github.com/openbabel/openbabel issues | Ecosyste.ms: OpenCollective

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

chw90 opened this issue 12 months ago

Kekulize bonds when converting sdf to mol2

andt88 opened this issue 12 months ago

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

gryffNx opened this issue about 1 year ago

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

NooraAz opened this issue about 1 year ago

Parsing error issue with obabel generated pdbqt files in vina

AlexisGGk opened this issue about 1 year ago

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

dspoel opened this pull request about 1 year ago

pyttest_babel test passes on clean build

jfkonecn opened this pull request about 1 year ago

pytest_babel test fails on clean build

jfkonecn opened this issue about 1 year ago

Upgrade hinformat.cpp InterX

ileontyev opened this pull request about 1 year ago

_formatstodict is broken

gorrie06 opened this issue about 1 year ago

python depend failed

mintuos opened this issue about 1 year ago

slurmstepd-falkor7: error: Step 1141809.0 exceeded memory limit (41393168 > 20971520), being killed srun: Exceeded job memory limit

ivzzognam opened this issue about 1 year ago

slurmstepd-falkor7: error: Step 1141810.0 exceeded memory limit (52917772 > 20971520), being killed srun: Exceeded job memory limit

ivzzognam opened this issue about 1 year ago

OpenBabel determines incorrect sum formula

schatzsc opened this issue about 1 year ago

cml conversion to smiles - extra implicit hydrogens added to files with explicit hydrogens

kmlefran opened this issue about 1 year ago

Add more cjson features, including conformer energies

ghutchis opened this pull request about 1 year ago

Fix parsing "Gaussian" vibration output from xtb program

ghutchis opened this pull request about 1 year ago

Frequencies from g98 file converted incorrectly

matterhorn103 opened this issue about 1 year ago

Is there any routine to check the 3D validity of a molecule

AlexisGeorgiou opened this issue about 1 year ago

numerous vulnerabilities reported by cisco TALOS

ajakk opened this issue about 1 year ago

Proper aromatic support for CML

fredrikw opened this pull request about 1 year ago

Remove redundant SSSR rings based on bond paths

fredrikw opened this pull request about 1 year ago

--delete option is not working properly

ivok2002 opened this issue about 1 year ago

CML Aromatic Bonds not being written

kmlefran opened this issue about 1 year ago

openbabel.org with ERR_TOO_MANY_REDIRECTS

j3mdamas opened this issue about 1 year ago

Not generating the same torsion lists for conformers

pyrodancer123 opened this issue about 1 year ago

`openbabel.org` site is down

chenrui333 opened this issue about 1 year ago

openbabel not honoring keyword option for mopac conversion

peabreu opened this issue about 1 year ago

Unexpected behaviour in SSSR routine - wrong sub rings

Mblakey opened this issue about 1 year ago

Make sure to add cell vectors & space group info to CJSON

ghutchis opened this pull request about 1 year ago

access record count by the compiled obabel executable

nbehrnd opened this issue about 1 year ago

I meet a problem when i use --gen3D in openbabel 3.1.1

zengdashi opened this issue over 1 year ago

Support for segment names in pdb files

dkoes opened this pull request over 1 year ago

Wrong enegy values when converting Gaussian .log files to .xyz files

Astro-Aionia opened this issue over 1 year ago

Add support for range-based for loops

timvdm opened this pull request over 1 year ago

Fix bug in distance geometry code

timvdm opened this pull request over 1 year ago

obconformer does not find the most stable conformation of a cyclic compound (e.g. cyclohexane chair)

e-kwsm opened this issue over 1 year ago

obabel uses single thread

avinashkarkada opened this issue over 1 year ago

Ambiguous stereochemistry in -opng

Quaddroo opened this issue over 1 year ago

There was a problem with file 2020_refined_lig_sdf/1e1v_ligand.sdf: Sanitization error: Can't kekulize mol.

Dadiao-shuai opened this issue over 1 year ago

By default do not wrap atomic coordinates to the unit cell

ghutchis opened this pull request over 1 year ago

curl: (60) SSL certificate problem: certificate has expired

ivzzognam opened this issue over 1 year ago

problem openbabel installation

ivzzognam opened this issue over 1 year ago

Command obrms not found

1980whisky opened this issue over 1 year ago

Bonded charged hydrogen atoms are silently removed from the SMILES output

vaitkus opened this issue over 1 year ago

Molecular formula calculation from SMILES sometimes does not include H atoms from brackets

vaitkus opened this issue over 1 year ago

XYZ to SDF no formal charges

JSLJ23 opened this issue over 1 year ago

How to use OBGraphSym.GetSymmetry

545487677 opened this issue over 1 year ago

visualization of Markush structures

nbehrnd opened this issue over 1 year ago

Import Openbabel error from Python calling

tgupta2222 opened this issue over 1 year ago

Assertion failure in rapidjson when using output of Avogadro2

jakiki6 opened this issue over 1 year ago

Error with python bindings while compilation

tgupta2222 opened this issue over 1 year ago

Valence error (pdb->pdbqt->pdb)

