Trivial change.
Trivial change.
Trivial change.
Trivial change.
Merge branch 'tICA' of github.com:SimTk/msmbuilder into tICA
Added files from schwancrtools (svn repo) for doing tICA
Added arglib_crs which contains the argparse stuff for PCA metric. This will be updated once the new-metric-parser branch is finished/stable
Added functionality to read chunks of hdf files instead of the entire file to Serializer.py and the corresponding Trajectory.py functions. Additionally, assigning.py has a new method called streaming_assign_with_checkpoint which assigns without reading the entire trajectory in
This commit (plus the previous) addresses issue #8. Specifically this adds the corresponding Conformation.py to use the changes in Serializer.py
Trivial change.
Trivial change.
Added files from schwancrtools (svn repo) for doing tICA
Added arglib_crs which contains the argparse stuff for PCA metric. This will be updated once the new-metric-parser branch is finished/stable
Merge branch 'tICA' of github.com:SimTk/msmbuilder into tICA
Headers in Serializer, Trajectory and Conformation.
Fixes to tICA, tICA_train.py, arglib.py, and metric_parser.py to make the new arglib cooperate with the tICA metric. This also introduces functionality to use a 'layered' metric, which is a metric that manipulates the output of another metrics prepare_trajectory method.
Fixes to tICA_train.py to look more like msmbuilder scripts and cooperate with new arglib. I also added a unit test and reference data for the tICA_train.py script in TestWrappers.py
removed new_tests/test_tica.py, since I added a test in TestWrappers
Merge issues, when pulling from master. I really hope this is not pushing to master. I think I did it right though.
Bugfix in metrics.parsers.py introduced in merge. Only because I have 'layered' metrics now.