msmbuilder/msmbuilder issues and pull requests

#1141 - Getting the mapping for a HMM

Issue - State: open - Opened by orthonalmatrix over 3 years ago - 1 comment

#1140 - added cosine distance metric to libdistance

Pull Request - State: open - Opened by koileee over 3 years ago

#1139 - Website down?

Issue - State: closed - Opened by ahy3nz almost 4 years ago - 1 comment

#1138 - change readme

Issue - State: open - Opened by brookehus almost 4 years ago - 3 comments

#1137 - clustering for my data

Issue - State: open - Opened by momarzouksobeh almost 4 years ago

#1136 - simtk module problem

Issue - State: open - Opened by momarzouksobeh almost 4 years ago

#1135 - During run the tICA vs. PCA example, I found that I need this library but I couldn't get by Conda or pip

Issue - State: open - Opened by momarzouksobeh almost 4 years ago

#1134 - Using msmbuilder dataset for .h5 files

Issue - State: open - Opened by aasthajhunjhunwala over 4 years ago

#1133 - Issue with module import from scikit-learn

Issue - State: open - Opened by jacknicoludis over 4 years ago - 1 comment

#1132 - Key error: 'run' when run in Python notebook.

Issue - State: closed - Opened by ghost over 4 years ago

#1131 - [Question] sample_discrete algorithm

Issue - State: closed - Opened by tombo512 over 4 years ago

#1130 - Key Error `run` trying to use Numbered Runs Parser

Issue - State: closed - Opened by ghost almost 5 years ago

#1129 - how to create "meta.pandas.pickl" file

Issue - State: open - Opened by qasimpars almost 5 years ago - 1 comment

#1128 - Sampling conformations from microstates

Issue - State: open - Opened by rsatijaUT almost 5 years ago

#1127 - Fspeptide example in "http://msmbuilder.org/development/examples/index.html" why is the timescale different for fspeptide (in RAM) and fspeptide(using dataset)

Issue - State: open - Opened by anuginu about 5 years ago

#1126 - New release/build?

Issue - State: open - Opened by dwhswenson about 5 years ago - 1 comment

#1125 - Bump minimum cython to 0.28

Pull Request - State: closed - Opened by rmcgibbo about 5 years ago

#1124 - Multiple `Error compiling Cython file` with 3.8.0

Issue - State: closed - Opened by fcannini about 5 years ago - 2 comments

#1123 - ImportError after installation

Issue - State: open - Opened by vshiv18 about 5 years ago - 9 comments

#1122 - RuntimeError with featurize.py in tutorial

Issue - State: open - Opened by proteinevolver over 5 years ago

#1121 - Update test_ghmm.py

Pull Request - State: open - Opened by cxhernandez over 5 years ago
Labels: bug

#1120 - Update to latest version of MDTraj

Pull Request - State: open - Opened by cxhernandez over 5 years ago

#1119 - Update build_docs.sh

Pull Request - State: closed - Opened by cxhernandez over 5 years ago
Labels: bug, docs

#1118 - An unexpected error has occurred with MSMBuilder (version 3.7.0)

Issue - State: closed - Opened by ghost over 5 years ago

#1117 - NameError: name 'tica_trajs' is not defined

Issue - State: closed - Opened by ghost over 5 years ago

#1116 - Contribution of each feature to components in PCA(or tICA)

Issue - State: open - Opened by ortizdiego166 over 5 years ago

#1115 - NameError: name 'check_iter_of_sequences' is not defined

Issue - State: open - Opened by kritikamehta15 over 5 years ago

#1114 - Units of TICA

Issue - State: open - Opened by sbhakat over 5 years ago

#1113 - ValueError: The eigenvalue range specified is not valid

Issue - State: open - Opened by girodat almost 6 years ago

#1112 - A question about tICA in MSMBuilder

Issue - State: open - Opened by Juanrong almost 6 years ago

#1111 - fix typo

Pull Request - State: closed - Opened by sunhwan almost 6 years ago - 1 comment

#1110 - Download links for Jupyter Notebook examples result in 404

Issue - State: open - Opened by jaimergp almost 6 years ago

#1109 - Pool issue

Issue - State: closed - Opened by girodat almost 6 years ago - 4 comments

#1108 - Contact featurizer memoryError unspecified

Issue - State: closed - Opened by orthonalmatrix almost 6 years ago - 6 comments

#1107 - Update to model_selection

Pull Request - State: closed - Opened by cxhernandez almost 6 years ago

#1106 - Import issue after installation

Issue - State: closed - Opened by girodat almost 6 years ago - 3 comments

#1105 - Dumping snapshots from the Macrostate

Issue - State: open - Opened by sbhakat almost 6 years ago

#1104 - Modified import of ParameterGrid for compatibility with sklearn 0.20 and below.

