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openbabel

We're on a mission to speak the many languages of chemical data
Collective - Host: opensource - https://opencollective.com/openbabel - Code: https://github.com/openbabel/openbabel

unclear origin of timestamp by `obabel --version`

github.com/openbabel/openbabel - nbehrnd opened this issue 4 days ago

Can not convert pdbqt to mol2

github.com/openbabel/openbabel - He-Ziping opened this issue 4 days ago

fix(py): fix invalid escape sequence

github.com/openbabel/openbabel - e-kwsm opened this pull request 11 days ago

test: remove ADD_PYTHON_TEST

github.com/openbabel/openbabel - e-kwsm opened this pull request 11 days ago

test: use preferred format of add_test

github.com/openbabel/openbabel - e-kwsm opened this pull request 11 days ago

test name conflict: test_conversion_1

github.com/openbabel/openbabel - e-kwsm opened this issue 11 days ago

build!: use CMake FindPython

github.com/openbabel/openbabel - e-kwsm opened this pull request 11 days ago

pybindtest_obconv_writers test spuriously fails due to floating-point error

github.com/openbabel/openbabel - e-kwsm opened this issue 12 days ago

build(intel): use CMake IPO and strip at linkage for Release build

github.com/openbabel/openbabel - e-kwsm opened this pull request 12 days ago

Fix memory issues in ABINIT parser

github.com/openbabel/openbabel - tyler92 opened this pull request 14 days ago

Fix memory issues in AOFORCE parser

github.com/openbabel/openbabel - tyler92 opened this pull request 15 days ago

Support reactions in Ruby swig wrapper

github.com/openbabel/openbabel - romanbsd opened this pull request 15 days ago

Fix crash when converting some bad CML to inchi

github.com/openbabel/openbabel - romanbsd opened this pull request 15 days ago

Fix stack-buffer-overflow for SMILES format parser

github.com/openbabel/openbabel - tyler92 opened this pull request 15 days ago

Add support for dipole moment and reformat with clang-format

github.com/openbabel/openbabel - ghutchis opened this pull request 15 days ago

Bump actions/setup-python from 4 to 5

github.com/openbabel/openbabel - dependabot[bot] opened this pull request 16 days ago

Bump peter-evans/create-pull-request from 3.8.0 to 7.0.5

github.com/openbabel/openbabel - dependabot[bot] opened this pull request 16 days ago

Bump actions/checkout from 2 to 4

github.com/openbabel/openbabel - dependabot[bot] opened this pull request 16 days ago

Bump github/codeql-action from 2 to 3

github.com/openbabel/openbabel - dependabot[bot] opened this pull request 16 days ago

Bump actions/upload-artifact from 1 to 4

github.com/openbabel/openbabel - dependabot[bot] opened this pull request 16 days ago

Add GitHub dependabot scanning for GitHub actions

github.com/openbabel/openbabel - ghutchis opened this pull request 16 days ago

Fix stack-buffer-overflow for MOPAC format parser

github.com/openbabel/openbabel - tyler92 opened this pull request 16 days ago

Implement fuzz_convert fuzzer

github.com/openbabel/openbabel - tyler92 opened this pull request 16 days ago

Issue with Molecule Partitioning During PDB to PDBQT Conversion in Open Babel

github.com/openbabel/openbabel - hezhizhang-269 opened this issue 18 days ago

Fix memory leak in Smilesformat

github.com/openbabel/openbabel - UnionTech-Software opened this pull request 19 days ago

Ensure chains and residues are retained in FASTA generation

github.com/openbabel/openbabel - ghutchis opened this pull request 22 days ago

hydrogen atom order in mol2 file

github.com/openbabel/openbabel - eisoab opened this issue about 1 month ago

New build: obgui failing

github.com/openbabel/openbabel - Javaslinger opened this issue about 1 month ago

could not set working directory in WSL

github.com/openbabel/openbabel - miroi opened this issue about 1 month ago

Segfault when converting a specific InChI to SMILES

github.com/openbabel/openbabel - rickhelmus opened this issue about 2 months ago

support for Python3.12

github.com/openbabel/openbabel - jonathaw opened this issue 2 months ago

Can I capture warning messages into a log file during executing pybel?

