* Fixes#9068
* fix a problem with empty labels in s-group parsing
* fix empty column names in smiles suppliers
* add the check to setPODVal()
---------
Co-authored-by: = <=>
* Parsing SCSR
* add scsrol to mol
* removed bad include file
* loosen distGeom test slightly
* add wrap test for SCSRMol
* Add test for scsr in python
* tests added for scsr and strict parsing removed
* remove extra stuff
* More fully specified use of SCSRMol for PR CI build
* Added flags for SCSR expansion to not include any leaving groups
* Added MolFromScsrParams to Wrap for python
* added SCSRMol destructor
* Added two tests for RNA macromols, and fixed a bug they revealed
* Added new tests abd expected files
* changes as per PR review
* SCSR Chnages for leaving groups
* fixed testScsr.py
* hydrogen bond treatment
* in SCSR expand, allow Hbond to be autoatically detected
* changes as per code review
* Adding new test file
* chages for SCSR contructors, destructors for CI build
* fixed pyton for SCSR hydrogen bond modes, and added tests
* Added new test files
* fixed edge case for SCSR
* fix checksum for inchi
* consistent capitalization of SCSR throughout
* switch to enum class
* make things shorter
* simplify
* get rid of the ATTCHORD class
* New section for SCSR in RDKit_book
* addeed section to RDKit_Book
* SCSRMol is no longer exposed in Python
* fix leak in MolFromSCSRFile()
light refactoring
* expose MolFromSCSRFile() to python
make the MolFromSCSR functions work with default args
a bit more testing
* removed C++ access to SCSRMol
* CXMsiles now ouputs hbonds, fix to template matching, and a few other things
* Addl fix for bad aromaticity in Hbond rings
* Test files needed
* Test files needed
* try to fix a CI build errors
* CI error fix
* Added missing test file
* CMake version - for CI build
* remove full file compoarison from macromol test file
* accidental change to debug restored to release
* Code review changes
* As per PR review
---------
Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
* 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
* RWMol: replace atom in stereo groups
Fix https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=36998, a
use-after-free in initFromOther.
* Fix out-of-bounds write in iterateCIPRanks
If the rank has not changed in the current iteration, the cipEntries
vectors might not have increased in size. Accessing `numIts + 1`
resulted in an out-of-bounds write. This commit skip the cipEntries
update when the rank is unchanged.
Fix https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=28660
* Fix use of uninitialized values in MolSGroupParsing
`stream >> count` may silently fail without an exception. In that case,
`count` was uninitialized but used. This commit initalizes `count` to 0,
as well as other variables that may be read without being initialized.
Fix https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=25220
Fix https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=25225
* Fix vector size cast in streamReadVec
In 32-bit systems, the implicit conversions from 64-bit to a 32-bit
size_t could lead to an underallocation of the vector. This would follow
by a out-of-bounds write while trying to populate the vector. Now, the
code throws an exception in case of a cast that would change the size.
Fix https://bugs.chromium.org/p/oss-fuzz/issues/detail?id=28034
* RWMol: improve atom replacement in stereo groups
This code is cleaner and more efficient.
* Add test for replaceAtom and stereo groups
* resolves oss-fuzz #24399
* clean up some undefined behavior
* fix some UB in mergeQueryHs
* be more defensive
* defensive programming
* fix a _cxsmilesBondIdx bug
* more defensive programming
* stop removing substance groups with replaceAtom()
change default for keepSGroups argument to replaceBond()
* enable logging output for the fileparserscatch
* basics of parsing SMARTSQ SubstanceGroups
* Fixes#4476
test coming in the next commit
* handle multi-atom SMARTS as recursive
more testing
Test #4476
* a bit of cleanup
* get the tests working
* additional testing
* Update Code/GraphMol/FileParsers/MolFileParser.cpp
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
* - eliminate some documentation ambiguity about the role of the strictParsing flag
- fix some inconsistencies between SGroup parsing function prototype declarations and implementations
- add a workaround for accepting malformed V2000 'M SAP' entries affecting older version of MarvinJS (only if strictParsing is set to false)
- if strictParsing is set to false, malformed V2000/V3000 SGroups are ignored rather than causing the parsing to fail
- fix a couple typos in warnings
* changes in response to review
* backup
* compiles
* progress, but not there yet
* basics now working
* start towards adding another test
* test having two variation points
* add actual enumeration and the corresponding tests
* docs and cleanup
* cleanups to get the mac build working
* attempt to get win32 dll builds to work
* dlls are fun
* Add FixedMolSizeMolBundle class
* changes in response to review
Also: add warnings for bad input in ParseV3000Array
* a bit of refactoring
* additional testing
* does not work, backup
* LINKNODES work now
* cleanup
* allow silencing reaction validation warnings during initialization
* docs
* fix (and test) handling of empty enumerations
* silence warnings when doing alchemy
* first pass at a Python wrapper for the enumerator
* Add Java wrappers for MolBundle and the MolEnumerator
* cleanup some comment formatting
* stop returning local memory in exceptions
* remove a couple unnecessary copies in loops
* fix a bug in the way the default MMFF aromatic parameters are constructed
* remove a bunch of loop-variable warnings
* remove a bunch of clang warnings
* disable clang warnings in python wrappers
* remove some warnings when building the python wrappers
* Progress on #3168
* Fixes#3167
* Fixes#3169
* deal with CBONDS too
* test PATOMS
* Fixes#3175
* a bit of code simplification and test updates
still needs more testing
* more testing
* handle s-group hierarchy
also a couple of other changes in response to the review
* add forgotten test file
* changes in response to review
* SGroups with more than one attachment point are now properly parsed
Thanks to Roger S for the example and fix.
* Update Code/GraphMol/FileParsers/file_parsers_catch.cpp
Co-Authored-By: Ric <ricrogz@users.noreply.github.com>
Co-authored-by: Ric <ricrogz@users.noreply.github.com>
* 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
* Fixes#2277
* changes in response to review
the big one is to move the PXA parser into the normal mol file parsing
* move the PXA changes to the writer as well
* SCN actually only needs 7 characters
* add test
* fixes in response to review
* handle blanks (instead of zeros) in the counts line.
The ctfile.pdf doc says we should do this
* Make the SGroup reader more robust w.r.t. bad data
The current behavior leads to uncaught exceptions when a line is too short.
This should clear that up so that we always throw the usual FileParseException
* make error messages a bit easier to read
* Implementation of SGroups
* remove sample files test
* update gitignore with test outputs
* fix RevisionModifier
* re-enable tests
* backup commit; things seem to work so far
* some refactoring; obvious s group tests pass now
* more refactoring
* everything now out of the public API
* not sure why this was still in there
* rename functions; all tests now pass
* remove getNextFreeSGroupId; readd comment in copy SGroups
* clang-format
* squash-merge current master
* squash merge master
* Address comments on PR
- Update to current master.
- Move SGroup parse time checks to SGroupChecks namespace.
- Store SGroups in ROMOl as vector<SGroups>.
- SGroup methods return referenes instead of pointers.
- Use atom/bond/sgroup indexes for properties instead of pointers.
- Have SGroups inherit from RDProps; move properties to RDProps.
- Remove trivial/unused methods.
- Add a link to the SD specification atop SGroup.h
