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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I have the biased and unbiased data. How can I calculate ttrajs, dtraj and bias for thermo.tram?

#1415 Moutoshi closed 5 years ago
1
[coordinates] do not allow pdb trajectories

#1414 marscher closed 5 years ago
1
Loading a PDB trajectory fails

#1413 rafwiewiora closed 5 years ago
2
[setup] pep517 compatible, doc fixes, minor bug fixes

#1412 marscher closed 5 years ago
2
Error upgrading to v2.5.5

#1411 moldyn-nagel closed 5 years ago
9
[fragmented_traj_reader] check indices are in bound with trajectory lengths prior iterating

#1410 marscher closed 4 years ago
2
Loglikelihood of observation under an HMM model

#1409 bamal closed 5 years ago
1
[logging] use a loader in yaml version >= 5.1 to fix deprecation warning

#1408 marscher closed 5 years ago
0
YAMLLoadWarning

#1407 euhruska closed 5 years ago
1
cktest bug?

#1406 euhruska closed 5 years ago
3
Not able to get the benzamidine-trypsin trajectory-link https://codeload.github.com/markovmodel/PyEMMA_IPython/zip/devel not working. Kindly provide the trajectory dataset

#1405 anuginu closed 5 years ago
1
"k" and "stride" in pyemma.coordinates.cluster_kmeans

#1404 lunnali closed 5 years ago
1
TICA and MSM Lag time Enquiry

#1403 lunnali closed 5 years ago
2
Compiling PyEMMA in powerPC

#1402 cescgina closed 5 years ago
6
Improper LaTeX rendering in tutorial notebooks

#1401 p16i opened 5 years ago
1
[doc] updated install instructions

#1400 marscher closed 5 years ago
0
Outdated installation document using miniconda

#1399 p16i closed 5 years ago
5
pyemma ignores histidine protonation state

#1398 compchemeric closed 5 years ago
1
Vamp fix varcut cutoff

#1397 marscher closed 5 years ago
0
Topology cache via python3 LRU functionality

#1396 marscher closed 5 years ago
0
Python3 only

#1395 marscher closed 5 years ago
1
Make left singular functions the default in VAMP

#1394 fabian-paul closed 5 years ago
2
Serialization docs

#1393 marscher closed 5 years ago
4
PyEMMA load and save objects

#1392 franknoe closed 5 years ago
1
[coordinates/patches] removed code branch for unreleased mdtraj

#1391 marscher closed 5 years ago
1
[msm] split up seperate MSM estimators into individual files

#1390 marscher closed 5 years ago
1
Consider using Scikit-CI to lower maintainence burden

#1389 marscher closed 5 years ago
1
added random seed option for double well

#1388 brookehus closed 5 years ago
5
[serialization] fixes

#1387 marscher closed 5 years ago
1
[doc] use sphinx-issues to link to github

#1386 marscher closed 5 years ago
2
minor bugfix "import warning" -> "import warnings"

#1385 fabian-paul closed 5 years ago
3
[config] forcefully enable coordinates_check_output

#1384 marscher closed 5 years ago
2
estimation failed due to alpha <= 0

#1383 jiajiexiao closed 5 years ago
5
Fix len for ascii trajs

#1382 marscher closed 5 years ago
1
[eig_qr] allocate memory directly in fortran-order

#1381 marscher closed 5 years ago
2
fix docstring format

#1380 sunhwan closed 5 years ago
1
Thermo merge

#1379 marscher closed 5 years ago
0
[coordinates/source] do not probe h5 file for mdtraj.HDF5TrajectoryFile

#1378 marscher closed 6 years ago
2
[msm/its] added 'only_timescales' option

#1377 marscher closed 6 years ago
2
[plots] fixed vmin, vmax kwarg pass to subsequent function call

#1376 thempel closed 6 years ago
1
Dtraj stats allow parallel no pg

#1375 marscher closed 6 years ago
1
HMSM: number of hidden states

#1374 and-tos closed 6 years ago
7
Implied timescales from dTRAM/TRAM object

#1373 yunhuige closed 6 years ago
4
No pkg resources outside tests, fix indexing in fragmented traj reader

#1372 marscher closed 6 years ago
0
[fragmented reader] future warning

#1371 marscher closed 6 years ago
0
K-means mini batch clustering very slow

#1370 and-tos closed 6 years ago
4
Python 3.7 support

#1369 j3mdamas closed 6 years ago
3
time step unit in TICA, timescales_msm

#1368 and-tos closed 6 years ago
2
relative entropy between two MSM matrices

#1367 euhruska opened 6 years ago
2
Tica model analog to vamp model

#1366 marscher closed 5 years ago
4

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