1 Release published by 1 person

• Release_2024_09_4 2024_09_4 (Q3 2024) Release

  published Dec 20, 2024

11 Pull requests merged by 5 people

• Fix for removing bad stereo indications from Atropisomer parsing

  #7984 merged Dec 22, 2024

• Bad radical values are now ignored for MRV generation

  #8130 merged Dec 21, 2024

• SynthonSpace search timeout

  #8070 merged Dec 21, 2024

• GetAtomsMatchingQuery: Tell where to find query options for

  #8132 merged Dec 21, 2024

• Add section How to Build RDKit Documentation Locally

  #8120 merged Dec 20, 2024

• bump the max runtime for the slower CI builds to 120 minutes

  #8122 merged Dec 19, 2024

• Minor MinimalLib cleanup

  #8112 merged Dec 19, 2024

• allow specified chiral features to SSS match unspecified features

  #8115 merged Dec 18, 2024

• normalizeDepiction() should always center coordinates on the coordinate centroid, irrespective of the canonicalize parameter

  #8107 merged Dec 18, 2024

• Use endian-aware read/write for length of string.

  #8105 merged Dec 18, 2024

• SynthonSearch synth check

  #8109 merged Dec 18, 2024

5 Pull requests opened by 3 people

• Fixes two out-of-bounds bugs in the InChI wrapper

  #8126 opened Dec 20, 2024

• Expand on Explicit Valence Error - Partial Sanitization recipe

  #8131 opened Dec 21, 2024

• fix: apply modernize-use-nullptr

  #8134 opened Dec 22, 2024

• Explain how to run doctests locally

  #8135 opened Dec 22, 2024

• style: apply readability-braces-around-statements

  #8136 opened Dec 24, 2024

67 Issues closed by 4 people

• Find externally installed maeparser and coordgenlibs dynamic libraries

  #2104 closed Dec 24, 2024

• Allow ctest to run memcheck on tests

  #2107 closed Dec 24, 2024

• Port EnumerateStereoisomers to C++

  #2110 closed Dec 24, 2024

• ImportError: DLL load failed: The specified module could not be found.

  #2112 closed Dec 24, 2024

• testEnumeration ..................***Exception: SegFault

  #2114 closed Dec 24, 2024

• Compilation issue with RDKit on CentOs 7

  #2118 closed Dec 24, 2024

• Add fingerprint bit rendering support for the new fingerprint generators

  #2120 closed Dec 24, 2024

• 2018_09_1b1: catch.hpp missing?

  #2125 closed Dec 24, 2024

• MemoryError from rdMolStandardize.Cleanup

  #2136 closed Dec 24, 2024

• Mix of aromatic atoms and aliphatic bonds incorrectly passes sanitization

  #2139 closed Dec 24, 2024

• Segfault for recent conda-forge install

  #2143 closed Dec 24, 2024

• MCS misses a ring with equivalent atoms

  #2166 closed Dec 24, 2024

• Look into pybind11

  #2214 closed Dec 24, 2024

• Bogus aromatic heterocycle incorrectly passing sanitization

  #2218 closed Dec 24, 2024

• Bug in C# Wrapper RDKit.Initialize()

  #2222 closed Dec 24, 2024

• AssignAtomChiralTagsFromStructure can cause MolToMolBlock to fail

  #2227 closed Dec 24, 2024

• Atom list queries written to mol file improperly

  #2231 closed Dec 24, 2024

• _checkAmideEster14 does not detect amide in bounds matrix initialization (bug)

  #2189 closed Dec 23, 2024

• Cartridge: v11 JIT fails during install for adapter.cpp/adapter.bc

  #2192 closed Dec 23, 2024

• Change color of DrawString func

  #2194 closed Dec 23, 2024

• No error on a molecule with incorrect valence

  #2195 closed Dec 23, 2024

• Incorrect MolBlock to SMILES conversion of hydrides

  #2196 closed Dec 23, 2024

• Aromatic issues: Quinodimethane is considered Aromatic while Benzoquinone is not?

  #2198 closed Dec 23, 2024

• sdf to SMILES

  #2199 closed Dec 23, 2024

• RDKit python on MacOS High Sierra from source

  #2201 closed Dec 23, 2024

• Feature Request: extend 3d conformation useBasicKnowledge to force chair\boat\twisted conformation for heterocycles

  #2204 closed Dec 23, 2024

• osx rdkit conda build pulls the wrong (most recent) boost

  #2205 closed Dec 23, 2024

• RDKit segfaults on macOS

  #2207 closed Dec 23, 2024

• Docs/Book/conf.py lacks sphinx.ext.imgconverter for LaTeX-handling of .svg images

  #2212 closed Dec 23, 2024

• Method-chain-able construction of fingerprints from a pandas dataframe.

  #2316 closed Dec 23, 2024

• How to set the AtomMapNumber in your reaction?

  #2325 closed Dec 23, 2024

• Correct index position (subscript tspan in SVG images)

  #2333 closed Dec 23, 2024

• Switch Draw.MolToImage and Draw.MolsToImage to use new drawing code when possible

  #2336 closed Dec 23, 2024

• Potentially a bug in reactions on molecules with more than one fragment

  #2344 closed Dec 23, 2024

• Installation problem.