AustinApple opened this issue over 1 year ago

Add some features for Organometallic molecules

Jesnm01 opened this pull request over 1 year ago

Issue with building Openbabel-3.1.1

tgupta2222 opened this issue over 1 year ago

It can not convert elements such as Li, Mg from gro to pdb

y805939188 opened this issue over 1 year ago

Missing file: data/ring-fragments-index.txt

oboril opened this issue over 1 year ago

Fix potential crash reading and writing CJSON files

ghutchis opened this pull request over 1 year ago

obabel output tabs and spaces

dgcovell opened this issue over 1 year ago

Incorrect? atom types in SDF -> Mol2 conversion (O.3 vs O.2)

AlexW12344 opened this issue over 1 year ago

parse cdxml

xinwoyouyou opened this issue over 1 year ago

obrms improvements

dkoes opened this pull request over 1 year ago

Bug in SMARTS string for CH-acidic and/or CH-acidic_strong

FLessi opened this issue over 1 year ago

Hello

FLessi opened this issue over 1 year ago

Hi there!

FLessi opened this issue over 1 year ago

2 tests fail

yurivict opened this issue over 1 year ago

Non standard residue names get reset after calling `GetResidue()`.

bisejdiu opened this issue over 1 year ago

OpenBabel cannot write output file

vidinjo opened this issue over 1 year ago

Fixed alignment of partial charges for PDBQT-files

flatstik opened this pull request over 1 year ago

Failed to kekulize from MOL2 to PDB

flatstik opened this issue over 1 year ago

Some source code packages could not find Python3 library during installation

HoaSoup opened this issue over 1 year ago

fix bug when read gro file as first residue idx is 0

DStarEpoch opened this pull request over 1 year ago

Linking fails

meerfrau opened this issue over 1 year ago

Fix bug in pubchem json coordinate writing

magnusrahm opened this pull request over 1 year ago

Erroneously aligned columns on pdbqt -type conversions <-- merge request

flatstik opened this issue over 1 year ago

.xyz -> .smi bug when converting oximes.

apshay opened this issue over 1 year ago

So many errors on make test in openbabel 3.1.1

jmechua-itsrdc opened this issue over 1 year ago

updated runner python setup

Mblakey opened this pull request over 1 year ago

Wiswesser

Mblakey opened this pull request over 1 year ago

Wiswesser

Mblakey opened this pull request over 1 year ago

ERROR in compiling orcaformat.cpp

lcmj520 opened this issue almost 2 years ago

CIF: behaviour inconsistency between Hermann–Mauguin short and full notations if symmetry operations are insufficient

e-kwsm opened this issue almost 2 years ago

SMILES -> OXYZ coordinate generation --gen3D not correctly identifying forcefield

raulorteg opened this issue almost 2 years ago

InChI normalization schema

drjahu opened this issue almost 2 years ago

AddAtom argument constness

correaa opened this pull request almost 2 years ago

AddAtom/InsertAtom could return a pointer to the inserted atom

correaa opened this issue almost 2 years ago

Do fingerprints change between OpenBabel releases?

drjahu opened this issue almost 2 years ago

use simple cube format for molecules with single grid

correaa opened this pull request almost 2 years ago

Correct way to deal with dialects for output of CUBE files

correaa opened this issue almost 2 years ago

Test case fail because of syntax error in testdistgeom.py

zimb3l-priv opened this issue almost 2 years ago

Improper torsion calculation in GAFF

niko-pd opened this issue almost 2 years ago

bs format doesn't seem to work

chrisewels opened this issue almost 2 years ago

Allylic Radicals: Open Babel Error in Do 3D coordinate generation failed

jacosand opened this issue almost 2 years ago

OpenBabel3Config.cmake to keep include information

correaa opened this pull request almost 2 years ago

Errors while running CTest

d9748336 opened this issue almost 2 years ago

The edge prediction from xyz is suboptimal.

HongxinXiang opened this issue almost 2 years ago

Need Pip Support for v3.1.1.1

fyffep opened this issue almost 2 years ago

Install error. macOS Ventura

izxle opened this issue almost 2 years ago

refactor: remove deprecated std::bind2nd

e-kwsm opened this pull request almost 2 years ago

OpenBabel3Config.cmake: "The following imported targets are referenced but are missing: maeparse coordgen"

chedatomasz opened this issue almost 2 years ago