for length of string. (#8105)
* Use endian-aware read/write for length of string.
* Re-run clang-format.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
commit ce35b3c25b
Author: David Cosgrove <davidacosgroveaz@gmail.com>
Date: Wed Dec 18 04:12:07 2024 +0000
SynthonSearch synth check (#8109)
* Catch errors when creating products.
* Extra python test.
* Fix formatting.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
commit 63123278ca
Author: James Thompson <thompj@google.com>
Date: Tue Dec 17 15:26:41 2024 +0000
Vulnerability fixes
commit e640915d4e
Author: Nikitas Rontsis <nrontsis@gmail.com>
Date: Tue Dec 17 15:11:40 2024 +0000
Avoid unnecessary matching (#8111)
commit 5aed3d886b
Author: Greg Landrum <greg.landrum@gmail.com>
Date: Mon Dec 16 16:59:13 2024 +0100
Fixes#8096 (#8104)
* add test
* Fixes#8096
* change in response to review
commit 6dce5d4080
Author: Greg Landrum <greg.landrum@gmail.com>
Date: Sun Dec 15 05:58:20 2024 +0100
Fixes#1670 (#8093)
* add missing descriptors to Lipinski.py
Fixes#1670
* add to descriptor list
commit 3d2a43470f
Author: thomp-j <58603847+thomp-j@users.noreply.github.com>
Date: Wed Dec 18 09:08:57 2024 -0500
Update MolFileParser.cpp
Remove extra whitespace.
commit a8a718923c
Author: thomp-j <58603847+thomp-j@users.noreply.github.com>
Date: Wed Dec 18 09:08:09 2024 -0500
Update MolFileParser.cpp
Remove ill-advised ASCII filter when parsing SDF V3000
commit 270136d6c0
Author: thomp-j <58603847+thomp-j@users.noreply.github.com>
Date: Wed Dec 18 09:07:05 2024 -0500
Move Iterator bounds check to a PRECONDITION for parse_data_sgroup_attr.
commit 2d257b1194
Merge: d4561233474fc77f95
Author: thomp-j <58603847+thomp-j@users.noreply.github.com>
Date: Wed Dec 18 09:03:06 2024 -0500
Merge branch 'rdkit:master' into vuln_fix
commit d456123344
Merge: c11caffbd63123278c
Author: James Thompson <thompj@google.com>
Date: Wed Dec 18 13:59:48 2024 +0000
Merge branch 'vuln_fix' of https://github.com/thomp-j/rdkit_vuln into vuln_fix
commit c11caffbd7
Author: James Thompson <thompj@google.com>
Date: Tue Dec 17 15:26:41 2024 +0000
Vulnerability fixes
commit 74fc77f959
Author: Paolo Tosco <paolo.tosco.mail@gmail.com>
Date: Wed Dec 18 13:40:57 2024 +0100
normalizeDepiction() should always center coordinates on the coordinate centroid, irrespective of the canonicalize parameter (#8107)
* normalizeDepiction() should always center coordinates on the coordinate centroid, irrespective of the canonicalize parameter
* Update Code/GraphMol/Depictor/catch_tests.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* fix catch test
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
commit e589f173fd
Author: David Cosgrove <davidacosgroveaz@gmail.com>
Date: Wed Dec 18 04:14:11 2024 +0000
Use endian-aware read/write for length of string. (#8105)
* Use endian-aware read/write for length of string.
* Re-run clang-format.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
commit ce35b3c25b
Author: David Cosgrove <davidacosgroveaz@gmail.com>
Date: Wed Dec 18 04:12:07 2024 +0000
SynthonSearch synth check (#8109)
* Catch errors when creating products.
* Extra python test.
* Fix formatting.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
commit 63123278ca
Author: James Thompson <thompj@google.com>
Date: Tue Dec 17 15:26:41 2024 +0000
Vulnerability fixes
commit e640915d4e
Author: Nikitas Rontsis <nrontsis@gmail.com>
Date: Tue Dec 17 15:11:40 2024 +0000
Avoid unnecessary matching (#8111)
commit 5aed3d886b
Author: Greg Landrum <greg.landrum@gmail.com>
Date: Mon Dec 16 16:59:13 2024 +0100
Fixes#8096 (#8104)
* add test
* Fixes#8096
* change in response to review
commit 6dce5d4080
Author: Greg Landrum <greg.landrum@gmail.com>
Date: Sun Dec 15 05:58:20 2024 +0100
Fixes#1670 (#8093)
* add missing descriptors to Lipinski.py
Fixes#1670
* add to descriptor list
commit a4cdf5d21d
Author: Greg Landrum <greg.landrum@gmail.com>
Date: Sun Dec 15 05:58:03 2024 +0100
Fixes#8092 (#8094)
* Fixes#8092
cross-platform file stuff is just soooooo fun
* response to review
* works on windows
commit b7de0585ca
Author: Greg Landrum <greg.landrum@gmail.com>
Date: Sat Dec 14 18:21:55 2024 +0100
Add drawMols3D() and improve documentation for IPythonConsole (#8083)
* Fixes#8082
more docs
* changes in response to review
commit 736e309f10
Author: David Cosgrove <davidacosgroveaz@gmail.com>
Date: Sat Dec 14 17:21:29 2024 +0000
Fix empty results bug. (#8099)
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
commit c90cee9b77
Author: Greg Landrum <greg.landrum@gmail.com>
Date: Sat Dec 14 17:08:43 2024 +0100
Add Molecular Interaction Fields (#7993)
* Add RealValueVect.
