Ecosyste.ms: Issues

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

GitHub / Electrostatics/pdb2pqr issues and pull requests

#400 - Comparing web server output and Command line output

Issue - State: closed - Opened by HaydenGJ about 2 months ago

#399 - Protonation of nonstandard residues not occurring

Issue - State: open - Opened by HeheHahaHoHoHo 2 months ago - 2 comments

#398 - Issue using APBS plugin on polysaccharides

Issue - State: open - Opened by NoaBinnes 3 months ago

#394 - Ligand amide bond type not

Issue - State: open - Opened by and-tos 5 months ago - 1 comment

#393 - Pending Job Start

Issue - State: open - Opened by hillaryhe 5 months ago - 6 comments

#392 - pdb2pqr does not remove atoms as expected

Issue - State: open - Opened by CyberCatQ 7 months ago

#391 - Adding pKa-ANI as an option to assign titratable states

Pull Request - State: open - Opened by sastrys1 7 months ago - 4 comments

#389 - Using pKa-ANI to compute titration states at a given pH?

Issue - State: open - Opened by sastrys1 7 months ago - 2 comments

#387 - Fix mol2 parsing

Pull Request - State: open - Opened by nimijkrap 8 months ago - 1 comment

#386 - Error to process neutral Cter of ASN

Issue - State: open - Opened by micmar15sr 8 months ago - 2 comments

#385 - Update Sphinx versions.

Pull Request - State: closed - Opened by sobolevnrm 9 months ago - 1 comment

#384 - Upgrade Sphinx packages

Issue - State: closed - Opened by sobolevnrm 9 months ago

#383 - Allow hexadecimal ATOM id

Pull Request - State: open - Opened by SSchott 9 months ago

#382 - Add tests for failed titration state naming

Pull Request - State: closed - Opened by sobolevnrm 9 months ago - 2 comments

#381 - Non-integer residue charge with PEOEPB

Issue - State: open - Opened by sobolevnrm 9 months ago

#380 - Generate tests for amino acid naming

Issue - State: closed - Opened by sobolevnrm 9 months ago - 1 comment

#379 - Version 3.6.2 release candidate

Pull Request - State: closed - Opened by sobolevnrm 9 months ago - 4 comments

#378 - Update pkg_resources

Issue - State: closed - Opened by sobolevnrm 9 months ago - 1 comment

#377 - Release new version

Issue - State: closed - Opened by sobolevnrm 9 months ago

#376 - Error in ligand processing

Issue - State: open - Opened by adventureneed 10 months ago - 2 comments

#375 - inputget error on alphafold structures

Issue - State: open - Opened by shaharsu 10 months ago - 2 comments

#374 - Caculating electrrostatic potential over distance

Issue - State: open - Opened by hanahg 10 months ago - 4 comments

#373 - pdb2pqr modifies the chain names

Issue - State: open - Opened by ndonyapour 10 months ago - 4 comments

#372 - Fix `io.test_for_file` failing for editable installs

Pull Request - State: closed - Opened by sphuber 12 months ago - 1 comment

#371 - update docutils please?

Issue - State: open - Opened by pgbarletta about 1 year ago

#370 - Allow using hexadecimal ATOM id

Pull Request - State: closed - Opened by SSchott about 1 year ago - 5 comments

#369 - ValueError: 'P' is not in list

Issue - State: open - Opened by GuhLelouch about 1 year ago - 2 comments

#368 - Too far hydrogen generated from "charmmgui corrected" pdb?

Issue - State: open - Opened by jdandrade-gmx about 1 year ago - 3 comments

#367 - Replace XML-format data files with YAML

Issue - State: open - Opened by sobolevnrm about 1 year ago

#366 - Warn about unused PROPKA options

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

#364 - Fix broken link in "Other software docs"

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

#363 - Fix typo in visualization documentation

Issue - State: closed - Opened by sobolevnrm over 1 year ago

#362 - Validation of protonation states in the output PDB File

Issue - State: closed - Opened by samit1194 over 1 year ago - 1 comment

#361 - Error message heavy atoms missing

Issue - State: closed - Opened by bakpaotlrasin over 1 year ago - 1 comment

#359 - Residues being renamed TER

Issue - State: closed - Opened by quockerwodger over 1 year ago - 1 comment

#358 - naming inconsistency with CHARMM

Issue - State: open - Opened by pokhreln over 1 year ago - 6 comments

#357 - Pending job start

Issue - State: open - Opened by axm8099 over 1 year ago - 4 comments

#355 - chelation sites

Issue - State: closed - Opened by joaomcteixeira over 1 year ago

#353 - There are concatenated fields in PQR output

Issue - State: closed - Opened by wt12318 over 1 year ago - 1 comment

#352 - Version 3.6.1 release candidate.

Pull Request - State: closed - Opened by sobolevnrm over 1 year ago - 3 comments

#351 - Update copyright to 2023.

