Ecosyste.ms: Issues

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

GitHub / openmm/pdbfixer issues and pull requests

#303 - Added optimizeHydrogenBonds()

Pull Request - State: open - Opened by peastman about 2 months ago

#301 - Neutralise systems with formal charges from the PDB

Pull Request - State: open - Opened by Yoshanuikabundi 2 months ago - 3 comments

#300 - findMissingResidues does not detect residues missing from structure

Issue - State: closed - Opened by YoavShamir5 2 months ago - 10 comments

#298 - Fixed bug in added bonds to heterogens

Pull Request - State: closed - Opened by peastman 2 months ago - 1 comment

#297 - PDBFixer not writing out complete CONECT records for downloaded Templates

Issue - State: closed - Opened by sukritsingh 2 months ago - 10 comments

#296 - Support nonstandard residues

Pull Request - State: closed - Opened by peastman 3 months ago

#295 - Can add hydrogens to nonstandard residues

Pull Request - State: closed - Opened by peastman 3 months ago - 1 comment

#294 - Bugfixed chain ID assignment in addSolvent (#287)

Pull Request - State: closed - Opened by murfalo 3 months ago - 5 comments

#293 - Should PDBFixer write out SEQRES entries if provided in the input?

Issue - State: open - Opened by sukritsingh 4 months ago - 9 comments

#292 - [bug] Ensure numpy < 2 version

Pull Request - State: closed - Opened by awlange 4 months ago - 3 comments

#291 - PDBFixer adding repeated residues at the start.

Issue - State: closed - Opened by Ian-CP 5 months ago - 1 comment

#290 - Fixing out a very long chain with pdbfixer

Issue - State: closed - Opened by stan1233 5 months ago - 2 comments

#289 - openmm.OpenMMException: Particle coordinate is nan

Issue - State: open - Opened by VeScarecrow 5 months ago - 3 comments

#288 - How can I cite this tool if I use it

Issue - State: open - Opened by tang2552 6 months ago - 1 comment
Labels: question

#287 - Error when having more than 10 chain identifiers

Issue - State: closed - Opened by FAOlivieri 6 months ago - 7 comments

#285 - mmCIF output - `_atom_site.label_entity_id` not written

Issue - State: closed - Opened by Augustin-Zidek 8 months ago - 1 comment

#284 - fix add missing unknown (UNK) residues error

Pull Request - State: open - Opened by ndonyapour 9 months ago - 3 comments

#281 - PDBFixer cannot handle nucleic acids with residue name N

Issue - State: open - Opened by jamesmkrieger 11 months ago - 5 comments

#280 - Do we have method to mutate the iCode-containing residue?

Issue - State: open - Opened by Loci-Tran 12 months ago - 2 comments
Labels: enhancement

#278 - pH protonation valid

Issue - State: open - Opened by groponp about 1 year ago - 1 comment

#277 - Issue with Multiprocessing

Issue - State: closed - Opened by cplateVT about 1 year ago - 10 comments

#276 - Processed Receptor has Long Legs in PDB File

Issue - State: closed - Opened by syedzayyan about 1 year ago - 14 comments

#275 - PDBFixer API cannot fix mmCIF file

Issue - State: closed - Opened by trandinhquangloc about 1 year ago - 5 comments

#274 - Invalide chirality when fixing neural network generated structure

Issue - State: open - Opened by ryankzhu over 1 year ago - 3 comments

#273 - Updated version number to 1.9

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

#272 - PDBfixer with python=3.10 and openmm=7.7

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

#271 - pdbfixer doesn

Issue - State: closed - Opened by matteo-cagiada over 1 year ago

#269 - [Unexpected behaviour] Unexpected behavoiur when parsing mmCIF files

Issue - State: open - Opened by Croydon-Brixton over 1 year ago - 5 comments

#268 - Optimizations to _findNearestDistance()

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

#267 - Speed up _findNearestDistance

Pull Request - State: closed - Opened by edwag over 1 year ago - 4 comments

#266 - Missing b factors

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

#265 - Updated installation instructions

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

#264 - For those care about the running time

Issue - State: closed - Opened by Minys233 almost 2 years ago - 3 comments
Labels: enhancement

#263 - Allow initialization from topology, positions, and sequence.

Pull Request - State: open - Opened by jonathanking almost 2 years ago - 1 comment

#262 - Add forcefield argument to addMissingHydrogens.

