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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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plot_contour colorbar tick labels don't adjust to changes to vmax and vmin
#1615
marcushock
opened
10 months ago
0
What is the difference between a working directory and a path?
#1614
Wencesgiovanni
opened
10 months ago
2
estimating Bayesian MSM very slow
#1613
H-EKE
opened
11 months ago
4
Update install_miniconda+pyemma.sh
#1612
songyongshun
closed
10 months ago
0
What should i do when my fraction of sets and counts are less than 1?
#1611
hima111997
opened
1 year ago
0
error in notebook 07
#1610
hima111997
opened
1 year ago
0
how to use pyemma.plots.plot_cktest with 21 X 21 plot?
#1609
hima111997
opened
1 year ago
0
Is it possible to use pyemma.msm.its on the dtrajs after using TICA on the features?
#1608
hima111997
opened
1 year ago
0
add_sidechain_torsions produces an error
#1607
hima111997
opened
1 year ago
0
pyemma.plots.scatter_contour produce an error
#1606
hima111997
opened
1 year ago
0
How to get information from macrostates after constructing MSM in pyemma
#1605
dulalmondal123
opened
1 year ago
0
Bayesian Hidden Markov model got an unexpected keyword argument 'desc'
#1604
ShenWenHuibit
opened
1 year ago
1
Identifying the minimum free energy conformation based on binding energy values between two proteins
#1603
Chakrabort123
opened
1 year ago
0
How to extract the pdb for a minimum free energy state from the free energy plot as a function of IC1 and IC2?
#1602
Chakrabort123
opened
1 year ago
0
Are Unbiased Trajectories Required for dTRAM PMF profile estimations
#1601
Cal-JWRW
opened
1 year ago
0
Detecting the disconnectivity between states and how to deal with it
#1600
raylab-projects
opened
1 year ago
0
How to extract the structures not belonging to the free energy minimum
#1599
satyajitkhatua09
opened
1 year ago
1
RuntimeError: XTC read error: Compressed 3d coordinate
#1598
Harshitasahni
opened
1 year ago
0
its showing runtime error
#1597
Gourav-Chakraborty
opened
1 year ago
1
Replace usage of np.float with float
#1596
comecattin
closed
10 months ago
0
Missing dimensions when performing get_output() method
#1595
meh47336
opened
1 year ago
1
Few basic questions regarding building MSM using pyemma.
#1594
udnenhsirK
opened
1 year ago
1
Reminder for _progress_register error in mini batch kmenas
#1593
SianXiaoCHN
opened
1 year ago
0
Substitute uses of numpy.bool with numpy.bool_
#1592
evilsetg
closed
1 year ago
1
NotImplementedError: MSM estimation with connectivity='none' is currently not implemented.
#1591
Harshitasahni
closed
1 year ago
3
Implied timescales calculation hangs with multiprocessing
#1590
yuxuanzhuang
opened
1 year ago
0
Minor issue with newest numpy version
#1589
pitmanme
opened
1 year ago
5
IndexError: index 188 is out of bounds for axis 0 with size 184
#1588
vas2201
opened
1 year ago
3
numpy.bool removed from numpy --> AttributeError
#1587
mmfarrugia
opened
1 year ago
4
how to import solvent accessible surface area as a feature in pyemma?
#1586
satyajitkhatua09
closed
1 year ago
5
Got ValueError associated with dimensionality when using a tica object
#1585
ryankzhu
closed
1 year ago
4
OSError: "Unable to open file (file signature not found)" h5py/_objects.pyx:55 related error
#1584
suniliisc
opened
1 year ago
1
TICA on backbone atoms
#1583
qasimpars
opened
1 year ago
4
implied timescales with hmsm
#1582
drdoppio
opened
1 year ago
4
Eigenvalues associated with the eigenvectors of TICA
#1581
qasimpars
opened
1 year ago
5
how adjusting simulation timestep affects lag times
#1580
cgseitz
closed
1 year ago
7
Added an optional argument for specifying the tolerance in the class MSM
#1579
wehs7661
closed
1 year ago
2
Possibility of specifying the tolerance for the MSM class
#1578
wehs7661
closed
1 year ago
5
ignore
#1577
cgseitz
closed
1 year ago
0
No return when using pyemma.msm.its
#1576
yingioi0
closed
1 year ago
3
Unable to import pyemma after installation using jupyter notebook
#1575
debanjansen48
opened
1 year ago
26
Fix tests, use deeptime double well discrete data.
#1574
clonker
closed
1 year ago
2
Change ipywidgets version check to use __version__. Fixes #1571.
#1573
clonker
closed
1 year ago
4
PyEMMA on MAC M1 - installation not working
#1572
toth12
closed
1 year ago
3
ipywidgets.version_info is deprecated since version a6 causing progress.reporter__init__.py to fail
#1571
apayne97
closed
1 year ago
1
How to extract structure from near the center of the clusters?
#1570
buruiyu
closed
1 year ago
1
Basis of the active state fraction and active count fraction
#1569
Bazzinga18
closed
1 year ago
2
Different transition time in compare to experimental results.
#1568
Bazzinga18
closed
1 year ago
1
pyemma.util no attribute 'context'
#1567
pojeda
opened
2 years ago
4
Secondary structure in PyEMMA
#1566
rubinanoor9
closed
2 years ago
5
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