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

Can't convert file from PDB to PDBQT

phamthanhbinh157 opened this issue almost 2 years ago

Fixed a bug that C.ar was converted to C3 when reading mol2 files

gfzhou opened this pull request almost 2 years ago

Test stuck at test_automorphism_10

surak opened this issue about 2 years ago

openbabel installation error at google colab, windows OS

sathish-dream-ai opened this issue about 2 years ago

Static ZLIB dependency not found with -DBUILD_SHARED=OFF in maeparser

Mblakey opened this issue about 2 years ago

Subprocess-exited-with-error when installing 3.1.1.1 on MacOS

stuchalk opened this issue about 2 years ago

Assign implicit hydrogens when reading pdbqt

fredrikw opened this pull request about 2 years ago

Automatic partial charge

dagarcial opened this issue about 2 years ago

ci: add CIFuzz Github Action

DavidKorczynski opened this pull request about 2 years ago

MOL file bug

ignaspakamore opened this issue about 2 years ago

Please consider adding a testsuite for python bindings

yurivict opened this issue about 2 years ago

Python example wgtRotorSrch.py fails: AttributeError: 'NoneType' object has no attribute 'SetLogLevel'

yurivict opened this issue about 2 years ago

PDBQT to SDF

sbembenek18 opened this issue about 2 years ago

Add CodeQL workflow for GitHub code scanning

lgtm-com[bot] opened this pull request about 2 years ago

mmCIF output is missing mandatory values

gregcouch opened this issue about 2 years ago

Tanimoto score filter display incorrect Tanimoto coefficient values

aburjan opened this issue about 2 years ago

Error in generating 3D coordinates

bhogalinderjeet opened this issue about 2 years ago

Hydrogen addition and Hydrogen bonds

alexandrefassio opened this issue about 2 years ago

obminimize of github version cannot do multithread computation

HsuShihHsueh opened this issue about 2 years ago

document silent deps: maeparser and CoordgenLibs

ostueker opened this pull request over 2 years ago

If requested, supply atom index as atom classes

ghutchis opened this pull request over 2 years ago

Orca: Make sure to update geometry coordinates during parsing

ghutchis opened this pull request over 2 years ago

Fix 338

fredrikw opened this pull request over 2 years ago

cannot access addFragment() function

cplateVT opened this issue over 2 years ago

QUESTION: What is the likelihood that the openbabel python api is broken due to the new patch update and how int/str conversions are changed?

EChung0111 opened this issue over 2 years ago

Allow Output of atom indices with SMILES conversion (e.g. .xyz to .smi)

Thomas3R opened this issue over 2 years ago

Add missing include of <ctime> to fix build with glibc 2.36

schnitzeltony opened this pull request over 2 years ago

Support for 64bit OBDotNet.dll

ulink-uaa opened this issue over 2 years ago

Writing Rigid pdbqt files

EChung0111 opened this issue over 2 years ago

how to skip Warning: Stereochemistry is wrong, using the distance geometry method instead

DreamMemory001 opened this issue over 2 years ago

Include <ctime> for clock()

heirecka opened this pull request over 2 years ago

is re-assignment of a carbon-centred radical possible

nbehrnd opened this issue over 2 years ago

Allow GUI to compile with wxWidgets built with STL

super7ramp opened this pull request over 2 years ago

InChI additional arguments silently ignored

RaphaelRobidas opened this issue over 2 years ago

Cannot SetOutputStream in Python

xrobin opened this issue over 2 years ago

installing openbabel with Python bindings

Rojaettfolk opened this issue over 2 years ago

Feature Request: Incorporate the GAMESS US Z-Matrix Format

ocelotStride opened this issue over 2 years ago

Catch (swig) error exception in python for system exit.

