rdkit/rdkit issues and pull requests

#7779 - Many tests fail

Issue - State: open - Opened by yurivict 5 months ago - 5 comments
Labels: bug

#7779 - Many tests fail

Issue - State: open - Opened by yurivict 5 months ago - 4 comments
Labels: bug

#7778 - Fix issue in #7720

Pull Request - State: closed - Opened by ricrogz 5 months ago
Labels: bug, infrastructure

#7778 - Fix issue in #7720

Pull Request - State: closed - Opened by ricrogz 5 months ago
Labels: bug, infrastructure

#7777 - SDWriter did not write a mol to SD File

Issue - State: open - Opened by ruslankotl 6 months ago - 2 comments
Labels: bug

#7777 - SDWriter did not write a mol to SD File

Issue - State: open - Opened by ruslankotl 6 months ago - 2 comments
Labels: bug

#7776 - RDKit 2024.03.6 fails to build on Mac with certain options

Issue - State: closed - Opened by ankane 6 months ago - 6 comments
Labels: bug

#7776 - RDKit 2024.03.6 fails to build on Mac with certain options

Issue - State: closed - Opened by ankane 6 months ago - 6 comments
Labels: bug

#7775 - Fix typo in 4.5.0--4.6.0 sql upgrade script

Pull Request - State: closed - Opened by esiaero 6 months ago - 3 comments
Labels: bug

#7775 - Fix typo in 4.5.0--4.6.0 sql upgrade script

Pull Request - State: closed - Opened by esiaero 6 months ago - 3 comments
Labels: bug

#7774 - Fix 4.3.0--4.4.0 sql upgrade script

Pull Request - State: closed - Opened by esiaero 6 months ago - 1 comment
Labels: bug

#7774 - Fix 4.3.0--4.4.0 sql upgrade script

Pull Request - State: closed - Opened by esiaero 6 months ago - 1 comment
Labels: bug

#7773 - add mol processing API

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

#7773 - [WIP] add mol processing API

Pull Request - State: open - Opened by greglandrum 6 months ago - 3 comments

#7771 - use make_unique in GeneralFileReader

Pull Request - State: closed - Opened by greglandrum 6 months ago
Labels: Cleanup, not in release notes

#7771 - use make_unique in GeneralFileReader

Pull Request - State: closed - Opened by greglandrum 6 months ago
Labels: Cleanup, not in release notes

#7770 - Weired behaviour of SMARTS ring opening

Issue - State: closed - Opened by GurevichPE 6 months ago - 1 comment

#7770 - Weired behaviour of SMARTS ring opening

Issue - State: closed - Opened by GurevichPE 6 months ago - 1 comment

#7768 - Bond stereo information not permutation invariant

Issue - State: open - Opened by JanCBrammer 6 months ago

#7765 - Expose MMFF aromaticity model for SetAromaticity

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

#7765 - Expose MMFF aromaticity model for SetAromaticity

Pull Request - State: open - Opened by JLVarjo 6 months ago - 2 comments

#7764 - CNS-MPO implementation in Python

Pull Request - State: closed - Opened by Adam-maz 6 months ago - 3 comments

#7764 - I provided 2 scripts, which allow user to calculate CNS-MPO score bas…

Pull Request - State: open - Opened by Adam-maz 6 months ago

#7763 - Add callbacks to the multithreaded mol suppliers

Pull Request - State: closed - Opened by greglandrum 6 months ago
Labels: bug, enhancement

#7763 - Add callbacks to the multithreaded mol suppliers

Pull Request - State: closed - Opened by greglandrum 6 months ago
Labels: bug, enhancement

#7762 - Unreal conformers obtained after conformer generation and UFF optimization for molecules with -NO2 groups

Issue - State: open - Opened by longdragoon 6 months ago - 2 comments
Labels: bug, stale

#7762 - Unreal conformers obtained after conformer generation and UFF optimization for molecules with -NO2 groups

Issue - State: open - Opened by longdragoon 6 months ago - 2 comments
Labels: bug, stale

#7761 - Fix aliasing bug in MultithreadedSDMolSupplier and move GeneralFileReader to v2 API

Pull Request - State: open - Opened by greglandrum 6 months ago
Labels: bug, enhancement, changes results

#7761 - Fix aliasing bug in MultithreadedSDMolSupplier and move GeneralFileReader to v2 API

