Ecosyste.ms: Issues

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GitHub / drorlab/pensa issues and pull requests

#71 - Update to MDAnalysis 2.8 and Python 3.10

Pull Request - State: closed - Opened by martinvoegele 17 days ago

#70 - Update to Python 3.12 and MDAnalysis 2.8

Issue - State: closed - Opened by martinvoegele 18 days ago - 1 comment

#68 - XTC file not recognized with extract_coordinates

Issue - State: closed - Opened by piia600 19 days ago - 3 comments
Labels: enhancement

#67 - Tutorial issue

Issue - State: closed - Opened by piia600 27 days ago - 2 comments

#66 - Updated and tested all .rst tutorial files.

Pull Request - State: closed - Opened by martinvoegele 2 months ago

#64 - Tutorial updates

Pull Request - State: closed - Opened by martinvoegele 2 months ago

#63 - Added instruction to run bash scripts in readme for tutorial.

Pull Request - State: closed - Opened by LMorlok 6 months ago - 1 comment

#62 - Update installation instruction for tutorial

Issue - State: closed - Opened by LMorlok 6 months ago - 1 comment

#61 - define pandas version as 1.4

Pull Request - State: closed - Opened by martinvoegele 6 months ago

#59 - Update README.md

Pull Request - State: closed - Opened by sangttruong 6 months ago

#58 - Update README.md

Pull Request - State: closed - Opened by sangttruong 6 months ago

#57 - Use the MDAnalysis hydrogen bond module to calculate the bonds

Issue - State: closed - Opened by martinvoegele about 1 year ago
Labels: enhancement

#56 - Update about.rst

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

#54 - adapt eigenvector index in dot product

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

#52 - upgrade python 3.7 to 3.8

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

#51 - [TICA]: Change implementation to deeptime library

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

#50 - 44 adding hydrogen bonds

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

#49 - ValueError: could not convert string to float: 'timeseries'

Issue - State: closed - Opened by chyannn06 almost 2 years ago - 2 comments

#48 - Reimplementation of TICA

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

#47 - fix colab link

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

#46 - link to google colab is broken

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

#44 - Adding hydrogen bond features

Issue - State: closed - Opened by NeilJ-Thomson almost 2 years ago

#43 - Update contribute.rst

Pull Request - State: closed - Opened by eltociear about 2 years ago

#42 - Sidechain torsions and Backbone C-Alpha Distances Error

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

#41 - add an option to visualize avg values per residue

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

#40 - Option to visualize average values per residue

Issue - State: closed - Opened by martinvoegele over 2 years ago
Labels: enhancement

#39 - 37 add feature reader for nucleic acid torsions

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

#38 - 37 add feature reader for nucleic acid torsions

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

#37 - Add feature reader for nucleic acid torsions

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

#36 - 32 state specific information updates

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

#35 - 32 state specific information updates

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

#34 - group distances + variable naming scheme

Pull Request - State: closed - Opened by martinvoegele almost 3 years ago

#33 - 30 uncertainty analysis

Pull Request - State: closed - Opened by NeilJ-Thomson almost 3 years ago

#32 - State-Specific Information Updates

Issue - State: closed - Opened by NeilJ-Thomson about 3 years ago - 1 comment

#31 - PyMOL script to visualize metrics

Issue - State: open - Opened by martinvoegele about 3 years ago
Labels: enhancement

#30 - Adding Uncertainty Analyses

Issue - State: closed - Opened by NeilJ-Thomson over 3 years ago - 1 comment
Labels: enhancement

#29 - Add chain identifier to distance name.

Issue - State: closed - Opened by martinvoegele over 3 years ago - 1 comment

#28 - Pull v0.2.5 to branch 20

Pull Request - State: closed - Opened by martinvoegele over 3 years ago

#27 - v0.2.5

Pull Request - State: closed - Opened by martinvoegele over 3 years ago

#26 - Closes #24 general sorting function

Pull Request - State: closed - Opened by martinvoegele over 3 years ago

#25 - Closes #15 add overall metrics

Pull Request - State: closed - Opened by martinvoegele over 3 years ago

#24 - General function to sort a trajectory

Issue - State: closed - Opened by martinvoegele over 3 years ago

#23 - v0.2.4

Pull Request - State: closed - Opened by martinvoegele over 3 years ago

#22 - change default last frame to None

Pull Request - State: closed - Opened by martinvoegele over 3 years ago

#21 - MDA distance readers have unintuitive default last frame

Issue - State: closed - Opened by martinvoegele over 3 years ago

#20 - Combine DiffNets with existing functionality

Issue - State: closed - Opened by martinvoegele over 3 years ago - 2 comments
Labels: enhancement

#19 - Separate branch for DiffNets integration

Pull Request - State: closed - Opened by martinvoegele over 3 years ago

#18 - Integrate diffnets

Pull Request - State: closed - Opened by sangttruong over 3 years ago

#17 - 17 integrate diffnets

Pull Request - State: closed - Opened by Mickdub over 3 years ago

#16 - DiffNets Integration

Issue - State: closed - Opened by martinvoegele over 3 years ago - 2 comments

#15 - Metrics for overall ensemble comparison

Issue - State: closed - Opened by martinvoegele over 3 years ago - 1 comment

#14 - Contributing guide needed

Issue - State: closed - Opened by sangttruong over 3 years ago

#13 - Added align_coordinates function to preprocessing script.

Pull Request - State: closed - Opened by jmcavity over 3 years ago

#12 - Improvements for SSI functions

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

#11 - Update TODO.md

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

#10 - Update tica

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

#9 - Update TODO.md

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

#8 - fixing file paths in tutorial for dens/

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

#7 - Density preprocessing

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

#6 - SSI updates

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

#5 - Initial merge of SSI into PENSA base master

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

#4 - unit test

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

#3 - unit test

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

#2 - animation+tica

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

#1 - listing on "MDAnalysis: used by page"?

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