Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / rdkit/rdkit issues and pull requests

#8030 - disable UBSAN builds in CI

Pull Request - State: closed - Opened by greglandrum 3 months ago - 1 comment
Labels: infrastructure, not in release notes

#8029 - improve defaults for the shape-based alignment

Pull Request - State: closed - Opened by greglandrum 3 months ago - 2 comments
Labels: enhancement, changes results

#8028 - RDKit postgreSQL cartridge is_valid_smiles return false

Issue - State: closed - Opened by sitanshubhunia 3 months ago - 3 comments
Labels: not a bug

#8026 - Question Mark Drawn In Molecule

Issue - State: closed - Opened by lounsbrough 3 months ago - 11 comments

#8025 - Synthon fingerprint search

Pull Request - State: closed - Opened by DavidACosgrove 3 months ago - 2 comments

#8018 - LabuteASA Descriptor Misinterprets Implicit Hydrogen

Issue - State: open - Opened by swteer 3 months ago - 1 comment
Labels: bug

#8017 - Chiral-at-P stereochemistry bug(s?)

Issue - State: open - Opened by supersciencegrl 3 months ago
Labels: bug

#8016 - Fix probe molecule transformation for ShapeAlign

Pull Request - State: closed - Opened by greglandrum 3 months ago
Labels: bug

#8016 - Fix probe molecule transformation for ShapeAlign

Pull Request - State: closed - Opened by greglandrum 3 months ago
Labels: bug

#8015 - Fix some minor issues reported by ubsan and the compiler

Pull Request - State: open - Opened by ricrogz 3 months ago

#8015 - Fix some minor issues reported by ubsan and the compiler

Pull Request - State: open - Opened by ricrogz 3 months ago

#8014 - Fix shifting of a potentially negative number

Pull Request - State: closed - Opened by ricrogz 3 months ago - 2 comments
Labels: Cleanup

#8014 - Fix shifting of a potentially negative number

Pull Request - State: closed - Opened by ricrogz 3 months ago - 2 comments
Labels: Cleanup

#8013 - Avoid division by zero in AlignPoints

Pull Request - State: open - Opened by ricrogz 3 months ago

#8012 - remove no-op macros and dead code (pt 1)

Pull Request - State: closed - Opened by whosayn 3 months ago
Labels: Cleanup

#8011 - Avoid division by zero in DrawMol

Pull Request - State: closed - Opened by ricrogz 3 months ago
Labels: Cleanup

#8008 - Throw when attempting to normalize a Zero RDGeom::Point

Pull Request - State: open - Opened by ricrogz 3 months ago - 3 comments
Labels: Cleanup

#8007 - Fix potential division by zero in UFF TorsionAngle

Pull Request - State: closed - Opened by ricrogz 3 months ago
Labels: bug

#8006 - xyz2mol implementation bug: DetermineBonds

Issue - State: open - Opened by simonmb 3 months ago - 1 comment
Labels: bug

#8005 - Mol to smiles docs

Pull Request - State: closed - Opened by DavidACosgrove 3 months ago
Labels: documentation

#8004 - expanded documentation in Chem and AllChem

Pull Request - State: closed - Opened by greglandrum 3 months ago
Labels: documentation

#8002 - fixes #8001

Pull Request - State: closed - Opened by greglandrum 3 months ago

#8001 - RMS pruning in conformer generation misses conformers above the threshold

Issue - State: closed - Opened by fwaibl 3 months ago - 1 comment
Labels: bug

#8000 - Implemented two more JSON parsers for CFFI and MinimalLib

Pull Request - State: closed - Opened by ptosco 3 months ago
Labels: enhancement

#7997 - something related to the completeAromaticRings in rdRascalMCES

Issue - State: closed - Opened by rongfengzou 3 months ago - 1 comment
Labels: bug

#7996 - Remove unused code from GraphMol/SmilesParse

Pull Request - State: closed - Opened by whosayn 3 months ago
Labels: Cleanup

#7995 - Can't generate all kekulization using rdkit

Issue - State: closed - Opened by xiaolinpan 3 months ago - 2 comments
Labels: not a bug

#7994 - Expose tautomer scoring functions to python

Pull Request - State: closed - Opened by bp-kelley 3 months ago - 2 comments
Labels: enhancement

#7993 - Add Molecular Interaction Fields

Pull Request - State: closed - Opened by greglandrum 3 months ago - 3 comments
Labels: enhancement

#7992 - Fix for kekuleAtrop wedge error

Pull Request - State: closed - Opened by tadhurst-cdd 3 months ago
Labels: bug

#7990 - Fixes #7989 Incorrect benzyl deprotection reaction

Pull Request - State: closed - Opened by bp-kelley 3 months ago - 2 comments

#7989 - Wrong SMARTS pattern in O-benzyl deprotection reaction

Issue - State: closed - Opened by marcobICR 3 months ago - 11 comments
Labels: bug

