Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / markovmodel/PyEMMA issues and pull requests
#1615 - plot_contour colorbar tick labels don't adjust to changes to vmax and vmin
Issue -
State: open - Opened by marcushock 10 months ago
#1614 - What is the difference between a working directory and a path?
Issue -
State: open - Opened by Wencesgiovanni 10 months ago
- 2 comments
#1613 - estimating Bayesian MSM very slow
Issue -
State: open - Opened by H-EKE 10 months ago
- 4 comments
#1612 - Update install_miniconda+pyemma.sh
Pull Request -
State: closed - Opened by songyongshun 11 months ago
#1611 - What should i do when my fraction of sets and counts are less than 1?
Issue -
State: open - Opened by hima111997 12 months ago
#1610 - error in notebook 07
Issue -
State: open - Opened by hima111997 12 months ago
#1609 - how to use pyemma.plots.plot_cktest with 21 X 21 plot?
Issue -
State: open - Opened by hima111997 12 months ago
#1608 - Is it possible to use pyemma.msm.its on the dtrajs after using TICA on the features?
Issue -
State: open - Opened by hima111997 12 months ago
#1607 - add_sidechain_torsions produces an error
Issue -
State: open - Opened by hima111997 12 months ago
#1606 - pyemma.plots.scatter_contour produce an error
Issue -
State: open - Opened by hima111997 12 months ago
#1605 - How to get information from macrostates after constructing MSM in pyemma
Issue -
State: open - Opened by dulalmondal123 about 1 year ago
#1604 - Bayesian Hidden Markov model got an unexpected keyword argument 'desc'
Issue -
State: open - Opened by ShenWenHuibit about 1 year ago
- 1 comment
#1603 - Identifying the minimum free energy conformation based on binding energy values between two proteins
Issue -
State: open - Opened by Chakrabort123 about 1 year ago
#1602 - How to extract the pdb for a minimum free energy state from the free energy plot as a function of IC1 and IC2?
Issue -
State: open - Opened by Chakrabort123 about 1 year ago
#1601 - Are Unbiased Trajectories Required for dTRAM PMF profile estimations
Issue -
State: open - Opened by Cal-JWRW about 1 year ago
#1600 - Detecting the disconnectivity between states and how to deal with it
Issue -
State: open - Opened by raylab-projects about 1 year ago
#1599 - How to extract the structures not belonging to the free energy minimum
Issue -
State: open - Opened by satyajitkhatua09 about 1 year ago
- 1 comment
#1598 - RuntimeError: XTC read error: Compressed 3d coordinate
Issue -
State: open - Opened by Harshitasahni about 1 year ago
#1597 - its showing runtime error
Issue -
State: open - Opened by Gourav-Chakraborty about 1 year ago
- 1 comment
#1596 - Replace usage of np.float with float
Pull Request -
State: closed - Opened by comecattin about 1 year ago
#1595 - Missing dimensions when performing get_output() method
Issue -
State: open - Opened by meh47336 about 1 year ago
- 1 comment
#1594 - Few basic questions regarding building MSM using pyemma.
Issue -
State: open - Opened by udnenhsirK about 1 year ago
- 1 comment
#1593 - Reminder for _progress_register error in mini batch kmenas
Issue -
State: open - Opened by SianXiaoCHN about 1 year ago
#1592 - Substitute uses of numpy.bool with numpy.bool_
Pull Request -
State: closed - Opened by evilsetg about 1 year ago
- 1 comment
#1591 - NotImplementedError: MSM estimation with connectivity='none' is currently not implemented.
Issue -
State: closed - Opened by Harshitasahni over 1 year ago
- 3 comments
#1590 - Implied timescales calculation hangs with multiprocessing
Issue -
State: open - Opened by yuxuanzhuang over 1 year ago
#1589 - Minor issue with newest numpy version
Issue -
State: open - Opened by pitmanme over 1 year ago
- 5 comments
#1588 - IndexError: index 188 is out of bounds for axis 0 with size 184
Issue -
State: open - Opened by vas2201 over 1 year ago
- 3 comments
#1587 - numpy.bool removed from numpy --> AttributeError
Issue -
State: open - Opened by mmfarrugia over 1 year ago
- 4 comments
#1586 - how to import solvent accessible surface area as a feature in pyemma?