PatReis opened this issue over 2 years ago

Wln writer

Mblakey opened this pull request over 2 years ago

WLN Reader Additions

Mblakey opened this pull request over 2 years ago

update interface pybel.py

zhongxiang117 opened this pull request over 2 years ago

AssignAromaticFlags example

MJoseom opened this issue over 2 years ago

Arginine fix

dkoes opened this pull request over 2 years ago

openbabel python import from conda environment fails due to undefined symbol

PanayotisManganaris opened this issue over 2 years ago

OpenBabel PHP Wrapper for PHP 8.x

cwolcott opened this issue over 2 years ago

How to use openbabel as c++ library on windows with visual studio 2019

retinavr opened this issue almost 3 years ago

Obgui failed to understand wildchars in input filename box.

alchemistcai opened this issue almost 3 years ago

Incomplete conversion when using string comparsion with the wild card `*` prefixed.

alchemistcai opened this issue almost 3 years ago

broken inclusion of model in .png files as string

nbehrnd opened this issue about 3 years ago

Exception after importing openbabel in Python

edmondop opened this issue over 3 years ago

Python bindings cannot be installed if OpenBabel installed with Brew on Macos

edmondop opened this issue over 3 years ago

pip install openbabel fails because of invalid version

samjeckert opened this issue over 3 years ago

Integrate cibuildwheel GHA for better PyPI deployment

radifar opened this issue over 3 years ago

Cannot open UFF.prm

MitosisAI opened this issue over 3 years ago

`xyz` is missing from ----INPUT FORMAT--- in OpenBabel GUI

othmanalbahri1 opened this issue over 3 years ago

Problem compiling static version of Open Babel 3.1.1 on Debian Buster

JSand134 opened this issue over 3 years ago

Simple ReadFile program leaks memory

correaa opened this issue over 3 years ago

Peptide in FASTA format to SMILES conversion problem

AnotherKiwi opened this issue over 3 years ago

can not import pybel from openbabel

mmccarthy1 opened this issue over 3 years ago

Open Babel Error in OpenBabel::OBBuilder::GetFragmentCoord Rigid fragment C1CCCNC1 in rigid-fragments.txt has all zero coordinates

StashOfCode opened this issue over 3 years ago

PDB conversion overload

cap-jmk opened this issue almost 4 years ago

Incorrect conversion of symbols

dlf57 opened this issue almost 4 years ago

How can I keep atom labels in the output PDB

shaoqx opened this issue almost 4 years ago

API documentation does not default to latest

RMeli opened this issue almost 4 years ago

Open Babel Error in Do 3D coordinate generation failed

nakatamaho opened this issue about 4 years ago

feature suggest, DataWarrior idcode format

nbehrnd opened this issue about 4 years ago

Option -e is not working with --gen3D

ivok2002 opened this issue about 4 years ago

obsym crashes with segmentation fault

e-kwsm opened this issue about 4 years ago

--gen3d get stucked

hust220 opened this issue over 4 years ago

Rigid fragment XXXX in rigid-fragments.txt has all zero coordinates

teriken opened this issue over 4 years ago

OBElements import is confusing in python

lpravda opened this issue over 4 years ago

Reimplement OpenBabel::OBRandom as a wrapper of std::mt19937_64

e-kwsm opened this pull request over 4 years ago

testdistgeom.py fails when run with Python 3

jcbollinger opened this issue over 4 years ago

Clean up tools/obabel.cpp

e-kwsm opened this pull request almost 5 years ago

Python bindings (OB3): No module named 'openbabel._openbabel'

odioidentisti2 opened this issue almost 5 years ago

Gen3D in python causing Segmentation fault

daemonice opened this issue about 5 years ago

Tidy up

e-kwsm opened this pull request about 5 years ago

pybel error when handling missing plugins

hmenager opened this issue about 5 years ago

Comment out unused parameters

e-kwsm opened this pull request about 5 years ago

Remove smart matching for rigid fragment

n-yoshikawa opened this pull request over 5 years ago

pip install openbabel under windows does not work

kovalp opened this issue over 5 years ago

Remove deprecated std::bind1st

e-kwsm opened this pull request over 5 years ago

Compilation failure

Vcald opened this issue over 5 years ago

Pybel reports Incorrect formal charge on Mol2 file

edwardclem opened this issue over 5 years ago

Fix incorrect use of `memcpy`.

sunoru opened this pull request about 6 years ago

problematic conversion from pdb to pdbqt

ghost opened this issue about 6 years ago

Incorrect Qeq charges

danieleongari opened this issue about 6 years ago

smi is not a recognised Open Babel format

yurivict opened this issue about 6 years ago

Gasteiger charge calculation should avoid use of GetType

baoilleach opened this issue almost 7 years ago

cannot pip install openbabel and install by myself

random-var-x opened this issue over 7 years ago

Problem with the negative charges when reading .cdx

genevievebo opened this issue over 8 years ago