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

#350 - Nathan/348

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

#349 - Release PDB2PQR 3.6.1

Issue - State: closed - Opened by sobolevnrm over 1 year ago - 1 comment

#348 - Fix broken PDB2PQR documentation

Issue - State: closed - Opened by sobolevnrm over 1 year ago

#346 - hydrogen atoms with zero radius ?!

Issue - State: closed - Opened by UnixJunkie over 1 year ago - 1 comment

#345 - PDB2PQR 3.6.0 release candidate.

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

#344 - Update copyright date to 2023

Issue - State: closed - Opened by sobolevnrm over 1 year ago

#343 - Update ChangeLog with modifications since last release.

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

#342 - Need to update PDB2PQR Python compatibility.

Issue - State: closed - Opened by sobolevnrm over 1 year ago

#341 - Update to PROPKA 3.5

Pull Request - State: closed - Opened by sobolevnrm over 1 year ago - 3 comments

#340 - Update ChangeLog with changes since last release

Issue - State: closed - Opened by sobolevnrm over 1 year ago

#339 - Update `setup.py` to force latest version of PROPKA

Issue - State: closed - Opened by sobolevnrm over 1 year ago

#338 - Run pdb2pqr as python library

Issue - State: open - Opened by dargen3 over 1 year ago - 1 comment

#337 - Another no PQR file in outputs issue

Issue - State: open - Opened by lbizzio over 1 year ago - 1 comment

#336 - tetrahedral hydrogen reconstruction issue

Issue - State: open - Opened by sunghh44 over 1 year ago

#335 - New PDB2PQR release

Issue - State: closed - Opened by sobolevnrm over 1 year ago - 12 comments

#334 - Possible race condition in main.run_propka()

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

#333 - Problems with Mn ion in enzyme

Issue - State: closed - Opened by mverissi over 1 year ago - 1 comment

#331 - format problems

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

#330 - Removed redundant ChangeLog file.

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

#329 - Remove ChangeLog.md

Issue - State: closed - Opened by sobolevnrm almost 2 years ago

#327 - missing modified phosphorylated threonine residue (THP1)

Issue - State: closed - Opened by sau1978 about 2 years ago

#326 - waiting for Pending Job Start too long

Issue - State: closed - Opened by Eridium1 about 2 years ago - 1 comment

#325 - Ligand with Amide Bonds

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

#323 - phospholipid problems

Issue - State: open - Opened by corbinsblack about 2 years ago

#322 - Protonation of histidine

Issue - State: closed - Opened by kexul about 2 years ago - 1 comment

#321 - OPM and pdb2pqr

Issue - State: open - Opened by khelmy55 about 2 years ago - 5 comments

#320 - Cannot add --display-coupled-residues flag to PDB2PQR webserver

Issue - State: closed - Opened by rediaz111 over 2 years ago - 1 comment

#319 - Biomolecue charge is non-integer --- pdb:4yki

Issue - State: closed - Opened by khelmy55 over 2 years ago - 1 comment

#318 - server stuck

Issue - State: closed - Opened by sunimei3 over 2 years ago - 8 comments

#316 - use pd2pqr in python3 script

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

#315 - Eliminated need to write to temporary file in disk

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

#314 - A bug of creating the Biomolecule instance

Issue - State: open - Opened by chemsh over 2 years ago

#313 - error during conversion of pdb file to pqr file format

Issue - State: open - Opened by rubinanoor9 over 2 years ago - 2 comments

#312 - Error reading four letters residues

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

#311 - atomic radius

Issue - State: closed - Opened by lex1213 over 2 years ago - 1 comment

#307 - Cyclic peptide support

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

#306 - Issue with cyclic peptides

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

#305 - Rename radian-to-degree constant

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

#304 - Hydrogen addition problems with non-experimental input structures

Issue - State: open - Opened by dargen3 over 2 years ago - 19 comments

#302 - AttributeError: 'NoneType' object has no attribute 'group_type'

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

#301 - Fix issues in protonated terminal residue naming

Pull Request - State: closed - Opened by stefdoerr over 2 years ago - 3 comments

#300 - NMR proteins with hydrogens fail preparation

Issue - State: open - Opened by stefdoerr over 2 years ago - 3 comments

#299 - Missing heavy atoms error erroring

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

#298 - Fix critical bug in python 3.8+ versions with temporary file creation

Pull Request - State: closed - Opened by stefdoerr over 2 years ago - 12 comments

#297 - Maintain original chain names unless there is a break

Pull Request - State: closed - Opened by stefdoerr over 2 years ago - 3 comments

#295 - Set up new version (3.5.2)

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

#294 - XML parser fix

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

#293 - Problem with DefinitionHandler

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

#292 - New PDB2PQR release

Issue - State: closed - Opened by sobolevnrm over 2 years ago - 7 comments

#291 - Fix bug and add support for integer resnames which exist in PDB

Pull Request - State: closed - Opened by stefdoerr over 2 years ago - 4 comments