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markovmodel
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PyEMMA
🚂 Python API for Emma's Markov Model Algorithms 🚂
http://pyemma.org
GNU Lesser General Public License v3.0
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Use spawn() for multiprocessing instead of fork()
#1565
sents
closed
2 years ago
4
Problems with loading more than two trajectories
#1564
orthonalmatrix
closed
2 years ago
2
Expose minRMSD metric directly
#1563
clonker
opened
2 years ago
2
Make data sources compatible to deeptime
#1562
clonker
opened
2 years ago
2
Migrate network plots to deeptime
#1561
clonker
closed
2 years ago
0
Examples how to migrate code from current PyEMMA API to deeptime
#1560
clonker
opened
2 years ago
1
Integrate dTRAM into deeptime
#1559
clonker
opened
2 years ago
2
Issue deprecation warnings
#1558
clonker
opened
2 years ago
2
Deprecations for coordinates api
#1557
clonker
closed
2 years ago
1
remove pybind submodule
#1556
clonker
closed
2 years ago
1
Remove msmtools
#1555
clonker
closed
2 years ago
1
unable to execute
#1554
debanjansen48
closed
1 year ago
2
Progress stuck after ITS estimation
#1553
satyajitkhatua09
closed
2 years ago
3
using radius of gyrationn in the custom featurizer
#1552
instaM
closed
2 years ago
4
minflux in plot_markov_model seems to be malfunctioning
#1551
orthonalmatrix
closed
2 years ago
4
Remove bhmm as dependency
#1550
clonker
closed
2 years ago
2
CK test doesn't justify HMM
#1549
Bazzinga18
closed
2 years ago
1
Changing the units of the rate in plot_markov_model
#1548
orthonalmatrix
closed
2 years ago
2
Python 3.10 release?
#1547
sroet
closed
1 year ago
4
Usage of pathlib in coordinates package
#1546
clonker
opened
2 years ago
1
Improved topology LRU cache
#1545
clonker
closed
2 years ago
1
Extracting PDB structures from TICA plot or PCA plot in PyEMMA 2.5.7
#1544
satyabrata400
closed
1 year ago
2
torsion feature for specific range
#1543
Bazzinga18
closed
2 years ago
2
Is transition time(mfpt) from one state to another may be different from time observed in MD simulations?
#1542
Bazzinga18
closed
1 year ago
4
Issue loading trajectory with pyemma.coordinates.source when topology file changes
#1541
AnjaConev
closed
2 years ago
6
update deeptime clustering include
#1540
clonker
closed
2 years ago
2
generate a synthetic trajectory from markov model
#1539
jeromeRlon
closed
2 years ago
2
XTC seek error: 13 when reading otherwise fine .xtc using coordinates.save_trajs
#1538
germanbarcenas
closed
2 years ago
26
To generate pdbs of each clusters at a particular timescale
#1537
Bazzinga18
closed
1 year ago
4
Metastable state distribution
#1536
rubinanoor9
closed
2 years ago
4
Error while calculating VAMP2 score at different lag times
#1535
Bazzinga18
closed
2 years ago
11
Assigning two features at a time
#1534
Bazzinga18
closed
2 years ago
6
Adaptive Sampling and Structure Extraction from TICA or PCA Plot
#1533
hl2500
closed
2 years ago
3
mfpt uncertainty
#1532
ccccclw
closed
2 years ago
2
use mambabuild in CI and fix rmsd computation in clustering
#1531
clonker
closed
2 years ago
1
solve some syntax warnings
#1530
sroet
closed
2 years ago
3
When to use periodic=False
#1529
Seral17
closed
2 years ago
3
Could not allocate enough memory to map all data
#1528
rubinanoor9
closed
2 years ago
3
How to deal with many short trajectories
#1527
KrishnenduSinha12
closed
1 year ago
4
Only pass copy of trajectory list to mdtraj.load and (CI) update macos image
#1526
clonker
closed
2 years ago
2
PyEMMA and GROMACS generate a bit different projection results
#1525
qasimpars
closed
2 years ago
1
Installation on M1 Mac
#1524
hl2500
closed
2 years ago
14
_bar_df wrong for loop boundary
#1523
MaaikeG
opened
2 years ago
3
Fix periodic width initialization in umbrella sampling
#1522
sefalkner
closed
2 years ago
1
IndexError: Index out of bound
#1521
rubinanoor9
closed
2 years ago
7
Tips on combining features across systems
#1520
cgseitz
closed
1 year ago
6
Loading Objects breaks '_default_chunksize' Attribute for 'get_output' Method
#1519
tim0marshall
closed
2 years ago
5
Is TRAM appropriate in this setting?
#1518
onehalfatsquared
closed
2 years ago
5
varify Markov model built by Umbrella sampling with PyEMMA
#1517
wyb2021
closed
2 years ago
1
Fresh conda install broken (at least for kmeans clustering) due to deeptime ImportError
#1516
rafwiewiora-silicon
closed
2 years ago
1
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