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Author SHA1 Message Date
Brian Kelley
a1cc87a8ef Change message to indicate removeHs might be the culprit 2025-11-06 11:24:57 -05:00
Brian Kelley
1451ef1cec Simpify to one sequences not equal error 2025-11-05 08:03:17 -05:00
Brian Kelley
cddb031a1e Fixes #8918 2025-11-02 12:43:19 -05:00
Brian Kelley
c756aff4f9 [CONTRIB]: Freewilson now keeps the coordinates passed in (#8868) 
* Freewilson now keeps the coordinates passed in

* Add better 3D reconstruction test
 2025-11-01 06:28:52 +01:00
David Cosgrove
b9b6078137 Extra explanation of getPosition() and getReagents(). (#8909) 2025-11-01 06:18:08 +01:00
Brian Kelley
c4678568a9 Use adjustQueryProperties logic when dealing with dummy atoms in cxsmiles (#8907) 2025-11-01 05:38:17 +01:00
David Cosgrove
a5347e725e Allow Multiple Core Hits in the Same Molecule in RGroupDecomposition (#8813) 
* 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>
 2025-10-29 21:50:19 +01:00
David Cosgrove
dad4d39803 Change docs in Python EmbedMultipleConfs. (#8900) 
Co-authored-by: David Cosgrove <david@cozchemix.co.uk>
 2025-10-28 02:09:14 +01:00
Greg Landrum
0ee90279b5 Partial fix to a problem with implicit Hs being written to SMARTS (#8893) 
* Partially resolve a problem with implicit Hs ending up in SMARTS

* update doctest

* document in release notes
 2025-10-24 07:50:06 +02:00
Greg Landrum
8844c55572 Fixes #8890 (#8891) 
stop stripping string properties
updates doc string
adds a test for autoConvertStrings
 2025-10-23 08:52:27 -04:00
Ricardo Rodriguez
e4c8ed7765 remove (#8872) 2025-10-23 11:21:36 +02:00
Greg Landrum
e625bdb95c make Point2D and Point3D constexpr (#8882) 
* constexpr Point, Point2D, and Point3D

* constexpr Vector

* cleanup

* rollback overzealous constexpring

* dial back the constexpr to get windows builds working

the math stuff isn't constexpr with MSVC++

* add [[nodiscard]]
 2025-10-23 10:57:33 +02:00
Greg Landrum
20907d3ba9 Fixes #8877 (#8886) 2025-10-22 07:59:35 -04:00
Andrew Dirksen
1ea159ce65 set up performance benchmarks (#8865) 2025-10-18 08:07:49 +02:00
Ricardo Rodriguez
d9850596aa Fixes #8726 (#8874) 
* 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>
 2025-10-17 16:51:22 +02:00
Greg Landrum
93d0f8bb74 Fixes #8776 (#8875) 
* Fixes #8776

don't call the pseudo-CIP perception code if we really don't need to

* allow calling the pseudo-CIP code from Python

* update doctests
 2025-10-17 05:52:27 +02:00
Andrew Dirksen
07e53b4fcd update .gitignore (#8871) 
* add to .gitignore

* one more .gitignore
 2025-10-16 04:59:04 +02:00
Paolo Tosco
2400a54a65 address #8840 by implementing dpi parameter in PandasTools.SaveXlsxFromFrame() (#8841) 
Co-authored-by: ptosco <paolo.tosco@novartis.com>
 2025-10-15 13:02:04 +02:00
Ricardo Rodriguez
af4e8cf01f propagate string_view (#8858) 2025-10-14 19:15:37 +02:00
Greg Landrum
5ea3994bd0 A fix and some refactoring for substructure highlighting in notebooks (#8851) 2025-10-11 20:36:20 +02:00
Greg Landrum
3a4d4df17e allow default radii in the DCLV calculation (#8836) 2025-10-11 20:35:20 +02:00
Greg Landrum
9fd5595f98 use bond labels in the ranking in MolFragmentToSmiles (#8861) 2025-10-10 14:58:45 +02:00
David Cosgrove
dfdddb3fc9 Add extra info about return value. (#8860) 2025-10-10 14:58:20 +02:00
Ricardo Rodriguez
7d1e662bc7 Use std::string_view for property keys (#8844) 
* string_view props API

