bowman-lab enspara issues

bowman-lab / enspara

Modeling molecular ensembles with scalable data structures and parallel computing

https://enspara.readthedocs.io

GNU General Public License v3.0

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issues

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Fixed rng in test that was failing randomly (due to rng seed?)

#239 Justin-J-Miller opened 2 months ago
0
Updated README and env.yaml to include mpi4py

#238 Justin-J-Miller closed 3 weeks ago
0
Mpi4py in documentation

#237 upasana-m closed 3 weeks ago
0
Fix for CARDS angle=360 issue.

#236 lgsmith closed 2 months ago
7
Subsample features

#235 Justin-J-Miller closed 2 months ago
1
Add tolerance exit for Kmedoids

#234 Justin-J-Miller opened 3 months ago
0
Add intermediate write out for kcenters during clustering?

#233 Justin-J-Miller opened 3 months ago
0
Allow for subsampling of featured trajectories

#232 Justin-J-Miller opened 3 months ago
2
Add app script to compute per-residue Shannon entropy

#231 sukritsingh closed 3 months ago
5
Update rtd2

#230 Justin-J-Miller closed 4 months ago
0
Possibly fixing Readthedocs?

#229 Justin-J-Miller closed 4 months ago
0
Cleaned up RNG calls in kmedoids function.

#228 Justin-J-Miller closed 4 months ago
0
Add intermediate saves

#227 Justin-J-Miller closed 5 months ago
0
Add intermediate saves

#226 Justin-J-Miller closed 5 months ago
0
Update docs, update auto tests

#225 Justin-J-Miller closed 4 months ago
2
Nose2py

#224 Justin-J-Miller closed 5 months ago
4
nose -> pytests?

#223 Justin-J-Miller closed 5 months ago
4
condense_sidechain_sasas assert -> exception

#222 justinrporter closed 11 months ago
0
SASA-Exposon calculation problem

#221 H-EKE closed 11 months ago
2
pockets.py returning None for no-pockets breaks FAST-pockets

#220 Justin-J-Miller closed 1 year ago
2
Warning when creating ragged arrays

#219 Justin-J-Miller closed 5 months ago
1
Fixed obsolteted import of 'Iterable' from collections.

#218 lgsmith closed 1 year ago
1
Enspara problems with Ragged Array flattening

#217 matthew-cruz closed 1 year ago
3
Issue with ra.py module

#216 BJWiley233 closed 1 year ago
4
Fix tests jan 2022

#215 justinrporter closed 5 months ago
11
Getting enspara installable on ARM machines

#214 sukritsingh closed 5 months ago
13
Fret from expt

#213 Justin-J-Miller closed 5 months ago
3
Fret from expt

#212 Justin-J-Miller closed 2 years ago
0
Updated synthetic_traj to use rng.choice; this doubles its speed.

#211 lgsmith closed 2 years ago
4
Fixed module prefixing within test_paths().

#210 lgsmith closed 5 months ago
1
Fix time clock

#209 lgsmith closed 3 years ago
1
Paths msmbuilder tpt

#208 lgsmith closed 3 years ago
7
Change np.hstack to np.concatenate

#207 EllaNguyen1711 opened 3 years ago
8
AttributeError: 'numpy.ndarray' object has no attribute 'toarray'

#206 sbhakat closed 3 years ago
4
Saving cluster centers with 'trj_filename'

#205 sbhakat closed 6 months ago
3
enspara not executing correctly

#204 MMLawal opened 3 years ago
8
Setup.py and documentation question

#203 matthew-cruz closed 3 years ago
3
Time update

#202 mizimmer90 closed 3 years ago
1
Resolve file not found error when center features path isn't absolute

#201 roblaine closed 1 year ago
3
Distance measurement as feature input

#200 PeptideSimulator01 opened 4 years ago
0
Pooled clustering followed by reassignment

#199 PeptideSimulator01 closed 5 months ago
1
No topology if different trajectories loaded

#198 PeptideSimulator01 closed 4 years ago
1
Kmedoids warm restart implementation

#197 Mickdub closed 4 months ago
2
Add extra info about clustering output to tutorial

#196 justinrporter closed 4 years ago
0
cluster.py fails if paths have no directory spec

#195 justinrporter opened 4 years ago
3
Number of frames distributed to centroids

#194 PeptideSimulator01 closed 4 years ago
1
Update pocket-detection.rst

#193 alexholehouse closed 4 years ago
1
updated pockets parallelization and default values

#192 mizimmer90 closed 4 years ago
0
Exposon init preference

#191 justinrporter closed 4 years ago
0
Deploy package to anaconda and pypi

#190 Longbowman closed 4 years ago
9