Ecosyste.ms: Issues

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

GitHub / Acellera/moleculekit issues and pull requests

#145 - Unable to find residue ... after preparation error

Issue - State: open - Opened by dargen3 about 2 months ago - 2 comments

#143 - RuntimeError if the chain field has multiple characters

Issue - State: closed - Opened by dargen3 3 months ago - 3 comments

#142 - Meaning of the _molkit_ff parameter in the systemPrepare function

Issue - State: closed - Opened by dargen3 3 months ago - 5 comments

#141 - Bond in mmCIF block _struct_conn is ignored

Issue - State: closed - Opened by dargen3 3 months ago - 2 comments

#139 - Wrong numbering of added hydrogens

Issue - State: closed - Opened by dargen3 4 months ago - 1 comment

#138 - Wrong atom numbering in the saved mmCIF file

Issue - State: closed - Opened by dargen3 5 months ago - 3 comments

#137 - error with hold_nonpeptidic_bonds=False

Issue - State: closed - Opened by dargen3 5 months ago - 4 comments

#136 - Charges from pdb2pqr

Issue - State: closed - Opened by dargen3 5 months ago - 3 comments

#135 - Fix wrapping bug

Pull Request - State: closed - Opened by stefdoerr about 1 year ago

#134 - free GC references so that objects are deleted faster

Pull Request - State: closed - Opened by stefdoerr about 1 year ago

#133 - `atomselect` improvements

Issue - State: open - Opened by stefdoerr about 1 year ago
Labels: enhancement

#132 - Improvements to parameterizable dihedral detection

Pull Request - State: closed - Opened by stefdoerr over 1 year ago

#131 - numpy version, infinite loop when calling Molecule

Issue - State: closed - Opened by duerrsimon over 1 year ago - 2 comments

#130 - Editing velocity files

Issue - State: closed - Opened by Saleh-OM4R over 1 year ago - 2 comments

#129 - CIF improvement

Pull Request - State: closed - Opened by stefdoerr over 1 year ago

#128 - fix a couple of cache-related exceptions

Pull Request - State: closed - Opened by tonigi over 1 year ago - 2 comments

#126 - Failed to parse selection resid<200

Issue - State: closed - Opened by tonigi almost 2 years ago - 3 comments

#125 - chore: drop redundant lgtm configuration

Pull Request - State: closed - Opened by SauravMaheshkar almost 2 years ago - 1 comment

#124 - chore: move configurations to `pyproject.toml`

Pull Request - State: closed - Opened by SauravMaheshkar almost 2 years ago - 1 comment

#123 - Fix bug in XTC read frames

Pull Request - State: closed - Opened by RaulPPelaez almost 2 years ago

#122 - `atomselect` doesn't recognize `numbonds`

Issue - State: open - Opened by raimis about 2 years ago - 1 comment

#121 - Conda package contains `.h` and `.cpp`

Issue - State: closed - Opened by raimis about 2 years ago - 7 comments

#120 - Windows fix

Pull Request - State: closed - Opened by stefdoerr about 2 years ago - 1 comment

#119 - Windows build

Pull Request - State: closed - Opened by stefdoerr about 2 years ago - 1 comment

#118 - ImportError

Issue - State: closed - Opened by lblaabjerg about 2 years ago - 3 comments

#117 - Align to best match in OPM

Pull Request - State: closed - Opened by stefdoerr about 2 years ago - 1 comment

#116 - FTR: Added atom and residue pair distance calculations

Pull Request - State: closed - Opened by stefdoerr about 2 years ago - 1 comment
Labels: enhancement

#115 - sdf for non-cannonical residues

Pull Request - State: open - Opened by alejandrovr about 2 years ago - 1 comment

#114 - Syntax error with atomselect

Issue - State: closed - Opened by JasmineDing01 over 2 years ago - 6 comments

#113 - atomselect fails on resnames that start with number

Issue - State: closed - Opened by duerrsimon over 2 years ago - 3 comments
Labels: bug