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

#261 - Add phosphorylated residues SEP and PTR (pSer and pTyr)

Pull Request - State: closed - Opened by sukritsingh almost 2 years ago - 25 comments

#260 - Residues are not recorded correctly

Issue - State: open - Opened by Ruibin-Liu almost 2 years ago - 1 comment

#259 - Adding phosphorylated residues to PDBFixer templates

Issue - State: open - Opened by sukritsingh almost 2 years ago - 12 comments
Labels: enhancement

#258 - Add nonstandard residue '5OW' to LYS

Pull Request - State: closed - Opened by Ruibin-Liu almost 2 years ago - 10 comments

#257 - Added nonstandard residue 'MK8'

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

#256 - Failed to find missing residues in 6VYC

Issue - State: closed - Opened by jw-feng almost 2 years ago - 6 comments

#255 - `fixer.findMissingResidues()` fails on 3ODU

Issue - State: closed - Opened by JSLJ23 almost 2 years ago - 2 comments

#254 - pypi version

Issue - State: open - Opened by Pantelispanka almost 2 years ago - 9 comments

#253 - Select residue atom positions for residues with alternate locations (altloc)

Issue - State: closed - Opened by JSLJ23 about 2 years ago - 4 comments

#252 - Cannot add missing atoms

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

#251 - Adding two terminal caps to a single residue

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

#248 - remove

Issue - State: closed - Opened by jaredsagendorf over 2 years ago

#247 - Enhancement requests if not already existing?

Issue - State: open - Opened by BJWiley233 over 2 years ago - 5 comments

#246 - fix CI badge; remove some old simtk

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

#245 - Added boxShape option to addSolvent()

Pull Request - State: closed - Opened by peastman over 2 years ago

#244 - No matching distribution found for openmm>=7.1 (from pdbfixer)

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

#243 - How to eliminate hydrogen

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

#242 - Potential Energy mantisa is same for all iteration.

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

#241 - one case cannot fix missing residue

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

#240 - question for PDBFixer

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

#239 - Updated manual to show current output of --help

Pull Request - State: closed - Opened by peastman over 2 years ago

#238 - User manual not updated

Issue - State: closed - Opened by BJWiley233 over 2 years ago - 1 comment

#236 - Rename chain

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

#235 - Fix DeprecationWarning (#233)

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

#234 - phosaa14SB.xml KeyError and Resolution

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

#232 - Index out of bounds error when calling fixer function

Issue - State: closed - Opened by Tonylac77 almost 3 years ago - 3 comments

#231 - Is bond order available via pdbfixer?

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

#230 - PDBFixer is changing chain names

Issue - State: open - Opened by raoufkeskes about 3 years ago - 1 comment

#229 - Updated version number to 1.8.1

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

#228 - Fixed error leading to duplicate bonds

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

#227 - PDBFixer not working some PDB file

Issue - State: open - Opened by AhmetGG about 3 years ago - 5 comments

#226 - Fix typos discovered by codespell

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

#225 - Revamp PDBFixer testing

Pull Request - State: closed - Opened by swails about 3 years ago - 5 comments

#224 - Convert to GitHub actions to re-enable continuous integration

Issue - State: closed - Opened by jchodera about 3 years ago - 1 comment
Labels: tests

#223 - Changes to work with OpenMM 7.6

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

#222 - GitHub Action to lint Python code

Pull Request - State: closed - Opened by cclauss about 3 years ago - 14 comments

#221 - Fix reading PDBx from filename

Pull Request - State: closed - Opened by dww100 about 3 years ago - 1 comment

#219 - PDBs from RCSB failed to reconstruct

Issue - State: open - Opened by slawek111 over 3 years ago - 7 comments

#218 - how to handle non standard amino acids e.g. PTR

Issue - State: open - Opened by michelsanner over 3 years ago - 5 comments

#217 - Documentation needed?

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

#216 - Updated version in setup.py

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

#215 - Support all lipid types from OpenMM 7.5

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

#214 - Fixed 'See our manual' link

Pull Request - State: closed - Opened by TrianguloY almost 4 years ago - 1 comment

#213 - After fixing my protein giving long tail

Issue - State: closed - Opened by Bio-Otto almost 4 years ago - 3 comments

#212 - See our manual link broken

Issue - State: closed - Opened by birbilis almost 4 years ago - 11 comments

#211 - Fix Travis builds

Pull Request - State: closed - Opened by peastman almost 4 years ago - 1 comment

#210 - Charges lost on ASP and GLU residues

Issue - State: open - Opened by tdudgeon almost 4 years ago - 1 comment

#209 - Histidines created with Hs at HD1 and HE1

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

#208 - Fixed box vectors for truncated octahedron

Pull Request - State: closed - Opened by peastman almost 4 years ago - 2 comments

#207 - combining fixed PDBs

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

#206 - Maintain wanted heterogens

Issue - State: open - Opened by ghost about 4 years ago - 4 comments
Labels: enhancement

#205 - How to select a single position for atoms with multiple alternate positions listed

Issue - State: open - Opened by ghost about 4 years ago - 3 comments
Labels: enhancement

#204 - Which force field is used and how to change?

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