Issue -
State: closed - Opened by satyajitkhatua09 over 1 year ago
- 5 comments
#1585 - Got ValueError associated with dimensionality when using a tica object
Issue -
State: closed - Opened by ryankzhu over 1 year ago
- 4 comments
#1584 - OSError: "Unable to open file (file signature not found)" h5py/_objects.pyx:55 related error
Issue -
State: open - Opened by suniliisc over 1 year ago
- 1 comment
Labels: wontfix
#1583 - TICA on backbone atoms
Issue -
State: open - Opened by qasimpars over 1 year ago
- 4 comments
Labels: wontfix
#1582 - implied timescales with hmsm
Issue -
State: open - Opened by drdoppio over 1 year ago
- 4 comments
#1581 - Eigenvalues associated with the eigenvectors of TICA
Issue -
State: open - Opened by qasimpars over 1 year ago
- 5 comments
#1580 - how adjusting simulation timestep affects lag times
Issue -
State: closed - Opened by cgseitz over 1 year ago
- 7 comments
#1579 - Added an optional argument for specifying the tolerance in the class MSM
Pull Request -
State: closed - Opened by wehs7661 over 1 year ago
- 2 comments
#1578 - Possibility of specifying the tolerance for the MSM class
Issue -
State: closed - Opened by wehs7661 over 1 year ago
- 5 comments
#1577 - ignore
Issue -
State: closed - Opened by cgseitz over 1 year ago
#1576 - No return when using pyemma.msm.its
Issue -
State: closed - Opened by yingioi0 almost 2 years ago
- 3 comments
#1575 - Unable to import pyemma after installation using jupyter notebook
Issue -
State: open - Opened by debanjansen48 almost 2 years ago
- 26 comments
Labels: wontfix
#1574 - Fix tests, use deeptime double well discrete data.
Pull Request -
State: closed - Opened by clonker almost 2 years ago
- 2 comments
#1573 - Change ipywidgets version check to use __version__. Fixes #1571.
Pull Request -
State: closed - Opened by clonker almost 2 years ago
- 4 comments
#1572 - PyEMMA on MAC M1 - installation not working
Issue -
State: closed - Opened by toth12 almost 2 years ago
- 3 comments
#1571 - ipywidgets.version_info is deprecated since version a6 causing progress.reporter__init__.py to fail
Issue -
State: closed - Opened by apayne97 almost 2 years ago
- 1 comment
#1570 - How to extract structure from near the center of the clusters?
Issue -
State: closed - Opened by buruiyu almost 2 years ago
- 1 comment
#1569 - Basis of the active state fraction and active count fraction
Issue -
State: closed - Opened by Bazzinga18 almost 2 years ago
- 2 comments
#1568 - Different transition time in compare to experimental results.
Issue -
State: closed - Opened by Bazzinga18 almost 2 years ago
- 1 comment
#1567 - pyemma.util no attribute 'context'
Issue -
State: open - Opened by pojeda about 2 years ago
- 4 comments
Labels: documentation
#1566 - Secondary structure in PyEMMA
Issue -
State: closed - Opened by rubinanoor9 about 2 years ago
- 5 comments
#1565 - Use spawn() for multiprocessing instead of fork()
Pull Request -
State: closed - Opened by sents about 2 years ago
- 4 comments
#1564 - Problems with loading more than two trajectories
Issue -
State: closed - Opened by orthonalmatrix about 2 years ago
- 2 comments
#1563 - Expose minRMSD metric directly
Issue -
State: open - Opened by clonker about 2 years ago
- 2 comments
#1562 - Make data sources compatible to deeptime
Issue -
State: open - Opened by clonker about 2 years ago
- 2 comments
Labels: enhancement, wontfix, coordinates
#1561 - Migrate network plots to deeptime
Issue -
State: closed - Opened by clonker about 2 years ago
#1560 - Examples how to migrate code from current PyEMMA API to deeptime
Issue -
State: open - Opened by clonker about 2 years ago
- 1 comment
Labels: wontfix
#1559 - Integrate dTRAM into deeptime
Issue -
State: open - Opened by clonker about 2 years ago
- 2 comments
Labels: wontfix
#1558 - Issue deprecation warnings
Issue -
State: open - Opened by clonker about 2 years ago
- 2 comments
Labels: wontfix, documentation, design-discussion
#1557 - Deprecations for coordinates api
Pull Request -
State: closed - Opened by clonker about 2 years ago
- 1 comment
#1556 - remove pybind submodule
Pull Request -
State: closed - Opened by clonker about 2 years ago
- 1 comment
#1555 - Remove msmtools
Pull Request -
State: closed - Opened by clonker about 2 years ago
- 1 comment
#1554 - unable to execute
Issue -
State: closed - Opened by debanjansen48 about 2 years ago
- 2 comments
#1553 - Progress stuck after ITS estimation
Issue -
State: closed - Opened by satyajitkhatua09 about 2 years ago
- 3 comments
#1552 - using radius of gyrationn in the custom featurizer
Issue -
State: closed - Opened by instaM over 2 years ago
- 4 comments
#1551 - minflux in plot_markov_model seems to be malfunctioning
Issue -
State: closed - Opened by orthonalmatrix over 2 years ago
- 4 comments
#1550 - Remove bhmm as dependency
Pull Request -
State: closed - Opened by clonker over 2 years ago
- 2 comments
#1549 - CK test doesn't justify HMM
Issue -
State: closed - Opened by Bazzinga18 over 2 years ago
- 1 comment
#1548 - Changing the units of the rate in plot_markov_model
Issue -
State: closed - Opened by orthonalmatrix over 2 years ago
- 2 comments
#1547 - Python 3.10 release?
