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

#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

#1610 - error in notebook 07

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

#1604 - Bayesian Hidden Markov model got an unexpected keyword argument 'desc'

Issue - State: open - Opened by ShenWenHuibit about 1 year ago - 1 comment

#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

#1592 - Substitute uses of numpy.bool with numpy.bool_

Pull Request - State: closed - Opened by evilsetg about 1 year ago - 1 comment

#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

#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

#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

#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

#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