Pull Request - State: closed - Opened by RobertArbon almost 6 years ago

#1103 - All tICA fittings give a LinAlgError

Issue - State: closed - Opened by ljmartin almost 6 years ago - 5 comments

#1102 - Fix const-ness of some functions for rate matrix code

Pull Request - State: closed - Opened by rmcgibbo almost 6 years ago

#1101 - Compilation failure with Cython 0.28.5 / Python 3.7

Issue - State: closed - Opened by rmcgibbo almost 6 years ago - 2 comments

#1100 - are tICs unit and orthogonal vectors?

Issue - State: open - Opened by DaMaoShan about 6 years ago

#1099 - Information on kerneltICA

Issue - State: closed - Opened by orthonalmatrix about 6 years ago - 2 comments

#1098 - Some questions about RawPositionsFeaturizer

Issue - State: open - Opened by sbhakat about 6 years ago - 2 comments

#1097 - Is the Kernel TICA implemented in some development version of MSMBuilder?

Issue - State: closed - Opened by sbhakat about 6 years ago - 1 comment

#1096 - [Question] Erratic timescale plots and what they mean

Issue - State: open - Opened by orthonalmatrix about 6 years ago

#1095 - msm.transmat to MSMExplorer

Issue - State: closed - Opened by girodat about 6 years ago - 2 comments

#1093 - Tutorial Help issue

Issue - State: open - Opened by lilianabello over 6 years ago

#1092 - Checking states are at minimums in the Free Energy landscape and wrt to which tICA axes

Issue - State: closed - Opened by orthonalmatrix over 6 years ago - 1 comment

#1091 - Fix vmfeat

Pull Request - State: closed - Opened by cxhernandez over 6 years ago - 2 comments

#1090 - center conformations of the macrostates

Issue - State: closed - Opened by musaoz over 6 years ago - 3 comments

#1089 - Dumping representative snapshots from microstate, macrostate

Issue - State: closed - Opened by sbhakat over 6 years ago - 4 comments

#1087 - too much data seems to stop the msmbuilder

Issue - State: open - Opened by orthonalmatrix over 6 years ago

#1086 - Number of microstates and Chaoman-Kolmogorov test

Issue - State: closed - Opened by Nidane over 6 years ago - 1 comment

#1085 - transition probabilities (Rates per ns)

Issue - State: closed - Opened by mkhoshle over 6 years ago - 3 comments

#1084 - Installing msmbuilder using pip3.5

Issue - State: closed - Opened by orthonalmatrix over 6 years ago - 5 comments

#1083 - Tutorial problem with python 3.5

Issue - State: closed - Opened by orthonalmatrix over 6 years ago

#1082 - Generate pkl file of MD trajectories

Issue - State: closed - Opened by daipayans over 6 years ago - 2 comments

#1081 - the unit of impliedtimescales plot and how to decide lagtime?

Issue - State: closed - Opened by Avon07 over 6 years ago - 6 comments

#1080 - TPT on a set of macrostates

Issue - State: closed - Opened by jeiros over 6 years ago - 6 comments

#1079 - Do I have enough samples?

Issue - State: closed - Opened by AlirezaTafazzol over 6 years ago - 10 comments

#1078 - Intel MKL ERROR: Parameter 5 was incorrect on entry to DGEEV.

Issue - State: open - Opened by lenhsherr over 6 years ago

#1077 - Add periodic option to contact featurizers

Pull Request - State: closed - Opened by HWaymentSteele over 6 years ago

#1076 - previous msmbuilder versions

Issue - State: closed - Opened by asgharrazavi over 6 years ago - 2 comments

#1075 - msmb fails to load dll on clean install

Issue - State: open - Opened by orthonalmatrix over 6 years ago - 1 comment

#1074 - cluster centers in the Kmeans

Issue - State: closed - Opened by asgharrazavi over 6 years ago - 2 comments

#1073 - MacroAssignments_ and labels_ are NoneType object while using APM.