github.com/openbabel/openbabel - mainguyenanhvu opened this issue 2 months ago

Atom type assignment depends on order of atoms

github.com/openbabel/openbabel - dspoel opened this issue 2 months ago

option -g for cif to create _geom_bond in command line

github.com/openbabel/openbabel - mersadkhan opened this issue 3 months ago

Is retaining an empty bond block in the sdf file necessary?

github.com/openbabel/openbabel - nbehrnd opened this issue 3 months ago

Windows installer creates certain files only for the current user

github.com/openbabel/openbabel - cihlarma opened this issue 3 months ago

Autodock command error

github.com/openbabel/openbabel - maham29 opened this issue 3 months ago

Autodock command error

github.com/openbabel/openbabel - maham29 opened this issue 3 months ago

Fetch more recent rapidjson codebase rather than last release

github.com/openbabel/openbabel - matterhorn103 opened this pull request 3 months ago

The PDBQT files appear distorted after being converted from the SDF format!

github.com/openbabel/openbabel - nilanjana1996 opened this issue 4 months ago

obminimize: could not setup force field.

github.com/openbabel/openbabel - nilanjana1996 opened this issue 4 months ago

obabel -p on protein PDB file fails to kekulize Tryptophans

github.com/openbabel/openbabel - kimjc95 opened this issue 4 months ago

Don't crash on an invalid InChI

github.com/openbabel/openbabel - romanbsd opened this pull request 4 months ago

Linking on Windows (VS 2022) with CMake - missing lib file

github.com/openbabel/openbabel - AngstromZA opened this issue 4 months ago

IntelLLVM does not support `-ipo1`

github.com/openbabel/openbabel - e-kwsm opened this issue 5 months ago

Fail to read molecule.pdb while covalent docking

github.com/openbabel/openbabel - Brett628 opened this issue 5 months ago

Direct Comparison of `OBMol` and PyBel.Molecule Objects

github.com/openbabel/openbabel - KunhuanLiu opened this issue 5 months ago

obminimize: could not setup force field.

github.com/openbabel/openbabel - hackerzone85 opened this issue 5 months ago

How to rearrange Pybel objects according to the order of atoms in a SMILES string.

github.com/openbabel/openbabel - kronos7777777 opened this issue 5 months ago

Errors in 3 D structure generation

github.com/openbabel/openbabel - LigandJed1 opened this issue 5 months ago

Converting to pdbqt gets rid of Hydrogen atom

github.com/openbabel/openbabel - Yannlefrancois opened this issue 5 months ago

Interoperability with MDAnalysis

github.com/openbabel/openbabel - lunamorrow opened this issue 5 months ago

a use-after-free issue on src/charges/fromfile.cpp#L114.

github.com/openbabel/openbabel - hokein opened this issue 6 months ago

Fix memory leak in InChi handling

github.com/openbabel/openbabel - romanbsd opened this pull request 6 months ago

Fix crash on specific CML format

github.com/openbabel/openbabel - romanbsd opened this pull request 6 months ago

Gasteiger Partial Charges Explanation

github.com/openbabel/openbabel - maciejwisniewski-drugdiscovery opened this issue 6 months ago

Converting reactions SMILES into cdxml format loses reactant/product information

github.com/openbabel/openbabel - RamziWeslati opened this issue 6 months ago

Restore compatibility with libxml 2.12.7

github.com/openbabel/openbabel - merkys opened this pull request 6 months ago

LICENSE clarification

github.com/openbabel/openbabel - hmacdope opened this issue 7 months ago

Formal releases or just continue to use the master branch

github.com/openbabel/openbabel - cwolcott opened this issue 7 months ago

Unexpected twisted double bond in output structure

github.com/openbabel/openbabel - arebruvold opened this issue 7 months ago

ReadyToInput member wasn't initialized

github.com/openbabel/openbabel - romanbsd opened this pull request 7 months ago

Clear ImplicitHydrogens on multi-fragment cdxml documents.

