markovmodel/PyEMMA

Issues

• plot_contour colorbar tick labels don't adjust to changes to vmax and vmin

  #1615 opened a year ago by marcushock
  0

• What is the difference between a working directory and a path?

  #1614 opened a year ago by Wencesgiovanni
  2

• estimating Bayesian MSM very slow

  #1613 opened a year ago by H-EKE
  4

• Bayesian Hidden Markov model got an unexpected keyword argument 'desc'

  #1604 opened 2 years ago by ShenWenHuibit
  1

• What should i do when my fraction of sets and counts are less than 1?

  #1611 opened a year ago by hima111997
  0

• error in notebook 07

  #1610 opened a year ago by hima111997
  0

• how to use pyemma.plots.plot_cktest with 21 X 21 plot?

  #1609 opened a year ago by hima111997
  0

• Is it possible to use pyemma.msm.its on the dtrajs after using TICA on the features?

  #1608 opened a year ago by hima111997
  0

• add_sidechain_torsions produces an error

  #1607 opened a year ago by hima111997
  0

• pyemma.plots.scatter_contour produce an error

  #1606 opened a year ago by hima111997
  0

• pyemma.util no attribute 'context'

  #1567 opened 3 years ago by pojeda
  4

• How to get information from macrostates after constructing MSM in pyemma

  #1605 opened 2 years ago by dulalmondal123
  0

• Identifying the minimum free energy conformation based on binding energy values between two proteins

  #1603 opened 2 years ago by Chakrabort123
  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 opened 2 years ago by Chakrabort123
  0

• Are Unbiased Trajectories Required for dTRAM PMF profile estimations

  #1601 opened 2 years ago by Cal-JWRW
  0

• Detecting the disconnectivity between states and how to deal with it

  #1600 opened 2 years ago by raylab-projects
  0

• NotImplementedError: MSM estimation with connectivity='none' is currently not implemented.

  #1591 opened 2 years ago by Harshitasahni
  3

• How to extract the structures not belonging to the free energy minimum

  #1599 opened 2 years ago by satyajitkhatua09
  1

• Unable to import pyemma after installation using jupyter notebook

  #1575 opened 2 years ago by debanjansen48
  26

• Integrate dTRAM into deeptime

  #1559 opened 3 years ago by clonker
  2

• Make data sources compatible to deeptime

  #1562 opened 3 years ago by clonker
  2

• OSError: "Unable to open file (file signature not found)" h5py/_objects.pyx:55 related error

  #1584 opened 2 years ago by suniliisc
  1

• TICA on backbone atoms

  #1583 opened 2 years ago by qasimpars
  4

• Expose minRMSD metric directly

  #1563 opened 3 years ago by clonker
  2

• RuntimeError: XTC read error: Compressed 3d coordinate

  #1598 opened 2 years ago by Harshitasahni
  0

• its showing runtime error

  #1597 opened 2 years ago by Gourav-Chakraborty
  1

• Missing dimensions when performing get_output() method

  #1595 opened 2 years ago by meh47336
  1

• Few basic questions regarding building MSM using pyemma.

  #1594 opened 2 years ago by udnenhsirK
  1

• Reminder for _progress_register error in mini batch kmenas

  #1593 opened 2 years ago by SianXiaoCHN
  0

• Implied timescales calculation hangs with multiprocessing

  #1590 opened 2 years ago by yuxuanzhuang
  0

• numpy.bool removed from numpy --> AttributeError

  #1587 opened 2 years ago by mmfarrugia
  4

• Minor issue with newest numpy version

  #1589 opened 2 years ago by pitmanme
  5

• IndexError: index 188 is out of bounds for axis 0 with size 184

  #1588 opened 2 years ago by vas2201
  3

• implied timescales with hmsm

  #1582 opened 2 years ago by drdoppio
  4

• how to import solvent accessible surface area as a feature in pyemma?

  #1586 opened 2 years ago by satyajitkhatua09
  5

• Secondary structure in PyEMMA

  #1566 opened 3 years ago by rubinanoor9
  5

• Got ValueError associated with dimensionality when using a tica object

  #1585 opened 2 years ago by ryankzhu
  4

• Eigenvalues associated with the eigenvectors of TICA

  #1581 opened 2 years ago by qasimpars
  5

• how adjusting simulation timestep affects lag times

  #1580 opened 2 years ago by cgseitz
  7

• Examples how to migrate code from current PyEMMA API to deeptime

  #1560 opened 3 years ago by clonker
  1

• Possibility of specifying the tolerance for the MSM class

  #1578 opened 2 years ago by wehs7661
  5

• ignore

  #1577 opened 2 years ago by cgseitz
  0

• No return when using pyemma.msm.its

  #1576 opened 2 years ago by yingioi0
  3

• ipywidgets.version_info is deprecated since version a6 causing progress.reporter__init__.py to fail

  #1571 opened 2 years ago by apayne97
  1

• PyEMMA on MAC M1 - installation not working

  #1572 opened 2 years ago by toth12
  3

• How to extract structure from near the center of the clusters?

  #1570 opened 2 years ago by buruiyu
  1

• Basis of the active state fraction and active count fraction

  #1569 opened 2 years ago by Bazzinga18
  2

• Different transition time in compare to experimental results.

  #1568 opened 2 years ago by Bazzinga18
  1

• Problems with loading more than two trajectories

  #1564 opened 3 years ago by orthonalmatrix
  2

• Migrate network plots to deeptime

  #1561 opened 3 years ago by clonker
  0