#112 - SmallMolLib unexpected behaviour

Issue - State: closed - Opened by alejandrovr over 2 years ago - 4 comments

#111 - Update getFingerprint in moleculekit

Issue - State: closed - Opened by NikSchap2107 over 2 years ago - 2 comments

#110 - Add sasa option to the atom selection language

Issue - State: closed - Opened by ajasja over 2 years ago - 2 comments

#109 - Atomselect reimplementation

Pull Request - State: closed - Opened by stefdoerr over 2 years ago - 1 comment

#108 - Bondguesser

Pull Request - State: closed - Opened by stefdoerr over 2 years ago - 1 comment

#107 - Protein atoms regarded as nonprotein atoms by atomselect()

Issue - State: closed - Opened by computbiolgeek almost 3 years ago - 2 comments

#106 - PIP incompatibility: filename has '1.2.0', but metadata has '0'

Issue - State: closed - Opened by tonigi almost 3 years ago - 5 comments

#105 - 2-D xgboost tool

Pull Request - State: closed - Opened by alejandrovr almost 3 years ago - 1 comment

#104 - Finding difference between voxels of two different protein

Issue - State: closed - Opened by wdorji almost 3 years ago - 1 comment

#103 - Fixing non-canonical residue protonation

Pull Request - State: closed - Opened by stefdoerr almost 3 years ago

#101 - Small molecule CIFs can have ? coordinates

Issue - State: closed - Opened by stefdoerr almost 3 years ago - 1 comment
Labels: bug

#100 - Add support for preparing non-canonical residues with backbone modifications

Issue - State: closed - Opened by stefdoerr almost 3 years ago - 1 comment

#99 - better parameters for align

Pull Request - State: closed - Opened by alejandrovr almost 3 years ago

#98 - added new matching in molvs tautomer

Pull Request - State: closed - Opened by rubbs14 almost 3 years ago

#97 - Fix issue with terminal histidine protonation

Issue - State: closed - Opened by stefdoerr almost 3 years ago - 2 comments
Labels: bug

#96 - Fix printing of newlines in getOpenBabelProperties

Pull Request - State: closed - Opened by duerrsimon almost 3 years ago - 1 comment

#95 - testing rst artifact generation

Pull Request - State: closed - Opened by stefdoerr almost 3 years ago - 1 comment

#94 - Add database of residues to moleculekit

Issue - State: closed - Opened by stefdoerr about 3 years ago - 1 comment
Labels: enhancement

#93 - Refactor dihedral detection code

Issue - State: open - Opened by stefdoerr about 3 years ago
Labels: enhancement

#92 - systemprepare error

Issue - State: closed - Opened by MaciejMajew about 3 years ago - 3 comments

#91 - conda installation fails with PackageNotFoundError

Issue - State: closed - Opened by cisert about 3 years ago - 1 comment

#90 - viewVoxelFeatures usage in python script.

Issue - State: closed - Opened by shikhar2333 about 3 years ago - 1 comment

#89 - Throw meaningful error if VMD is not available in view()

Issue - State: closed - Opened by stefdoerr about 3 years ago - 1 comment
Labels: enhancement

#88 - Avoid multiple, redundant queries to PDB

Issue - State: closed - Opened by alejandrovr about 3 years ago - 4 comments

#87 - various minor speed optimizations for moleculekit

Pull Request - State: closed - Opened by stefdoerr about 3 years ago - 1 comment

#86 - RuntimeError: Zero box size detected in `Molecule.box`. Cannot wrap simulation.

Issue - State: closed - Opened by aqred1 about 3 years ago - 1 comment

#85 - Updated all license headers

Pull Request - State: closed - Opened by stefdoerr about 3 years ago

#84 - Build nonstandard

Pull Request - State: closed - Opened by stefdoerr about 3 years ago

#83 - reading ligand cif

Issue - State: closed - Opened by MaciejMajew about 3 years ago - 4 comments

#82 - systemPrepare issues with terminal HIS residues

Issue - State: closed - Opened by stefdoerr about 3 years ago - 2 comments
Labels: bug

#81 - Error "pdb2pqr" not installed

Issue - State: closed - Opened by laurasansc about 3 years ago - 8 comments

#80 - New preparation

Pull Request - State: closed - Opened by stefdoerr over 3 years ago - 1 comment

#79 - flipping side chain orientations

Issue - State: open - Opened by alejandrovr over 3 years ago - 4 comments

#78 - OpenBabel warning

Issue - State: closed - Opened by nnguyen19 over 3 years ago - 2 comments

#77 - What are the VoxelDescriptors?