github.com/openbabel/openbabel - fredrikw opened this pull request 7 months ago

segfault when converting particular CDXML file

github.com/openbabel/openbabel - jasondbiggs opened this issue 7 months ago

Fix ASAN reported integer overflow

github.com/openbabel/openbabel - romanbsd opened this pull request 8 months ago

Support conversion to CMLR

github.com/openbabel/openbabel - romanbsd opened this pull request 8 months ago

Fix memory leaks for xmlChar allocated by libxml

github.com/openbabel/openbabel - romanbsd opened this pull request 8 months ago

documentation .bgf file format is missing

github.com/openbabel/openbabel - nbehrnd opened this issue 8 months ago

Correct identification of atom types of ionized molecules

github.com/openbabel/openbabel - husakm opened this issue 8 months ago

When I convert the ligands to pdbqt, the q values are 0

github.com/openbabel/openbabel - apaydinemre opened this issue 8 months ago

openbabel==3.1.1 from conda-forge has incorrectly versioned BABEL_LIBDIR

github.com/openbabel/openbabel - mjw99 opened this issue 8 months ago

<< Compilation stop in: "Built target plugin_charges" >>

github.com/openbabel/openbabel - icamps opened this issue 9 months ago

Overlapping atoms after UFF optimisation

github.com/openbabel/openbabel - jennijones opened this issue 9 months ago

pip install openbabel failing in windows

github.com/openbabel/openbabel - X265065 opened this issue 9 months ago

obabel error on reading "Cl" as "l"

github.com/openbabel/openbabel - zubairhussain123 opened this issue 9 months ago

Change check for rpc/xdr.h

github.com/openbabel/openbabel - fredrikw opened this pull request 9 months ago

Openbabel not found in Jupyter Notebook

github.com/openbabel/openbabel - jennijones opened this issue 9 months ago

Fix failing test in testobconv_writers

github.com/openbabel/openbabel - fredrikw opened this pull request 10 months ago

Add RDFile support

github.com/openbabel/openbabel - tkzv opened this issue 10 months ago

How to batch convert crystal format(.cif) to 3dmesh format (.obj) by using openbabel？

github.com/openbabel/openbabel - SteelDominic opened this issue 10 months ago

crystal(.cif,.pdb.etc)covert to print 3d format .stl ,open babel cannot cov

github.com/openbabel/openbabel - SteelDominic opened this issue 10 months ago

Make CorrectForPH respect perceived chains.

github.com/openbabel/openbabel - fredrikw opened this pull request 10 months ago

Adding hydrogens with -p messes up the entire structure (not only residue numbers and names)

github.com/openbabel/openbabel - kalinni opened this issue 10 months ago

errors in --gen3d

github.com/openbabel/openbabel - cassguff opened this issue 10 months ago

Make OpenBabel read pymatgen format

github.com/openbabel/openbabel - correaa opened this issue 10 months ago

obabel add SMILES stereocenter `@`/`@@` to achiral unsaturated spiro compounds

github.com/openbabel/openbabel - e-kwsm opened this issue 10 months ago

Failed to compiling the python bindings.

github.com/openbabel/openbabel - hongyi-zhao opened this issue 10 months ago

Creating a reduced version of openbabel for Python 3.11

github.com/openbabel/openbabel - sdr0598 opened this issue 10 months ago

obrms is not computing RMSDs for all conformations in a multimol2 file

github.com/openbabel/openbabel - isabellaguedes opened this issue 11 months ago

E0020 The identifier ""strcasecmp"" is not defined plugin.h

github.com/openbabel/openbabel - chris9672 opened this issue 11 months ago

Box and atom coordinate scaling not consistent when converting from GROMACS to LAMMPS

github.com/openbabel/openbabel - chw90 opened this issue 11 months ago

Kekulize bonds when converting sdf to mol2

github.com/openbabel/openbabel - andt88 opened this issue 11 months ago

Unable to compile Align-It with openbabel at the end of make

github.com/openbabel/openbabel - gryffNx opened this issue 11 months ago

Parse error on line 4 (ATOM) : Unknown or inappropriate tag

github.com/openbabel/openbabel - NooraAz opened this issue 11 months ago

Parsing error issue with obabel generated pdbqt files in vina

github.com/openbabel/openbabel - AlexisGGk opened this issue 11 months ago

Implemented code for atom-typing to support the Alexandria force field.

github.com/openbabel/openbabel - dspoel opened this pull request 11 months ago

pyttest_babel test passes on clean build

github.com/openbabel/openbabel - jfkonecn opened this pull request 12 months ago

pytest_babel test fails on clean build

github.com/openbabel/openbabel - jfkonecn opened this issue 12 months ago

Upgrade hinformat.cpp InterX

github.com/openbabel/openbabel - ileontyev opened this pull request almost 1 year ago

_formatstodict is broken

github.com/openbabel/openbabel - gorrie06 opened this issue about 1 year ago