Ecosyste.ms: Issues

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

GitHub / prody/ProDy issues and pull requests

#1632 - Select app help fix

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

#1631 - Question about Coevolution Analysis

Issue - State: closed - Opened by obasekigit almost 2 years ago - 17 comments
Labels: Feature request

#1630 - add cif datafiles to setup

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

#1626 - DNA Mutual Information

Issue - State: closed - Opened by cag1343 almost 2 years ago - 1 comment

#1625 - Biopython deprecation warning with ProDy plugin on VMD

Issue - State: closed - Opened by cpayal almost 2 years ago - 5 comments

#1624 - fix tests

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

#1623 - Allowing setFlags to take scalar values

Pull Request - State: closed - Opened by SHZ66 almost 2 years ago - 9 comments

#1622 - Package data does not include newly added *.cif test files

Issue - State: closed - Opened by merkys almost 2 years ago - 1 comment

#1619 - store hydrogen bonds between beta-strands

Issue - State: open - Opened by jamesmkrieger almost 2 years ago - 1 comment
Labels: Feature request

#1619 - store hydrogen bonds between beta-strands

Issue - State: open - Opened by jamesmkrieger almost 2 years ago - 1 comment
Labels: Feature request

#1605 - account for PDB FTP deprecation

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

#1602 - showOverlapTable problem

Issue - State: closed - Opened by Yago52 almost 2 years ago - 2 comments

#1599 - Error message when running Prody in VMD 1.9.4a53 Windows 10

Issue - State: open - Opened by tanoury1 almost 2 years ago - 2 comments

#1596 - Interpro Pfam transition

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

#1594 - test cases failed on Debian riscv64

Issue - State: open - Opened by yuzibo almost 2 years ago - 20 comments

#1592 - Question about atom selection in prody

Issue - State: closed - Opened by obasekigit about 2 years ago - 11 comments

#1591 - showMode(gnm[0]) problem in jupyter notebook

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

#1587 - Powering down the Pfam website

Issue - State: closed - Opened by boneta about 2 years ago - 8 comments

#1572 - Domain Bar

Issue - State: closed - Opened by Yago52 about 2 years ago - 24 comments

#1557 - PCA Analysis

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

#1554 - Restore SVD in some cases

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

#1553 - add seaborn kernel density estimation to showProjection

Issue - State: closed - Opened by jamesmkrieger over 2 years ago
Labels: Feature request

#1549 - WIP: Motif search

Pull Request - State: open - Opened by mkonstanty over 2 years ago - 1 comment

#1546 - fail to import prody

Issue - State: closed - Opened by nongbaoting over 2 years ago - 16 comments

#1515 - Extend ClustENM kwargs for more functionality

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

#1499 - modehunter interpolateModel

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

#1482 - fetchPDB should check in folder for files of other formats too

Issue - State: closed - Opened by jamesmkrieger over 2 years ago
Labels: Feature request

#1480 - cealign non-ca fix

Pull Request - State: closed - Opened by jamesmkrieger over 2 years ago - 5 comments

#1467 - Normal mode analysis from VMD

Issue - State: open - Opened by Atulsingh17 over 2 years ago - 18 comments

#1431 - NMWiz connected chains

Issue - State: open - Opened by dim-99 almost 3 years ago - 1 comment
Labels: Enhancement, NMWiz

#1431 - NMWiz connected chains

Issue - State: open - Opened by dim-99 almost 3 years ago - 1 comment
Labels: Enhancement

#1430 - Excluding contacts from flanking residues

Issue - State: closed - Opened by paulaberry almost 3 years ago - 3 comments
Labels: Enhancement

#1430 - Excluding contacts from flanking residues

Issue - State: closed - Opened by paulaberry almost 3 years ago - 3 comments
Labels: Enhancement

#1425 - Read in arbitrary coordinate set (x, y, z)

Issue - State: closed - Opened by b2jia almost 3 years ago - 11 comments
Labels: how-to

#1422 - Dali PCA equivalent (correspondence analysis) on aligned pdbs

Issue - State: open - Opened by williamb009 almost 3 years ago - 9 comments
Labels: Feature request

#1412 - Prody job submission error

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

#1408 - PCA Percent Contribution

Issue - State: closed - Opened by william61001 about 3 years ago - 16 comments
Labels: Feature request

#1406 - added gromos rmsd clustering

Pull Request - State: closed - Opened by jamesmkrieger about 3 years ago - 5 comments
Labels: Enhancement

#1401 - Is there a way to disable logger output in notebook?

Issue - State: open - Opened by zllion about 3 years ago - 10 comments

#1400 - Error of fetchPDBclusters()

Issue - State: closed - Opened by KeiYura about 3 years ago - 9 comments

#1399 - deprecation prep

Pull Request - State: open - Opened by jamesmkrieger about 3 years ago - 1 comment

#1398 - Revert "GitHub actions"

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

#1372 - fix up requirements

Pull Request - State: closed - Opened by hrnciar over 3 years ago - 7 comments

#1346 - System size limitation in writeNMD and/or NMWiz

Issue - State: open - Opened by cgseitz over 3 years ago - 17 comments

#1344 - added trajectory wrap method

Pull Request - State: open - Opened by jamesmkrieger over 3 years ago - 8 comments
Labels: Enhancement

#1327 - pip install cannot build wheels

Issue - State: closed - Opened by mccool-ryan over 3 years ago - 24 comments

#1318 - sampleModes docs fix

Pull Request - State: open - Opened by jamesmkrieger over 3 years ago - 2 comments

#1309 - New Hybrid Modules

Pull Request - State: open - Opened by jamesmkrieger over 3 years ago - 6 comments
Labels: Enhancement

#1292 - New file with protein and protein-ligand interaction is added.

