Electrostatics/apbs-pdb2pqr issues and pull requests

#634 - Remove stray documentation.

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

#633 - Move documentation

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

#632 - Move PDB2PQR-specific docs to separate repo

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

#630 - Remove APBS code from this repo

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

#629 - Remove PDB2PQR code from this repo

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

#628 - Remove APBS code from this repo

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

#627 - Update README.md and documentation for this repo

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

#626 - Create separate apbs repo

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

#625 - Mark/logging caching

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

#624 - Remove PDB2PQR code from this repo

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

#623 - Positive potential on hydrophobic protein interfaces

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

#622 - Restore ligand functionality to PDB2PQR

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

#619 - Move PDB2PQR back to its own repo?

Issue - State: closed - Opened by sobolevnrm about 4 years ago - 10 comments

#618 - Clean up README.md

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

#615 - NotImplementedError: PDB2PKA not implemented.

Issue - State: closed - Opened by arikat about 4 years ago - 12 comments

#612 - This resolves issue 611

Pull Request - State: closed - Opened by kozlac about 4 years ago - 1 comment

#610 - Separate tests by functionality

Pull Request - State: closed - Opened by sobolevnrm about 4 years ago - 1 comment

#605 - Find dat folder.

Pull Request - State: closed - Opened by kozlac about 4 years ago - 6 comments

#601 - Remove binaries from Git repo

Issue - State: closed - Opened by sobolevnrm about 4 years ago - 9 comments

#600 - PyMOL 2.4.0 APBS plug-in not recognising PDB2PQR

Issue - State: closed - Opened by DBradley27 about 4 years ago - 4 comments

#599 - APBS and Python3

Issue - State: closed - Opened by sagitter about 4 years ago - 7 comments

#595 - Large apbs .dx file downloads fail from web server due to server-side error?

Issue - State: closed - Opened by sherif10002 about 4 years ago - 8 comments
Labels: bug

#592 - Possibly reinstate PDB2PKA ligand support

Issue - State: closed - Opened by sobolevnrm about 4 years ago

#589 - Double-check Cmake build

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

#588 - Replace C++ clique-finding with Python

Issue - State: closed - Opened by sobolevnrm about 4 years ago

#582 - Please fix really ugly code

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

#575 - Problem with pdb2pqr.utilities.getFFfile

Issue - State: closed - Opened by sobolevnrm about 4 years ago - 1 comment
Labels: bug

#574 - PDB2PQR doesn't recognize HETATM with --drop-water

Issue - State: closed - Opened by sobolevnrm about 4 years ago - 2 comments
Labels: bug

#573 - PDB2PQR --assign-only does not assign charges or radii

Issue - State: closed - Opened by sobolevnrm about 4 years ago
Labels: bug, critical

#571 - PDB2PQR tests don't actually work

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

#570 - Add testing for extensions

Issue - State: closed - Opened by sobolevnrm about 4 years ago
Labels: enhancement

#569 - Clean up old branches

Issue - State: closed - Opened by sobolevnrm about 4 years ago - 1 comment
Labels: backlog

#561 - Eliminate use of sys.stdout and sys.stderr

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

#558 - Clean up vestigal Opal & web server files

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

#551 - PROPKA 3.0 vs 3.1

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

#547 - Update doc/installing.rst

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

#546 - Merge license files

Issue - State: closed - Opened by sobolevnrm about 4 years ago

#543 - Combine APBS & PDB2PQR code bases into single version

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

#540 - AMBER fix of {N,C}CYS atom HSG to HG

Pull Request - State: closed - Opened by j3mdamas about 4 years ago - 2 comments

#537 - baker.css no longer available for docs

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

#534 - Unable to use inputgen.py with python3

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

#516 - Python 3 compatibility for pdb2pqr

Pull Request - State: closed - Opened by speleo3 almost 6 years ago - 6 comments

#504 - We need documentation for tolsp.

Issue - State: closed - Opened by sobolevnrm almost 7 years ago

#451 - Why use atomname HSG in terminal CYS? And why atomname HN in CYM?

Issue - State: closed - Opened by j3mdamas almost 8 years ago - 8 comments

#440 - Python 3 compatibility and propka3.1 support

Pull Request - State: closed - Opened by tonigi about 8 years ago - 7 comments

#416 - move files in google docs to github

Issue - State: closed - Opened by lizutah over 8 years ago
Labels: documentation

#311 - Add Ball & Stick rendering to 3dmol web viewer

Issue - State: closed - Opened by karinaliles almost 9 years ago - 1 comment
Labels: 3dmol

#310 - Add backbone rendering to 3dmol web viewer

Issue - State: closed - Opened by karinaliles almost 9 years ago - 1 comment
Labels: 3dmol

#306 - More robust geometric flow: RPBE paradigm

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: geometric flow

#305 - More robust geometric flow: Deterministic convergence

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: geometric flow

#304 - Size-modified PB re-integration: APBS release

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: apbs

#303 - Size-modified PB re-integration: Testing with benchmarks

Issue - State: closed - Opened by lizutah almost 9 years ago

#302 - Nonlocal PB: paper for DNA-ion interactions

Issue - State: closed - Opened by lizutah almost 9 years ago

#301 - Nonlocal PB: APBS release

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: apbs

#300 - Nonlocal PB: collaborate with Jay Bardhan

Issue - State: closed - Opened by lizutah almost 9 years ago

#299 - Classical density functional theory: cDFT APBS paper

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: apbs

#298 - Classical density functional theory: cDFT APBS release

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: apbs

#297 - Classical density functional theory: Tramanto integration

Issue - State: closed - Opened by lizutah almost 9 years ago

#296 - Classical density functional theory: Sushko implementation

Issue - State: closed - Opened by lizutah almost 9 years ago

#295 - PDB2PQR 2.1 paper written

Issue - State: closed - Opened by lizutah almost 9 years ago - 1 comment
Labels: pdb2pqr

