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
#302 - app.Modeller._loadStandardHydrogenDefinitions() AttributeError: type object 'Modeller' has no attribute '_loadStandardHydrogenDefinitions'
Issue -
State: closed - Opened by MichaelAbel1 about 2 months ago
- 2 comments
#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
#299 - `PDBFixer.addSolvent` often incorrectly neutralises systems with charged ligands as though they were neutral
Issue -
State: open - Opened by Yoshanuikabundi 2 months ago
- 7 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
#286 - Mutating to non-standard amino acids not present in available force field libraries
Issue -
State: open - Opened by amin-sagar 7 months ago
- 5 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
#283 - The repair of two ends of peptide didn't return the desired result
Issue -
State: open - Opened by bdx114514 10 months ago
#282 - How to avoid conflicts with other atoms of the protein when undergoing amino acid mutations?
Issue -
State: closed - Opened by 9527567 10 months ago
- 2 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
#279 - findMissingAtoms raises AttributeError if findMissingResidues has not been called first
Issue -
State: open - Opened by nielskm 12 months ago
- 1 comment
#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
#270 - Is there any molecular dynamics or docking research published using pdbfixer?
Issue -
State: open - Opened by RuikangSun over 1 year ago
- 5 comments
#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
#250 - Which parameter set(periodicity, offset, k) does PeriodicTorsionForce use in soft.xml?
Issue -
State: closed - Opened by psp3dcg about 2 years ago
- 8 comments
#249 - Version 1.8.1 fails to addSolvent() when boxShape kwarg is present. Also in openmm-setup
Issue -
State: closed - Opened by pguillem 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
#237 - PDB file lines read in as Models, throws "AttributeError: 'Model' object has no attribute 'decode'"
Issue -
State: open - Opened by ddcas9 almost 3 years ago
- 5 comments
#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
#233 - PDBFixer issue (Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.)
Issue -
State: closed - Opened by markuslacher almost 3 years ago
#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
#220 - addMissingAtoms() adds a linear chain of residues to protein termini in PDB ID 2a07
Issue -
State: closed - Opened by lancelot-droid over 3 years ago
- 4 comments
#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