Ecosyste.ms: Issues

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GitHub / POVME/POVME3 issues and pull requests

#49 - How to choose the center of inclusion sphere?

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

#48 - Many common questions have been answered in "closed" issues!

Issue - State: open - Opened by j-wags over 2 years ago

#47 - povme installation error

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

#45 - Question about error in 'Clustering and PCA example'

Issue - State: closed - Opened by computational-chemist about 3 years ago - 1 comment

#44 - Error in analysis workflow example

Issue - State: closed - Opened by computational-chemist about 3 years ago - 1 comment

#43 - Error on using POVME3

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

#42 - A "cone-like" error occurred during the calculation

Issue - State: closed - Opened by Alzheimer98 about 3 years ago - 2 comments

#40 - ValueError in one out of three simulation trial

Issue - State: closed - Opened by hengi110 almost 4 years ago - 3 comments

#39 - bump version for setup_miniconda action

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

#38 - Refactor testing to use GitHub Actions, add tests for python 3.6 and 3.8

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

#37 - Does POVME work for RNA?

Issue - State: closed - Opened by j-wags over 4 years ago

#35 - Make compatible with Python 3

Pull Request - State: open - Opened by j-wags about 5 years ago - 3 comments

#34 - Update to Python 3

Pull Request - State: closed - Opened by Seanny123 about 5 years ago - 2 comments

#33 - Update POVME3 to Python3

Issue - State: open - Opened by Seanny123 about 5 years ago - 6 comments
Labels: enhancement, help wanted

#32 - Get volume and poc

Issue - State: closed - Opened by pgbarletta over 5 years ago - 1 comment

#31 - Fix #30, update README

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

#30 - README.md basic example visualization issue

Issue - State: closed - Opened by Petr-A over 5 years ago - 2 comments

#29 - POVME_pocket_id.py error ( index 0 is out of bounds for axis 0 with size 0)

Issue - State: closed - Opened by MBenabderrahmane almost 7 years ago - 2 comments

#28 - generic temporary work folder causing overwriting issues

Issue - State: open - Opened by rhs2132 over 7 years ago - 1 comment
Labels: enhancement, help wanted

#27 - Circleci fixing and pocketPointsPCA addition to analysis_workflow_example

Pull Request - State: closed - Opened by j-wags over 7 years ago - 1 comment

#26 - Povme3 refactor

Pull Request - State: closed - Opened by inevibitable over 7 years ago

#25 - Make clustering include outputs like g_cluster

Issue - State: open - Opened by j-wags about 8 years ago
Labels: enhancement, help wanted

#24 - analyzeClusterMembershipInGroups had segfault

Issue - State: closed - Opened by j-wags about 8 years ago - 3 comments

#23 - Change analyzeclustermembershipingroups to show frames starting at 1 instead of 0

Issue - State: open - Opened by j-wags about 8 years ago
Labels: enhancement, help wanted

#22 - Change inclusion cylinder to be defined as (base1x, b1y, b1z, b2x, b2y, b2z, radius)

Issue - State: open - Opened by j-wags about 8 years ago
Labels: enhancement, help wanted

#21 - Make workflow work with ~10 frames from trajectory to show example before running for real

Issue - State: open - Opened by j-wags over 8 years ago
Labels: enhancement, help wanted

#20 - Take care of numpy warning once and for all

Issue - State: open - Opened by j-wags over 8 years ago
Labels: enhancement, help wanted

#19 - Feature color normalization causes intensities to stack up at the edge of the box

Issue - State: open - Opened by j-wags over 8 years ago
Labels: enhancement, help wanted

#18 - Surface area varies a lot when I change grid resolution, even though volume stays about the same

Issue - State: open - Opened by j-wags over 8 years ago
Labels: enhancement, help wanted

#17 - Add option to binding_site_overlap to output raw score matrix

Issue - State: open - Opened by j-wags over 8 years ago
Labels: enhancement, help wanted

#16 - When loading an inclusion/seed region ensure that new points are snapped to a grid of appropriate resolution

Issue - State: open - Opened by j-wags over 8 years ago
Labels: enhancement, help wanted

#15 - Make POVME work with DNA pockets

Issue - State: open - Opened by j-wags over 8 years ago
Labels: enhancement, help wanted

#14 - Check for appropriate protonation so coloring doesn't break/we can do charge

Issue - State: open - Opened by j-wags over 8 years ago
Labels: enhancement, help wanted

#13 - Does POVME handle crystal waters?

Issue - State: closed - Opened by j-wags over 8 years ago
Labels: question

#12 - Ensure that frame extraction in cluster.py doesn't have an off-by-1 error

Issue - State: closed - Opened by j-wags over 8 years ago - 1 comment

#11 - Fix inclusion cylinder and cube, and VMD plugin as it relates to them

Issue - State: open - Opened by j-wags over 8 years ago
Labels: enhancement, help wanted

#10 - Merge in j-wags/POVME

Issue - State: closed - Opened by j-wags over 8 years ago

#9 - Finish POVME tutorial

Issue - State: closed - Opened by j-wags over 8 years ago

#8 - Make all subpackage integration tests be run in tests.sh

Issue - State: open - Opened by j-wags over 8 years ago
Labels: enhancement, help wanted

#7 - Make .vmdrc file creator

Issue - State: open - Opened by j-wags over 8 years ago
Labels: enhancement, help wanted

#6 - Convert as many tests as possible to unittest framework

Issue - State: open - Opened by j-wags over 8 years ago
Labels: help wanted

#5 - Replace pymolecule with something more standard (maybe mdtraj?)

Issue - State: open - Opened by j-wags over 8 years ago
Labels: enhancement, help wanted

#4 - Include a good pocket finder in dependencies (maybe fpocket?)

Issue - State: open - Opened by j-wags over 8 years ago
Labels: enhancement, help wanted

#3 - Update sample_POVME_input_each.ini

Pull Request - State: closed - Opened by j-wags over 8 years ago

#2 - Update setup.py

Pull Request - State: closed - Opened by j-wags over 8 years ago

#1 - Update README.md

Pull Request - State: closed - Opened by j-wags over 8 years ago - 1 comment