Pull Request - State: closed - Opened by greglandrum 6 months ago - 4 comments
Labels: bug, enhancement, changes results

#7760 - Bad two colour wedge

Pull Request - State: closed - Opened by DavidACosgrove 6 months ago

#7759 - More stable SMILES canonicalization function

Issue - State: open - Opened by gentle1999 6 months ago - 3 comments
Labels: enhancement

#7759 - More stable SMILES canonicalization function

Issue - State: open - Opened by gentle1999 6 months ago - 3 comments
Labels: enhancement

#7758 - add useChirality flag to SaltRemover

Pull Request - State: closed - Opened by JuniorSen 6 months ago - 1 comment

#7758 - add useChirality flag to SaltRemover

Pull Request - State: closed - Opened by JuniorSen 6 months ago - 1 comment

#7757 - Fixes #7501 dative bonds in cdxml

Pull Request - State: open - Opened by bp-kelley 6 months ago - 1 comment

#7757 - Fixes #7501 dative bonds in cdxml

Pull Request - State: closed - Opened by bp-kelley 6 months ago - 2 comments

#7756 - Add cdxml dative bonds

Pull Request - State: closed - Opened by bp-kelley 6 months ago

#7756 - Add cdxml dative bonds

Pull Request - State: closed - Opened by bp-kelley 6 months ago

#7755 - Dev/remove iter from vector wrappers

Pull Request - State: closed - Opened by bp-kelley 6 months ago

#7755 - Dev/remove iter from vector wrappers

Pull Request - State: open - Opened by bp-kelley 6 months ago

#7754 - Proposal/Minimallib CI

Pull Request - State: open - Opened by MichelML 6 months ago - 5 comments
Labels: stale

#7754 - Proposal/Minimallib CI

Pull Request - State: open - Opened by MichelML 6 months ago - 5 comments
Labels: stale

#7753 - Azure pipeline for minimal lib

Issue - State: open - Opened by MichelML 6 months ago - 1 comment
Labels: enhancement, stale

#7752 - Get pytest to run without incurring in a circular import when RDKit Python modules are installed out-of-tree

Pull Request - State: open - Opened by ptosco 6 months ago - 3 comments
Labels: stale

#7750 - SaltRemover loses E/Z configuration

Issue - State: closed - Opened by JuniorSen 6 months ago - 3 comments
Labels: enhancement

#7750 - SaltRemover loses E/Z configuration

Issue - State: closed - Opened by JuniorSen 6 months ago - 3 comments
Labels: enhancement

#7749 - Fix vectToString such that it outputs valid JSON

Pull Request - State: open - Opened by ptosco 6 months ago - 1 comment
Labels: enhancement

#7749 - Fix vectToString such that it outputs valid JSON

Pull Request - State: closed - Opened by ptosco 6 months ago - 1 comment
Labels: enhancement

#7748 - Exposure to minilib: molzip

Pull Request - State: open - Opened by StLeonidas 6 months ago - 3 comments
Labels: stale

#7748 - Exposure to minilib: molzip

Pull Request - State: open - Opened by StLeonidas 6 months ago - 3 comments
Labels: stale

#7747 - Suppress large amounts of 'macro redefined' warnings in clang/emcc builds

Pull Request - State: open - Opened by ptosco 6 months ago - 1 comment
Labels: infrastructure, stale

#7746 - AtomValenceException for transition metal anion

Issue - State: closed - Opened by simonmb 6 months ago - 5 comments

#7746 - AtomValenceException for transition metal anion

Issue - State: open - Opened by simonmb 6 months ago - 1 comment

#7745 - Enumerate Resonance Structures for Radical Species

Issue - State: open - Opened by KShebek 6 months ago - 1 comment
Labels: enhancement, stale

#7745 - Enumerate Resonance Structures for Radical Species

Issue - State: open - Opened by KShebek 6 months ago - 1 comment
Labels: enhancement, stale

#7744 - Complement JSMol with JSMolShared

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

#7743 - Expose two additional boolean flags for mol creation to MinimalLib

Pull Request - State: closed - Opened by ptosco 6 months ago
Labels: enhancement

#7743 - Expose two additional boolean flags for mol creation to MinimalLib

Pull Request - State: closed - Opened by ptosco 6 months ago
Labels: enhancement

#7742 - Code cleanup, minor refactoring and typos

Pull Request - State: open - Opened by ptosco 6 months ago
Labels: Cleanup

#7742 - Code cleanup, minor refactoring and typos

Pull Request - State: closed - Opened by ptosco 6 months ago - 1 comment
Labels: Cleanup