#291 - Binary support for different platforms for pKa

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: pdb2pqr

#287 - surface-based free energy evaluation

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: apbs

#283 - Better FEM support with mesh generation tool

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: apbs

#282 - Improved FEM support with new FEM library

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: apbs

#281 - Surface energy evaluation for RPBE

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: apbs

#280 - Integration of RPBE into finite element library (FEM)

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: apbs

#278 - Visualization improvements

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: enhancement, pdb2pqr, apbs

#277 - Python front end for APBS

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: apbs

#276 - APBS 2.0 paper written/submitted

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: pdb2pqr, apbs

#275 - APBS and PDB2PQR integration

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: pdb2pqr, apbs

#274 - GPU APBS paper

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: apbs

#273 - Biophysical J review written/submitted

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: pdb2pqr, apbs, documentation

#270 - create webcasts

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: pdb2pqr, apbs, documentation, intern

#269 - Workshop

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: pdb2pqr, apbs, documentation

#268 - add "write" parameter to Geometric Flow code

Issue - State: closed - Opened by lizutah almost 9 years ago - 1 comment
Labels: apbs, geometric flow

#265 - linearized PB support for geoflow

Issue - State: closed - Opened by lizutah almost 9 years ago
Labels: apbs, geometric flow

#257 - localize MALOC dependencies

Issue - State: closed - Opened by lizutah about 9 years ago
Labels: apbs, infrastructure

#256 - GPU sparse solver support

Issue - State: closed - Opened by lizutah about 9 years ago
Labels: apbs, infrastructure

#255 - Trilinos numerical library support

Issue - State: closed - Opened by lizutah about 9 years ago
Labels: apbs, infrastructure

#254 - PETSc numerical library support

Issue - State: closed - Opened by lizutah about 9 years ago
Labels: apbs, infrastructure

#248 - more examples for website

Issue - State: closed - Opened by lizutah about 9 years ago
Labels: pdb2pqr, apbs, documentation, intern

#245 - Color discrepancies between jmol/3dmol and pymol

Issue - State: closed - Opened by pzli3 about 9 years ago - 1 comment
Labels: 3dmol

#241 - Create ADSETMEAS plugin

Issue - State: closed - Opened by kmonson about 9 years ago - 5 comments
Labels: pdb2pqr, mailing list question, intern

#237 - APBS databus

Issue - State: closed - Opened by lizutah about 9 years ago
Labels: apbs

#229 - cDFT APBS implementation

Issue - State: closed - Opened by sobolevnrm about 9 years ago
Labels: enhancement, apbs

#228 - Nonlocal PB solver for APBS?

Issue - State: closed - Opened by sobolevnrm about 9 years ago - 2 comments
Labels: enhancement, apbs

#227 - Write paper about geometric flow nonlinear Poisson-Boltzmann support

Issue - State: closed - Opened by sobolevnrm about 9 years ago
Labels: geometric flow

#226 - Robust Poisson-Boltzmann support for geometric flow

Issue - State: closed - Opened by sobolevnrm about 9 years ago
Labels: enhancement, apbs, geometric flow

#225 - Replace geoflow Poisson solver

Issue - State: closed - Opened by sobolevnrm about 9 years ago
Labels: enhancement, apbs, geometric flow

#223 - Enable output and visualization from geoflow

Issue - State: closed - Opened by sobolevnrm about 9 years ago
Labels: enhancement, user experience, geometric flow

#221 - Consider paper on geometric flow computational tool

Issue - State: closed - Opened by sobolevnrm about 9 years ago

#219 - Make geometric flow more robust

Issue - State: closed - Opened by sobolevnrm about 9 years ago
Labels: apbs, user experience, geometric flow

#218 - Size-modified PB re-integration: implement Nuo's method for SMPBE

Issue - State: closed - Opened by sobolevnrm about 9 years ago - 2 comments
Labels: enhancement, apbs

#212 - updated pKA value

Issue - State: closed - Opened by lizutah about 9 years ago
Labels: enhancement, pdb2pqr

#208 - Read pdb files with multiple model entries into PDB2PQR

Issue - State: closed - Opened by lizutah over 9 years ago
Labels: pdb2pqr, intern

#191 - Geometric Flow is missing OPLS support

Issue - State: closed - Opened by keith923 over 9 years ago - 3 comments
Labels: enhancement, apbs, geometric flow

#164 - Electrostatic results for Geometric Flow are a tad off

Issue - State: closed - Opened by keith923 almost 10 years ago - 1 comment
Labels: bug, apbs, geometric flow

#163 - FEM Problem

Issue - State: closed - Opened by keith923 almost 10 years ago - 1 comment
Labels: bug, apbs, backlog, test

#162 - adding pymol support info

Issue - State: closed - Opened by lizutah almost 10 years ago
Labels: pdb2pqr, apbs, documentation

#29 - Geometric flow test suite for APBS

Issue - State: closed - Opened by sobolevnrm about 10 years ago - 8 comments
Labels: apbs, geometric flow, documentation

GitHub / Electrostatics/apbs-pdb2pqr issues and pull requests