Issue - State: open - Opened by zshamsi2 over 6 years ago - 1 comment

#1072 - Unexpected error occurred with MSMBuilder (version 3.8.0) when experiment with Tutorial Command Line

Issue - State: closed - Opened by Yesssun over 6 years ago - 1 comment

#1071 - Macrostate or microstate structure and Transition Pathways ?

Issue - State: open - Opened by Avon07 over 6 years ago - 26 comments

#1070 - [question] how to distill intermediate structures from MSM ?

Issue - State: open - Opened by Nidane over 6 years ago - 1 comment

#1069 - update mvca citation

Pull Request - State: closed - Opened by brookehus over 6 years ago

#1068 - [questions] how to deal with .mdcrd trajectory instead of .xtc ?

Issue - State: closed - Opened by Nidane over 6 years ago - 27 comments

#1067 - Problems about MSMBuilder especially for .mdcrd trajectory, thanks

Issue - State: closed - Opened by Nidane over 6 years ago - 10 comments

#1066 - MSMExplorer: No module named 'basesetup'

Issue - State: closed - Opened by AlirezaTafazzol over 6 years ago - 4 comments

#1065 - [question] 'Unlikely unit cell vectors detected in PDB file likely '

Issue - State: closed - Opened by AlirezaTafazzol over 6 years ago - 2 comments

#1064 - Free energy projections on Feature different from that used for MSM

Issue - State: closed - Opened by enaziga over 6 years ago - 2 comments

#1063 - Update notebook_sphinxext.py

Pull Request - State: closed - Opened by cxhernandez over 6 years ago

#1062 - SparseTICA supports commute mapping

Pull Request - State: closed - Opened by jeiros over 6 years ago - 1 comment

#1061 - GaussianHMM parameter estimation runs indefinitely

Issue - State: open - Opened by tmaula over 6 years ago - 1 comment

#1060 - Error tica.py line 405

Issue - State: closed - Opened by oni-sama14 over 6 years ago - 1 comment

#1059 - fit method of MarkovStateModel: ValueError: Likelihood not converged. Error code=-3

Issue - State: closed - Opened by jeiros almost 7 years ago - 5 comments

#1058 - change bayes factors name

Pull Request - State: closed - Opened by brookehus almost 7 years ago

#1057 - Implement RobustScaler with trimmed means

Issue - State: open - Opened by cxhernandez almost 7 years ago

#1056 - lag time and macrostate structures

Issue - State: closed - Opened by mohanpradhan almost 7 years ago - 2 comments

#1055 - Question about msm.io.sampling sample_msm

Issue - State: closed - Opened by jeiros almost 7 years ago - 7 comments

#1054 - Performing tICA on a single trajectory

Issue - State: closed - Opened by sbhakat almost 7 years ago - 10 comments

#1053 - No lumping in msmbuilder website?

Issue - State: open - Opened by jeiros almost 7 years ago - 1 comment
Labels: docs

#1052 - Change MDTraj required version to 1.9.

Pull Request - State: closed - Opened by nhstanley almost 7 years ago - 1 comment

#1051 - Add sasa describe (again)

Pull Request - State: closed - Opened by nhstanley almost 7 years ago - 4 comments

#1050 - Implementation of BACE

Pull Request - State: closed - Opened by brookehus almost 7 years ago - 2 comments

#1049 - option to fit only

Pull Request - State: closed - Opened by brookehus almost 7 years ago

#1048 - Make it so that zippy_maker returns ordered unique lists.

Pull Request - State: closed - Opened by nhstanley almost 7 years ago

#1047 - Implement inverse_transform when appropriate

Issue - State: open - Opened by cxhernandez almost 7 years ago

#1046 - HMM generation getting stuck

Issue - State: closed - Opened by Trayder almost 7 years ago - 1 comment

#1021 - Using subset of common atoms for rmsd-based clustering

Issue - State: closed - Opened by jeiros about 7 years ago - 13 comments

#1020 - Question about HierarchyParser

Issue - State: open - Opened by jeiros about 7 years ago - 1 comment

#1018 - Change to FeatureSelector 'which_feat' setter.

Pull Request - State: closed - Opened by RobertArbon over 7 years ago - 1 comment

GitHub / msmbuilder/msmbuilder issues and pull requests