#7741 - Reconstruction of a big molecule out of SMILES. Valence issue

Issue - State: open - Opened by iGulitch 6 months ago - 8 comments
Labels: bug, stale

#7739 - Bad 2-colour wedge

Issue - State: open - Opened by DavidACosgrove 6 months ago
Labels: bug

#7739 - Bad 2-colour wedge

Issue - State: closed - Opened by DavidACosgrove 6 months ago
Labels: bug

#7738 - Don't do the fancy merging of solid wedges and bond lines for triple …

Pull Request - State: closed - Opened by DavidACosgrove 6 months ago - 1 comment

#7737 - refactor: use [[maybe_unused]] attribute

Pull Request - State: open - Opened by e-kwsm 6 months ago - 7 comments

#7736 - Excessive Memory Consumption during MCS Calculation with `rdFMCS.FindMCS`

Issue - State: open - Opened by J-Kazusa 6 months ago - 1 comment
Labels: bug

#7736 - Excessive Memory Consumption during MCS Calculation with `rdFMCS.FindMCS`

Issue - State: open - Opened by J-Kazusa 6 months ago - 2 comments
Labels: bug, stale

#7735 - bad_alloc was found while trying to load Chem moduel in with Python import

Issue - State: open - Opened by TristonC 6 months ago - 2 comments
Labels: bug

#7735 - bad_alloc was found while trying to load Chem moduel in with Python import

Issue - State: closed - Opened by TristonC 6 months ago - 4 comments
Labels: bug

#7734 - Restore the ability to build RDKit_minimal.js after #7700

Pull Request - State: closed - Opened by ptosco 6 months ago - 1 comment
Labels: bug, not in release notes

#7734 - Restore the ability to build RDKit_minimal.js after #7700

Pull Request - State: closed - Opened by ptosco 6 months ago - 1 comment
Labels: bug, not in release notes

#7732 - Allow atom map numbers to be ignored when generating canonical SMILES

Pull Request - State: closed - Opened by DavidACosgrove 6 months ago - 1 comment
Labels: enhancement

#7731 - Python 3.13 support: _Py_IsFinalizing() has been removed from Python 3.13.

Issue - State: open - Opened by kuelumbus 6 months ago - 2 comments
Labels: bug

#7731 - Python 3.13 support: _Py_IsFinalizing() has been removed from Python 3.13.

Issue - State: closed - Opened by kuelumbus 6 months ago - 2 comments
Labels: bug

#7729 - Ensure 13 bounds constraints are added to angles that are part of an improper torsion

Pull Request - State: closed - Opened by nmaeder 6 months ago - 1 comment
Labels: bug

#7729 - Ensure 13 bounds constraints are added to angles that are part of an improper torsion

Pull Request - State: closed - Opened by nmaeder 6 months ago - 1 comment
Labels: bug

#7728 - Fixes #7725

Pull Request - State: open - Opened by greglandrum 6 months ago

#7728 - Fixes #7725

Pull Request - State: closed - Opened by greglandrum 6 months ago - 1 comment

#7726 - Embed Molecule numerical instability edge case?

Issue - State: open - Opened by fredtony 6 months ago - 2 comments
Labels: bug, stale

#7725 - Double-bond geometry lost from CXSMILES?

Issue - State: closed - Opened by greglandrum 6 months ago
Labels: bug

#7722 - Update TorsionAngle.cpp - vector cross products involved in the gradient calculation.

Pull Request - State: closed - Opened by buerbaumer 6 months ago - 3 comments

#7721 - doc: fix -Wdocumentation-html

Pull Request - State: closed - Opened by e-kwsm 6 months ago - 1 comment
Labels: documentation, Cleanup

#7720 - Some cmake cleanup work

Pull Request - State: closed - Opened by greglandrum 6 months ago - 2 comments
Labels: Cleanup, infrastructure

#7719 - Speed up boost vector iterators

Pull Request - State: closed - Opened by bp-kelley 6 months ago - 10 comments
Labels: enhancement

#7717 - Could NOT find Boost (missing: Boost_INCLUDE_DIR python) (Required is at least version "1.58.0") - when installing from source

Issue - State: closed - Opened by MKCarter 6 months ago - 2 comments

GitHub / rdkit/rdkit issues and pull requests