markovmodel PyEMMA issues

markovmodel / PyEMMA

🚂 Python API for Emma's Markov Model Algorithms 🚂

http://pyemma.org

GNU Lesser General Public License v3.0

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issues

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pyemma.coordinates.source unable to accept a list with length more than 2

#1465 lucl13 closed 4 years ago
3
In an irreproducible conda environment, tICA outputs all zeros

#1464 rafwiewiora closed 4 years ago
3
No possibility to understand what are the clusters considered for HMM

#1463 pl992 closed 4 years ago
2
Eigenvalues

#1462 toth12 closed 4 years ago
3
Extracting representative structures from the metastable states

#1461 eric-jm-lang closed 4 years ago
2
Why is the free energy landscape re-weighted using the stationary probabilities from the MSM?

#1460 eric-jm-lang closed 4 years ago
2
TRAM estimation without unbiased data

#1459 heureka185 closed 3 years ago
1
Transition Matrix Singular

#1458 toth12 closed 4 years ago
4
[coordinates] fix bug in SideChainTorsions.describe

#1457 thempel closed 4 years ago
1
Installing PyEMMA with OpenBLAS on AMD

#1456 cabergh closed 4 years ago
3
PCCA for non-reversible Markov Chains

#1455 Marius1311 closed 4 years ago
1
Bug pcca and cktest for msm built using statdist option

#1454 pl992 closed 4 years ago
4
add python 3.8 to the build matrices

#1453 clonker closed 4 years ago
1
How to calculate the statistical error of the equilibrium distribution obtained from the MSM?

#1452 lucl13 closed 4 years ago
2
Bug in sidechain torsion naming in featurizer

#1451 mandar5335 closed 4 years ago
1
[plots] plot cktest now can handle multiple cktests

#1450 cristinamelnic closed 4 years ago
4
Fixes #1443

#1449 fabian-paul closed 4 years ago
6
fixes issue #1443

#1448 fabian-paul closed 4 years ago
0
Can this be used? Please help??

#1447 ghost closed 4 years ago
6
setup.py needs --remote option in git submodule update?

#1446 fabian-paul closed 4 years ago
2
[msm] remove dead code

#1445 thempel closed 4 years ago
1
dTRAM and WHAM with more than one bias

#1444 rekbet closed 4 years ago
6
mfpt questions

#1443 Sizhang92190 closed 4 years ago
16
Modifying `add_minrmsd_to_ref` to return the RMSD value corresponding for the frame of the reference trajectory that gave the lowest RMSD

#1442 eric-jm-lang closed 4 years ago
3
contact counting for GroupMinDIstancesFeature, ResidueMinDistanceFeature

#1441 thempel closed 5 years ago
1
[util] improve performance of type check

#1440 clonker closed 5 years ago
4
MSM estimation 10x slower when dtraj is a list vs array

#1439 rafwiewiora closed 5 years ago
1
tqdm breaks jupyter notebook

#1438 Ginok1 closed 5 years ago
2
Custom feature for global angle (dihedral) caluclation using Center of mass atoms.

#1437 srp106 closed 5 years ago
1
version : Pyemma 2.5.7 TypeError: expected str, bytes or os.PathLike object, not list

#1436 srp106 closed 5 years ago
2
Pyemma : TICA analysis AttributeError: 'function' object has no attribute 'children'

#1435 srp106 closed 5 years ago
2
[progress-reporter] removed custom styling for notebook progress bars

#1434 marscher closed 5 years ago
1
progress bars in notebooks do not work with tqdm>=4.36.1

#1433 marscher closed 5 years ago
0
Problem with PCCA+

#1432 tanmoyp635 closed 5 years ago
1
SampledModel set_model_params overrides dt_model and conf parameters

#1431 thempel opened 5 years ago
6
issue plotting metastable states

#1430 wemd closed 5 years ago
9
some quick questions in dtram estimation

#1429 yunhuige closed 4 years ago
5
Error during featurizer step of tutorial notebook 00

#1428 mandar5335 closed 5 years ago
7
issue loading dcd file with pyemma.coordinates.load

#1427 wemd closed 5 years ago
2
Solving of eigenvalue problems yield bogus results with OpenBLAS-0.3.5 on SkyLake X CPUs

#1426 thempel closed 5 years ago
3
Separating bound from unbound Microstates

#1425 and-tos closed 5 years ago
1
msm.its UnicodeDecodeError

#1424 and-tos closed 5 years ago
8
different dimension between msm.pi and eigvec

#1423 arboryang closed 5 years ago
0
Trajectories with different box sizes

#1422 and-tos closed 5 years ago
4
similar looking TICs

#1421 and-tos closed 5 years ago
1
[doc] build notebooks with nbsphinx. [ci skip]

#1420 marscher closed 5 years ago
1
conda installation with strict-channel-priority and Py 3.5 fails

#1419 dwhswenson closed 5 years ago
2
fix numpy array hashing, added impl for scipy.sparse, added test

#1418 marscher closed 5 years ago
2
global setting for parallelisation

#1417 ppxasjsm closed 5 years ago
3
CK test Error

#1416 sundelinllnl closed 5 years ago
5

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