Issue -
State: closed - Opened by sroet over 2 years ago
- 4 comments
#1546 - Usage of pathlib in coordinates package
Issue -
State: open - Opened by clonker over 2 years ago
- 1 comment
Labels: enhancement, design-discussion
#1545 - Improved topology LRU cache
Pull Request -
State: closed - Opened by clonker over 2 years ago
- 1 comment
#1544 - Extracting PDB structures from TICA plot or PCA plot in PyEMMA 2.5.7
Issue -
State: closed - Opened by satyabrata400 over 2 years ago
- 2 comments
Labels: wontfix
#1543 - torsion feature for specific range
Issue -
State: closed - Opened by Bazzinga18 over 2 years ago
- 2 comments
#1542 - Is transition time(mfpt) from one state to another may be different from time observed in MD simulations?
Issue -
State: closed - Opened by Bazzinga18 over 2 years ago
- 4 comments
Labels: wontfix
#1541 - Issue loading trajectory with pyemma.coordinates.source when topology file changes
Issue -
State: closed - Opened by AnjaConev over 2 years ago
- 6 comments
#1540 - update deeptime clustering include
Pull Request -
State: closed - Opened by clonker over 2 years ago
- 2 comments
#1539 - generate a synthetic trajectory from markov model
Issue -
State: closed - Opened by jeromeRlon over 2 years ago
- 2 comments
#1538 - XTC seek error: 13 when reading otherwise fine .xtc using coordinates.save_trajs
Issue -
State: closed - Opened by germanbarcenas over 2 years ago
- 26 comments
#1537 - To generate pdbs of each clusters at a particular timescale
Issue -
State: closed - Opened by Bazzinga18 over 2 years ago
- 4 comments
Labels: wontfix
#1536 - Metastable state distribution
Issue -
State: closed - Opened by rubinanoor9 over 2 years ago
- 4 comments
#1535 - Error while calculating VAMP2 score at different lag times
Issue -
State: closed - Opened by Bazzinga18 over 2 years ago
- 11 comments
#1534 - Assigning two features at a time
Issue -
State: closed - Opened by Bazzinga18 over 2 years ago
- 6 comments
#1533 - Adaptive Sampling and Structure Extraction from TICA or PCA Plot
Issue -
State: closed - Opened by hl2500 over 2 years ago
- 3 comments
#1532 - mfpt uncertainty
Issue -
State: closed - Opened by ccccclw over 2 years ago
- 2 comments
#1531 - use mambabuild in CI and fix rmsd computation in clustering
Pull Request -
State: closed - Opened by clonker over 2 years ago
- 1 comment
#1530 - solve some syntax warnings
Pull Request -
State: closed - Opened by sroet over 2 years ago
- 3 comments
#1529 - When to use periodic=False
Issue -
State: closed - Opened by Seral17 over 2 years ago
- 3 comments
#1528 - Could not allocate enough memory to map all data
Issue -
State: closed - Opened by rubinanoor9 over 2 years ago
- 3 comments
Labels: wontfix
#1527 - How to deal with many short trajectories
Issue -
State: closed - Opened by KrishnenduSinha12 over 2 years ago
- 4 comments
Labels: wontfix
#1526 - Only pass copy of trajectory list to mdtraj.load and (CI) update macos image
Pull Request -
State: closed - Opened by clonker over 2 years ago
- 2 comments
#1525 - PyEMMA and GROMACS generate a bit different projection results
Issue -
State: closed - Opened by qasimpars over 2 years ago
- 1 comment
#1524 - Installation on M1 Mac
Issue -
State: closed - Opened by hl2500 over 2 years ago
- 14 comments
#1523 - _bar_df wrong for loop boundary
Issue -
State: open - Opened by MaaikeG over 2 years ago
- 3 comments
Labels: wontfix
#1522 - Fix periodic width initialization in umbrella sampling
Pull Request -
State: closed - Opened by sefalkner over 2 years ago
- 1 comment
#1521 - IndexError: Index out of bound
Issue -
State: closed - Opened by rubinanoor9 over 2 years ago
- 7 comments
Labels: tech-support
#1520 - Tips on combining features across systems
Issue -
State: closed - Opened by cgseitz over 2 years ago
- 6 comments
Labels: wontfix
#1519 - Loading Objects breaks '_default_chunksize' Attribute for 'get_output' Method
Issue -
State: closed - Opened by tim0marshall over 2 years ago
- 5 comments
#1518 - Is TRAM appropriate in this setting?
Issue -
State: closed - Opened by onehalfatsquared over 2 years ago
- 5 comments
Labels: wontfix
#1517 - varify Markov model built by Umbrella sampling with PyEMMA
Issue -
State: closed - Opened by wyb2021 over 2 years ago
- 1 comment
#1516 - Fresh conda install broken (at least for kmeans clustering) due to deeptime ImportError
Issue -
State: closed - Opened by rafwiewiora-silicon over 2 years ago
- 1 comment