Issue - State: closed - Opened by nnguyen19 over 3 years ago - 1 comment

#76 - Warning when `atomselect`-ing from molecules with >=100 atoms

Issue - State: closed - Opened by cisert over 3 years ago - 6 comments

#75 - fatal error: 'ios' file not found on MacOS

Issue - State: closed - Opened by tonigi almost 4 years ago

#74 - Deprecation of numpy.int

Issue - State: closed - Opened by raimis almost 4 years ago - 1 comment

#73 - Error voxelizing protein with 'GLY'

Issue - State: closed - Opened by zarif101 almost 4 years ago - 7 comments

#72 - Python 3.8 package

Issue - State: closed - Opened by raimis almost 4 years ago - 1 comment

#71 - Try to fix the cython deployment

Pull Request - State: closed - Opened by stefdoerr almost 4 years ago

#70 - How to cite moleculekit?

Issue - State: closed - Opened by mgarort almost 4 years ago - 2 comments

#69 - Hbonds calculator

Pull Request - State: closed - Opened by stefdoerr almost 4 years ago

#68 - Molecule from SDF file cannot be constructed if there are >100 atoms/bond

Issue - State: closed - Opened by cisert almost 4 years ago - 2 comments

#66 - viewVoxelFeatures uses hardcoded set of features

Issue - State: closed - Opened by cisert almost 4 years ago - 6 comments

#65 - Error in atom typing

Issue - State: closed - Opened by shikhar2333 about 4 years ago - 2 comments

#64 - Update installation conda command

Pull Request - State: closed - Opened by alejandrovr about 4 years ago

#63 - smallmol containing Hs

Issue - State: closed - Opened by z-linlinlin about 4 years ago - 6 comments

#62 - Azure CI

Pull Request - State: closed - Opened by stefdoerr about 4 years ago

#61 - Error on loading moleculekit (tmalign.dll?)

Issue - State: closed - Opened by NAEV95 about 4 years ago - 1 comment

#60 - Error with getVoxelDescriptors

Issue - State: closed - Opened by kamilla0503 about 4 years ago - 5 comments

#59 - Error .view() for ligand

Issue - State: closed - Opened by cuzzo87 about 4 years ago - 2 comments

#58 - Erro with voxelization

Issue - State: closed - Opened by cuzzo87 about 4 years ago - 3 comments

#57 - Error Smallmol reading file in jupyter-notebook

Issue - State: closed - Opened by cuzzo87 about 4 years ago - 8 comments

#56 - openbabel update

Pull Request - State: closed - Opened by PyeongKim over 4 years ago - 4 comments

#55 - element Cg not found

Issue - State: closed - Opened by PyeongKim over 4 years ago - 1 comment

#54 - VMD visualization does not pop up

Issue - State: closed - Opened by mgarort over 4 years ago - 8 comments

#53 - problem with prepareProtein

Issue - State: closed - Opened by drewaight over 4 years ago - 3 comments

#52 - additional tools

Pull Request - State: closed - Opened by alejandrovr over 4 years ago - 1 comment

#51 - tmalign.dll can't be found

Issue - State: closed - Opened by caiyingchun over 4 years ago - 1 comment

#50 - Issues with prepareProteinForAtomtyping

Issue - State: closed - Opened by zrt over 4 years ago - 1 comment

#49 - FIX: collision error, https://github.com/Acellera/moleculekit/issues/48

Pull Request - State: closed - Opened by churnikov almost 5 years ago - 1 comment

#48 - mol.append with collisions issue

Issue - State: closed - Opened by stefdoerr almost 5 years ago
Labels: bug

#47 - Issue with vmd viewer

Issue - State: closed - Opened by pkiruba almost 5 years ago - 1 comment

#46 - SmallMol issue with writing multiple frames

Issue - State: open - Opened by stefdoerr almost 5 years ago
Labels: bug

#45 - Error in Molecule and Smallmol while working with PDBBind dataset

Issue - State: closed - Opened by hassanmohsin almost 5 years ago - 8 comments