* wip

* fix leak

* add string_view to swig

* fix comment

* add backwards incompatibilty note

* fix rebase issue

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
 2025-10-09 16:14:48 +02:00
Greg Landrum
ad1fcb5b7b Use properties in the MolDrawOptions python wrappers to make setting/getting colours easier (#8857) 
* support direct property setting/getting in MolDraw2DOptions

* same thing for contourParams

* add getAtomPalette()
 2025-10-09 14:14:19 +02:00
Greg Landrum
00583fc1ab Fix a couple issues related to atom list handling in V3000 mol blocks (#8824) 
Fixes #8820
Fixes #8823
 2025-10-09 05:26:01 +02:00
Ricardo Rodriguez
350c22f7dd Install expat lib in static builds (#8832) 
* install expat in static builds

* specify destination

* also fix a windows build issue
 2025-10-09 05:25:11 +02:00
Brian Kelley
b0ef80d68d Allow labeled atoms to have working queries (#8849) 
* Allow labeled atoms to have working queries

* Remove stray keystrokes

* Fix typo

* Apply clang-format

* Move simpler checks first

---------

Co-authored-by: Brian Kelley <bkelley@glysade.com>
 2025-10-09 04:46:20 +02:00
Niels Maeder
686ca3fd6e same docs for same behaviour (#8854) 2025-10-09 04:44:58 +02:00
Ricardo Rodriguez
9eaa193186 Merge simple AND queries onto atoms. (#8830) 
* duplicate parser code

* regenerate smarts.tab files

* update test

* add release note

* restore pregenerated header

* Suggested changes (#23)

* add a generic flags interface to atoms and bonds

* suggested changes

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
 2025-10-09 04:38:42 +02:00
Niels Maeder
db93262a3e Add safeSetattr to more params / options objects (#8842) 
* add safeSetattr to varios params objects

* added safeSetattr to further params / options
 2025-10-08 16:15:20 +02:00
Rachael Pirie
b2fe43a9ad add Reaction From Smiles python wrapper (#8843) 
* add Reaction From Smiles python wrapper

* Update Code/GraphMol/ChemReactions/Wrap/rdChemReactions.cpp

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* fix Greg changes

---------

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>
 2025-10-08 16:13:06 +02:00
Ricardo Rodriguez
7b7a8a4e17 Refactor iostreams includes (#8846) 
* refactor iostreams includes

* restore ostream to MonomerInfo.cpp
 2025-10-08 16:08:01 +02:00
Ricardo Rodriguez
a4b63d7df5 Minor refactor of the python wrappers (#8847) 
* refactor python wrappers

* fix FilterHierarchyMatcher converted already registered warning
 2025-10-05 09:42:31 +02:00
Greg Landrum
66787fe604 new release prep (#8848) 2025-10-05 09:23:33 +02:00
Greg Landrum
6b30df1e40 run clang-tidy and clang-format on the chemdraw files (#8837) 
* git tidy

* clang-format
 2025-10-03 11:21:56 -04:00
Ricardo Rodriguez
158db5d1a7 link expat to ChemDraw_static (#8839) 2025-10-03 17:12:49 +02:00
Ricardo Rodriguez
fbf4990709 Fixes a leak in ChemDraw code (#8828) 
* clang format

* refactor code

* fix typos

* do not leak bonds when deleting in batch mode

* check sizes
 2025-10-02 06:04:24 +02:00
Paolo Tosco
485a88f3dc fix #8749 (#8835) 
Co-authored-by: ptosco <paolo.tosco@novartis.com>
 2025-10-02 05:58:04 +02:00
Paolo Tosco
23ffd85f60 - fix #8481 (#8808) 
- implement get_v2Kmolblock() in MinimalLib
- add the possibility to specify the MDL version preference as a get_molblock() forceMDLVersion JSON parameter, which is ignored by get_v3Kmolblock() and get_v2Kmolblock()
- changes in response to review