Pull Request - State: closed - Opened by karolamik13 over 3 years ago - 4 comments
Labels: Enhancement

#1226 - charmm-gui interface

Pull Request - State: open - Opened by jamesmkrieger almost 4 years ago - 1 comment
Labels: Enhancement

#1220 - Chain alignment fixes

Pull Request - State: open - Opened by jamesmkrieger almost 4 years ago - 1 comment

#1186 - add mmCIF writer and maybe others

Issue - State: closed - Opened by jamesmkrieger almost 4 years ago - 4 comments
Labels: Feature request

#1123 - Add interoperability with PDB REST API and chemical databases such as PubChem

Issue - State: closed - Opened by jamesmkrieger about 4 years ago - 7 comments
Labels: Feature request

#1116 - Need to reconcile clustering functionalities

Issue - State: closed - Opened by jamesmkrieger about 4 years ago - 1 comment
Labels: Enhancement

#1085 - added function printAtomicMatrix

Pull Request - State: open - Opened by jamesmkrieger over 4 years ago - 5 comments

#1073 - added markersizes to showProjection

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

#1070 - bug fix on color handling for showProjection

Pull Request - State: open - Opened by jamesmkrieger over 4 years ago

#1055 - Integrate NMA calculations using GPU

Issue - State: closed - Opened by jamesmkrieger over 4 years ago
Labels: Feature request

#979 - Create CODE_OF_CONDUCT.md

Pull Request - State: closed - Opened by SHZ66 over 4 years ago

#970 - Wrapper for DruGUI/VMD

Issue - State: closed - Opened by jamesmkrieger almost 5 years ago
Labels: Enhancement

#926 - Secondary structure monitoring in simulations

Issue - State: closed - Opened by jamesmkrieger almost 5 years ago - 2 comments
Labels: Feature request

#921 - Direct coupling analysis error

Issue - State: closed - Opened by lewisr34 about 5 years ago - 5 comments

#884 - Directions in NMWiz don't match directions from ProDy plots and overlaps

Issue - State: closed - Opened by jamesmkrieger over 5 years ago - 1 comment
Labels: Feature request

#827 - Revert "Revert "added calcSquareInnerProduct""

Pull Request - State: closed - Opened by jamesmkrieger over 5 years ago

#826 - Revert "added calcSquareInnerProduct"

Pull Request - State: closed - Opened by jamesmkrieger over 5 years ago

#703 - Add showAtomicBar

Issue - State: closed - Opened by jamesmkrieger over 6 years ago
Labels: Feature request

#687 - Revert "pfam fixes for missing xml"

Pull Request - State: closed - Opened by jamesmkrieger over 6 years ago

#491 - Where can I access oanm and ognm text files?

Issue - State: closed - Opened by mayeshh over 6 years ago - 5 comments

#448 - Revert "fixed a bug in parseCIF function"

Pull Request - State: closed - Opened by cihankayacihan almost 7 years ago

#426 - Revert "Revert "Several fixes""

Pull Request - State: closed - Opened by SHZ66 about 7 years ago

#425 - Revert "Several fixes"

Pull Request - State: closed - Opened by SHZ66 about 7 years ago

#334 - Projection plot

Issue - State: closed - Opened by natesh25 almost 8 years ago - 2 comments
Labels: Enhancement, NMWiz

#325 - Mass weighted covariance analysis

Issue - State: closed - Opened by Sanjoy-Paul about 8 years ago - 1 comment
Labels: Enhancement

#243 - support for CONECT in parsePDB and writePDB

Issue - State: closed - Opened by grinner about 9 years ago - 3 comments
Labels: Feature request

#243 - support for CONECT in parsePDB and writePDB

Issue - State: open - Opened by grinner about 9 years ago - 3 comments
Labels: Feature request

#202 - ParseDCD: Unrecognized DCD format

Issue - State: closed - Opened by jeeberhardt over 10 years ago - 6 comments

#186 - NMA with EM-data using pseudoatoms

Issue - State: closed - Opened by DavidHaselbach over 10 years ago - 11 comments
Labels: Feature request

#172 - Hierarchical coarse graining

Issue - State: closed - Opened by abakan-zz almost 11 years ago - 2 comments
Labels: Feature request

#171 - New Evol subcommands

Issue - State: closed - Opened by abakan-zz almost 11 years ago - 1 comment
Labels: Feature request

#159 - Omit gaps in MI calculations

Issue - State: closed - Opened by abakan-zz about 11 years ago
Labels: Feature request

#158 - Transformations with a descriptor

Issue - State: closed - Opened by abakan-zz about 11 years ago - 3 comments
Labels: Enhancement

#96 - Bond orders

Issue - State: closed - Opened by abakan-zz over 12 years ago - 2 comments
Labels: Feature request

#18 - Units

Issue - State: closed - Opened by abakan-zz over 13 years ago - 1 comment
Labels: Feature request