#7987 - Fixed #7986

Pull Request - State: closed - Opened by greglandrum 3 months ago

#7986 - Morgan fingerprints with chirality distinguish chiral atoms too early

Issue - State: closed - Opened by greglandrum 3 months ago
Labels: bug

#7985 - Make sure that FreeSASA can be built as DLL on Windows

Pull Request - State: open - Opened by ptosco 3 months ago - 1 comment

#7984 - Fix for removing bad stereo indications from Atropisomer parsing

Pull Request - State: closed - Opened by tadhurst-cdd 3 months ago - 1 comment
Labels: bug

#7983 - Stereogroup lost when importing chiral sulfoxide from v3000 molfile

Issue - State: open - Opened by spparel 3 months ago - 4 comments
Labels: bug

#7981 - Enrichment factor returns empty list

Issue - State: open - Opened by j-adamczyk 3 months ago - 2 comments
Labels: bug

#7979 - Update SMILES parsing syntax error to include bad token position

Pull Request - State: closed - Opened by whosayn 3 months ago - 6 comments
Labels: enhancement

#7978 - SynthonSpace Search

Pull Request - State: closed - Opened by DavidACosgrove 3 months ago - 3 comments
Labels: enhancement

#7975 - fix problems with template matching

Pull Request - State: closed - Opened by ZontaNicola 3 months ago - 5 comments

#7971 - DrawRDKitEnvs Can't kekulize mol.

Issue - State: closed - Opened by ivannnnnnnnnn 4 months ago - 2 comments
Labels: bug, stale

#7970 - MMFF optimization converts Pyridine geometry from planar to non-planar

Issue - State: closed - Opened by venkata-ramaswamy-cresset 4 months ago - 4 comments
Labels: bug

#7969 - Tautomer canonicalization loses sp3 stereo even when `SetRemoveSp3Stereo` is False

Issue - State: open - Opened by pechersky 4 months ago - 2 comments
Labels: bug, stale

#7968 - Move CI builds to macos-14

Pull Request - State: closed - Opened by greglandrum 4 months ago
Labels: infrastructure, not in release notes

#7965 - Upstream patches from rdkit-feedstock

Pull Request - State: closed - Opened by skearnes 4 months ago - 3 comments
Labels: stale

#7964 - Need to reserve space before assignment

Pull Request - State: closed - Opened by bp-kelley 4 months ago - 2 comments
Labels: bug

#7962 - Make sure that loggers can be enabled, disabled, captured and tee'd from MinimalLib

Pull Request - State: closed - Opened by ptosco 4 months ago - 1 comment
Labels: enhancement

#7961 - MMFFOptimizeMolecule removes aromatic property from some atoms

Issue - State: open - Opened by k-ujihara 4 months ago - 1 comment
Labels: bug

#7960 - Expose propertyFlags to CFFI and MinimalLib

Pull Request - State: closed - Opened by ptosco 4 months ago
Labels: enhancement

#7959 - Expose molzip functionality to MinimalLib

Pull Request - State: closed - Opened by ptosco 4 months ago - 5 comments
Labels: enhancement

#7957 - Fix incorrect CIP values for some aromatic atropisomers

Pull Request - State: closed - Opened by tadhurst-cdd 4 months ago
Labels: bug

#7956 - Add molecules names into ScaffoldNetwork

Pull Request - State: open - Opened by PatrickPenner 4 months ago

#7953 - Tautomer hash fix #7502 appears to introduce atom/bond order dependence

Issue - State: open - Opened by mcs07 4 months ago - 1 comment
Labels: bug, stale

#7952 - Fix misnamed test

Pull Request - State: closed - Opened by ricrogz 4 months ago
Labels: Cleanup, infrastructure

#7951 - Aromatic atropisomer error

Pull Request - State: open - Opened by tadhurst-cdd 4 months ago - 1 comment
Labels: bug

#7949 - Fix for trimethylcyclohexane error

Pull Request - State: closed - Opened by tadhurst-cdd 4 months ago - 1 comment
Labels: bug

#7948 - Wrong behaviour of the permutation tag for non-tetrahedral stereochemistry

Issue - State: closed - Opened by Strandgaard96 4 months ago - 2 comments
Labels: bug, stale

#7947 - RDKit postgreSQL cartridge infinity loop

Issue - State: closed - Opened by garaboncias 4 months ago - 2 comments
Labels: bug, stale

#7946 - Update RDKit_Book.rst

Pull Request - State: open - Opened by johnmay 4 months ago - 2 comments

#7944 - rxn.RunReactants mismatch directional bonds in a heterocycle ring

Issue - State: closed - Opened by m-hyin 4 months ago - 2 comments
Labels: bug

#7943 - One final round of mem errors

Pull Request - State: closed - Opened by ricrogz 4 months ago - 5 comments
Labels: Cleanup

#7942 - Updates to the Docs/Book directory

Pull Request - State: closed - Opened by greglandrum 4 months ago
Labels: enhancement, documentation