Co-authored-by: ptosco <paolo.tosco@novartis.com>
 2025-09-29 17:33:02 +02:00
tadhurst-cdd
f00a8cbb4c ScsrHbondMrvError (#8646) 
* fix MRV for Hbonds

* add test file

* add test file

* enforce chirality in DistGeom catch test

* Added test for correct hbond retention

* removed debug print statement

* retrigger checks

* testing  java AromaticTests

* testing java aromaticTests

* removed testing code
 2025-09-29 17:30:50 +02:00
Paolo Tosco
24b2039040 Implement returnDrawCoords JSON option in MinimalLib to return 2D drawing coordinates when SVG or canvas depictions are generated (#8815) 
Co-authored-by: ptosco <paolo.tosco@novartis.com>
 2025-09-29 09:36:06 +02:00
Ricardo Rodriguez
56df4de046 fix (#8829) 2025-09-29 09:25:14 +02:00
Rachael Pirie
2e1d946f6d DCLV updates (#8756) 
* first pass speed up of DCLV method

* drop to 320 surface points, add polar surface area v1

* suggested changes

* add John's GridKey implementation

* revert standard dots to float array

* pass simple variables by value

* stable pass radii as param

* final DCLV updates

- update max radius
- includeHs flag for polar surface area/volume
- fix silly include ligand mistake in checkExcludeAtoms
- update tests

* add missing break statements

* missing ;

* Greg changes 1

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Greg changes 2

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Greg changes 3

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Greg changes 4

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Greg changes 5

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Greg changes 6

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Greg changes 7

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* Greg changes 7

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* missing return false

* Greg changes 8

Co-authored-by: Greg Landrum <greg.landrum@gmail.com>

* fix incomplete doc string

* fix pytests

---------

Co-authored-by: greg landrum <greg.landrum@gmail.com>
 2025-09-26 16:40:11 +02:00
Brian Kelley
d304f9f416 Trim spaces from RDProp strings to simulate reading from SDFiles (#8760) 
* Trim spaces from RDProp strings to simulate reading from SDFiles

* Update documentation

* Use the correct doc strings

---------

Co-authored-by: Brian Kelley <bkelley@glysade.com>
 2025-09-26 06:14:23 +02:00
Greg Landrum
c15eb1a143 Fixes #8633 (#8794) 
* Fixes #8633

* changes in response to review
 2025-09-26 05:33:13 +02:00
Paolo Tosco
053a0283f7 Patch RapidJSON to make sure it builds on all platforms (#8818) 
* patch RapidJSON to make sure it builds on all platforms

* remove unnecessary sed command from Docker recipe

---------

Co-authored-by: ptosco <paolo.tosco@novartis.com>
 2025-09-26 05:28:46 +02:00
Brian Kelley
7e9293ed25 Fix an out of bounds access when replacing fragments (#8767) 
* Fix an out of bounds access when replacing fragments

* Add segfaulting US patent CDXs

* Return false when we can't find the bond idx for better handling

* Remove useless REQUIRE

* Only sniff when in format AUTO

* Add test for reading wrong format

---------

Co-authored-by: Brian Kelley <bkelley@glysade.com>
 2025-09-25 15:53:50 +02:00
Niels Maeder
4f2e61cbd3 expose exceeded timeout (#8816) 2025-09-25 14:07:43 +02:00
Joshua Black
64f7a5456f Stop External/rapidjson-1.1.0 and Code/RDGeneral going to ${CMAKE_SOURCE_DIR} (#8810) 
* set export.h and test.h to go to the correct places in RDKitUtils

* use cmake_source_dir so cmake files are picked up in list

* use cmake_current_source_dir in MolInterchange

* use rdkit variables to place rapidjson and headers in correct places
 2025-09-25 14:05:35 +02:00