  #2358 closed Dec 23, 2024

• value error: Sanitization error: Explicit valence for atom # 0 C, 5, is greater than permitted

  #2364 closed Dec 23, 2024

• yaehmop external git clone by cmake fails on ubuntu 16.04

  #2371 closed Dec 23, 2024

• Compute2DCoords gives inconsistent coordinates when not removing hydrogens

  #2386 closed Dec 23, 2024

• incorrect EEM charges for ionic compounds

  #2232 closed Dec 22, 2024

• Sulfones incorrectly recognized as potential chiral centers

  #2236 closed Dec 22, 2024

• ctest shows Failed results on Centos7.6

  #2249 closed Dec 22, 2024

• rdkit.Chem.Draw.rdMolDraw2D.MolDraw2D does not support setLineWidth

  #2251 closed Dec 22, 2024

• Wrong Chirality due to bad CIP ranking for cycles

  #2252 closed Dec 22, 2024

• Java wrappers missing get/set Typed Properties methods on molecule, atom and bond objects

  #2256 closed Dec 22, 2024

• DrawString and DrawMolecule overlap

  #2261 closed Dec 22, 2024

• Hs added to the wrong place when same molecule is generated from inchi

  #2263 closed Dec 22, 2024

• exhaustive definition of pharmacophore features from recent litterature

  #2265 closed Dec 22, 2024

• RDKitmaeparser double installed

  #2284 closed Dec 22, 2024

• Question about FindMCS

  #2288 closed Dec 22, 2024

• Stereo enumeration ignoring ring stereo and dependent stereochem

  #2298 closed Dec 22, 2024

• MolToPDBFile() produced incorrect Hs records.

  #8125 closed Dec 21, 2024

• Chiral Morgan Fingerprints should differ for geometric isomers

  #2388 closed Dec 21, 2024

• Incorrect 2D drawing of a molecule

  #2397 closed Dec 21, 2024

• AssignStereochemistry is removing valid cis/trans bond stereo

  #2404 closed Dec 21, 2024

• Compile failure on ArchLinux

  #2418 closed Dec 21, 2024

• Link to InChI is missing

  #2419 closed Dec 21, 2024

• chirality not supported in hashed atom pairs fingerprint

  #2428 closed Dec 21, 2024

• compilation failing

  #2432 closed Dec 21, 2024

• DrawMorganBits unable to draw certain fragments

  #2435 closed Dec 21, 2024

• WedgeMolBonds() is picking the wrong bond on some tetrahedral Cs

  #2439 closed Dec 21, 2024

• RDKit fails to parse SMILES if dot follows opening parenthesis

  #2442 closed Dec 21, 2024

• Update SMILES parsing syntax error to include bad token position

  #7980 closed Dec 20, 2024

• Too-closed geometry is generated when molecule is constructed from SMILES with period (disconnected structures)

  #2446 closed Dec 20, 2024

• Uncharger not behaving on some zwitterions.

  #2451 closed Dec 20, 2024

• 3D SDF generation from csv file

  #2453 closed Dec 20, 2024

• install failed

  #2468 closed Dec 20, 2024

• Make Chem.PropertyPickleOptions.AllProps default

  #2470 closed Dec 19, 2024

3 Issues opened by 3 people

• Two out-of-bounds bugs in inchi interface

  #8129 opened Dec 20, 2024

• AllChem.GenerateDepictionMatching2DStructure gives flipped orientation

  #8124 opened Dec 19, 2024

• symmetric ring finding not returning correct results for molecules with fragments

  #8121 opened Dec 19, 2024

54 Unresolved conversations

Sometimes conversations happen on old items that aren’t yet closed. Here is a list of all the Issues and Pull Requests with unresolved conversations.

• remove no-op macros and dead code (pt 4)

  #8037 commented on Dec 21, 2024 • 7 new comments

• Vulnerability fixes

  #8116 commented on Dec 18, 2024 • 3 new comments

• remove no-op macros and dead code (pt 3)

  #8036 commented on Dec 21, 2024 • 2 new comments

• Rascal synthon search

  #8097 commented on Dec 21, 2024 • 1 new comment

• Broken rings when applying ChemicalReaction

  #1333 commented on Dec 24, 2024 • 0 new comments

• 3d to 2d conversion (fused rings)

  #1321 commented on Dec 24, 2024 • 0 new comments

• MolPickler doesn't preserve atom properties

  #1320 commented on Dec 24, 2024 • 0 new comments

• Reorganize scripts in rdkit folders

  #1305 commented on Dec 24, 2024 • 0 new comments

• File rdkit/Chem/test_data/Crippen_contribs_regress.pkl is empty

  #1303 commented on Dec 24, 2024 • 0 new comments

• conformations not being generated for complex structure

  #1292 commented on Dec 24, 2024 • 0 new comments

• GenerateDepictionMatching2DStructure isn't matching 2D structure

  #1286 commented on Dec 24, 2024 • 0 new comments

• Use boost::vf2

  #1284 commented on Dec 24, 2024 • 0 new comments

• Bond#getQuery() in java wrapper returns object of type SWIGTYPE_p_Queries__QueryT_int_RDKit__Bond_const_p_true_t