#7941 - InsertMol does not update variable attachment points

Issue - State: closed - Opened by greglandrum 4 months ago - 2 comments
Labels: bug, stale

#7940 - InsertMol does not preserve link nodes

Issue - State: closed - Opened by greglandrum 4 months ago - 2 comments
Labels: bug, stale

#7939 - Add to Cookbook "Include a Bond Index" recipe and image

Pull Request - State: closed - Opened by bertiewooster 4 months ago - 5 comments
Labels: enhancement, documentation

#7938 - Remove deprecation warnings by switching MinimalLib to fingerprint generators

Pull Request - State: open - Opened by ptosco 4 months ago
Labels: Cleanup, infrastructure

#7937 - SimilarityMaps.GetSimilarityMapFromWeights scale option has no effect

Issue - State: closed - Opened by FrederikKjeldal 4 months ago - 2 comments
Labels: bug, stale

#7928 - SA Score updates

Pull Request - State: closed - Opened by DavidACosgrove 4 months ago
Labels: contrib, Cleanup

#7926 - Replace GetImplicitValence() and GetExplicitValence() with GetValence()

Pull Request - State: closed - Opened by greglandrum 4 months ago - 7 comments
Labels: Cleanup, API-change

#7924 - ... and more mem errors fixed

Pull Request - State: closed - Opened by ricrogz 4 months ago
Labels: Cleanup

#7922 - `DetermineBonds` causes a hard freeze for certain `Chem.Mol` inputs

Issue - State: open - Opened by amorehead 4 months ago - 8 comments
Labels: bug, stale

#7921 - RDK_BUILD_CAIRO_SUPPORT option missing from CMakeLists.txt in Version Version : 2024.03.6

Issue - State: closed - Opened by pippo1990 4 months ago - 2 comments
Labels: enhancement

#7920 - auto-close stale issues and PRs

Pull Request - State: closed - Opened by greglandrum 4 months ago - 1 comment
Labels: infrastructure, not in release notes

#7917 - Bug with assigning stereochemistry in multiprocessing

Issue - State: open - Opened by j-adamczyk 4 months ago - 2 comments
Labels: bug, stale

#7915 - Cns mpo

Pull Request - State: open - Opened by Adam-maz 4 months ago - 3 comments
Labels: stale

#7914 - export the targets with a python dependency to a different config file

Pull Request - State: open - Opened by rvianello 4 months ago - 3 comments

#7913 - Replace awful enum reflection macros with Better Enums

Pull Request - State: closed - Opened by ptosco 4 months ago
Labels: Cleanup, API-change

#7910 - Do the announced deprecations

Pull Request - State: closed - Opened by greglandrum 4 months ago
Labels: Cleanup, not in release notes

#7906 - MolToInchiKey inconsistency between rdkit versions

Issue - State: closed - Opened by radchenkods 4 months ago - 4 comments
Labels: bug

#7904 - Fixes #7699

Pull Request - State: closed - Opened by greglandrum 4 months ago

#7902 - Switch from awful macros to Better Enums for enum reflection

Pull Request - State: closed - Opened by ptosco 4 months ago - 1 comment
Labels: Cleanup, infrastructure

#7901 - UFF optimization leads to overlapping atoms

Issue - State: open - Opened by oboril 4 months ago - 9 comments
Labels: bug

#7900 - Update `PUBCHEMSHAPE_URL` and remove patch code

Pull Request - State: closed - Opened by eunos-1128 4 months ago - 1 comment
Labels: Cleanup

#7899 - Fix some more mem errors in 2024.09.1

Pull Request - State: closed - Opened by ricrogz 4 months ago - 9 comments
Labels: bug, Cleanup

#7898 - Restore "oops, exponential is a pain" code snippet in the RGD algorithm

Pull Request - State: closed - Opened by ptosco 4 months ago - 5 comments
Labels: bug, Cleanup

#7895 - Expose three ROMol methods which were not previously exposed to SWIG wrappers

Pull Request - State: closed - Opened by ptosco 4 months ago - 2 comments
Labels: enhancement

#7894 - MQN Implementation may differ from original paper in indices

Issue - State: closed - Opened by sroughley 4 months ago - 1 comment
Labels: bug

#7892 - Optimize Butina Clustering for Performance and Expand API

Pull Request - State: closed - Opened by evasnow1992 4 months ago - 5 comments
Labels: enhancement, optimization

#7889 - [IterateCIPRanks] Precompute neighbor indices and counts, sort them together for each atom

Pull Request - State: closed - Opened by scal444 4 months ago - 1 comment
Labels: enhancement, optimization

#7888 - IterateCIPRanks Algorithmic Improvements

Issue - State: open - Opened by scal444 4 months ago
Labels: enhancement

#7888 - IterateCIPRanks Algorithmic Improvements

Issue - State: closed - Opened by scal444 4 months ago - 1 comment
Labels: enhancement, optimization

#7885 - Fixes #7873

Pull Request - State: closed - Opened by bp-kelley 4 months ago