* Add UniformRealValueGrid3D
* Add Molecular Interaction Fields (MIFs)
* line endings
* cherry-pick f1bc94a4c8
* format
* Adapt tests for python3.
* Adapt RealValueVector pickling for python3.
* Speed-up of MIF calculations.
* Bugfix in MIFDescriptors.cpp.
* all tests pass
* clean up some memory leaks
* update copyrights
* rename
* rename the library
* complete the rename
* lost file
* another forgotten file
* cleanup
* clang-tidy
* clang-tidy
* windows DLL builds work
* python wrapper and tests cleanup
* convert to catch2 testing
* switch RealValueVect to use std::vector
* remove obsolete friend
* - Replace explicit loops with stdlib implicit equivalents
- Replace explicit types with auto where possible
- Avoid unnecessary copy operations where possible
- Replace raw pointers with exception-safe unique_ptr
- Replace C-style #define with constexpr
- Replace C-style casts with C++ casts
- Replace C-style arrays with std::vector
- Avoid code duplication with templated operators
- Replace VdWaals class taking multiple atom type definitions and force-field name as string parameter with force-field-specific classes deriving from an abstract VdWaals class
- Replace x,y,z doubles with Point3D class where possible
- Removed unused (and untested) DistanceToClosestAtom class
- Renamed some variables and functions for better clarity
- Converted tabs to spaces
- Made the mol parameter in cube read/write functions optional for convenience
- Made the Python wrappers more pythonic (e.g., avoid C++-style passing objects as parameters which are modified in place)
- Implemented alternative Python class constructors using boost::python::make_constructor rather than with external non-class functions
- The Python wrappers taking a sequence of Point3D now take a sequence of sequences, such that the output of Conformer.GetPositions() can be passed
- Made the Python wrapper sequence parsing more robust
- Removed duplicated code from Python wrappers
* - avoid an unnecessary copy
* progress
* works
* more cleanup
* all tests pass
* changes in response to review
---------
Co-authored-by: dfhahn <dfhahn@users.noreply.github.com>
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* Adds error message to parse_data_sgroup_attr PRECONDITION
* Fix bond smoothing - apply atom index offset to products.
Update Hash codes.
Tweak side_by_side_images.py.
* Added hash code for new file. Doh!
* Option to remove brackets from atom lists.
* Python wrapper.
* Change option name after review.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Fix bond smoothing - apply atom index offset to products.
Update Hash codes.
Tweak side_by_side_images.py.
* Added hash code for new file. Doh!
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* improve handling of esters, amides, etc. in the v2 tautomer hash
Fixes#8090
* cleanup
* extend that logic to aromatic systems
* documentation in response to review
* First pass at approximate FP check.
* Tidy and Python wrapper.
* More tidying.
* Add addFP and subtractFP to binary file.
* Minor tidy.
* In splits code, check for duplicate fragmentations.
* Update test results.
* Tidy.
* Set configurable limit on number of fragments generated from query.
* Stash prior to trying counts fps.
* Stash count fps.
* Back to bit fingerprints again.
* Extra comment.
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
* 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>
* fix SetPositions when using strided numpy array
previously SetPositions assumed that the provided numpy array used contiguous-C stride patterns
* cast to a const pointer to avoid compiler warning
* Expand on Explicit Valence Error - Partial Sanitization recipe, including adding molecular structures for the unsanitized and partially-sanitized iterations
* Format `argument=value`
* Fix typo in formatting
* Update label to *Original* Source
* Correct rdqueries import, and formatting of testoutput blocks
* Print out hybridization create doctests
* For GetAtomsMatchingQuery, note that "Atom query options are given in the rdkit.Chem.rdqueries module"
* wording change
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Add timeout to searches.
* Correct docstring.
* Include chrono header.
* Get it compiling with gcc.
* And then clang didn't like it...
* Revert to tmpnam as msktemp isn't available on Windows.
* Response to review.
Run time no longer saved in SearchResults.
Timeout check not tied to size of results.
Made the test timeout shorter.
* Fix the Python wrapper.
* Shamelessly steal the better timeout method from PR8110.
* suggested changes
* be more conservative about what does not time out
the CI machines can be surprisingly slow
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Handle DOS files.
* Smaller test file.
Add DOS file to .gitattributes.
* Update Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
- str_to_c() should check the ptr returned by malloc for non-nullness before using it
- change has_coords() mol_pkl parameter to const
- use assert.equal in JS tests where possible
Co-authored-by: ptosco <paolo.tosco@novartis.com>
* normalizeDepiction() should always center coordinates on the coordinate centroid, irrespective of the canonicalize parameter
* Update Code/GraphMol/Depictor/catch_tests.cpp
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* fix catch test
---------
Co-authored-by: ptosco <paolo.tosco@novartis.com>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* Handle DOS files.
* Smaller test file.
Add DOS file to .gitattributes.
* Update Code/GraphMol/SynthonSpaceSearch/substructure_search_catch_tests.cpp
---------
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