  #1279 commented on Dec 24, 2024 • 0 new comments

• Missing support of SMARTS component-level grouping

  #1261 commented on Dec 24, 2024 • 0 new comments

• Reaction binary format throws away stereo chemistry

  #1257 commented on Dec 24, 2024 • 0 new comments

• Errors when computing partial charges for PDB files

  #1253 commented on Dec 24, 2024 • 0 new comments

• Initialization of force-field parameter objects is not thread safe

  #1238 commented on Dec 24, 2024 • 0 new comments

• - made the UFF/MMFF singletons thread-safe using boost::call_once()

  #1250 commented on Dec 24, 2024 • 0 new comments

• Safer ranking-related performance computation

  #1306 commented on Dec 24, 2024 • 0 new comments

• Stereochemistry of implicit neighbours

  #6772 commented on Dec 20, 2024 • 0 new comments

• Remove meso stereogroups

  #7623 commented on Dec 20, 2024 • 0 new comments

• Fix a bug in findMesoCenters()

  #7686 commented on Dec 20, 2024 • 0 new comments

• Update RDKit_Book.rst

  #7946 commented on Dec 22, 2024 • 0 new comments

• fix problems with template matching

  #7975 commented on Dec 19, 2024 • 0 new comments

• remove no-op macros and dead code (pt 2)

  #8035 commented on Dec 20, 2024 • 0 new comments

• style: renormalize EOL

  #8056 commented on Dec 21, 2024 • 0 new comments

• Conformer embedding timeout

  #8110 commented on Dec 23, 2024 • 0 new comments

• faster rmsd calculations in rdkit

  #1460 commented on Dec 18, 2024 • 0 new comments

• Overlaping hydrogens in structure drawing

  #7790 commented on Dec 18, 2024 • 0 new comments

• SMILES parsing in CDK and OpenEye but not RDKit

  #8119 commented on Dec 18, 2024 • 0 new comments

• ImportError: cannot import name rdMolDraw2D

  #1681 commented on Dec 20, 2024 • 0 new comments

• Clashes in 2D layout with bridged systems

  #6753 commented on Dec 20, 2024 • 0 new comments

• rmsd lower bound

  #1458 commented on Dec 21, 2024 • 0 new comments

• Reorganisation of descriptor implementation on the Python side

  #1450 commented on Dec 21, 2024 • 0 new comments

• assignStereochemistry does not handle Atropisomers

  #8108 commented on Dec 21, 2024 • 0 new comments

• Problem with chirality, MolFromSmiles, and ReplaceSubstructs

  #1438 commented on Dec 22, 2024 • 0 new comments

• AdjustQueryParams adjustDegree should probably be heavy not explicit

  #1426 commented on Dec 22, 2024 • 0 new comments

• SMARTS string from MCS does not contain chiral tags

  #1405 commented on Dec 22, 2024 • 0 new comments

• MolToSmarts generates invalid SMARTS on aromatic selenium

  #1401 commented on Dec 22, 2024 • 0 new comments

• Failure to parse SMILES with digits inside parentheses

  #1395 commented on Dec 22, 2024 • 0 new comments

• Support for generation of RInChI

  #1391 commented on Dec 22, 2024 • 0 new comments

• Nonstandard spelling of piperidine and piperazine

  #1390 commented on Dec 22, 2024 • 0 new comments

• Many tests fail

  #7779 commented on Dec 22, 2024 • 0 new comments

• Fix _test_ring_only_select_1_7 in the MCS test

  #1373 commented on Dec 23, 2024 • 0 new comments

• Fix _test_ring_only_select_1_4 in the MCS test

  #1372 commented on Dec 23, 2024 • 0 new comments

• Check impact of matchValence in MCS matching

  #1371 commented on Dec 23, 2024 • 0 new comments

• really long (infinite?) processing of large highly cyclic smile

  #1360 commented on Dec 23, 2024 • 0 new comments

• Add optional UINT_VECT or std::vector<int> argument to Chirality::assignStereochemistry and ::findPotentialStereoBonds

  #1358 commented on Dec 23, 2024 • 0 new comments

• GetTotalNumHs() return zeros after Chem.AddHs()

  #1357 commented on Dec 23, 2024 • 0 new comments

• Add interactive conformation browser to Jupyter integration

  #1356 commented on Dec 23, 2024 • 0 new comments

• MergeQueryHs() not handling "modified" Hs properly

  #1350 commented on Dec 23, 2024 • 0 new comments

• FMCS code not working properly with maximizeBonds=False

  #1346 commented on Dec 23, 2024 • 0 new comments

• FMCS code failing when completeRingsOnly is true

  #1345 commented on Dec 23, 2024 • 0 new comments

• Update docs page for python params

  #1336 commented on Dec 24, 2024 • 0 new comments