Published March 29, 2016
| Version 3.4.0
Software
Open
msmbuilder: MSMBuilder 3.4
Creators
- 1. D.E. Shaw Research
- 2. Stanford University
- 3. DeepMile Networks
- 4. HKUST
- 5. University of Pittsburgh
Description
We're pleased to announce MSMBuilder 3.4. It contains a plethora of new features, bug fixes, and improvements.
API Changes- Range-based slicing on dataset objects is no longer allowed. Keys in the dataset object don't have to be continuous. The empty slice, e.g. ds[:] loads all trajectories in a list (#610).
- Ward clustering has been renamed AgglomerativeClustering in scikit-learn. Please use the new msmbuilder wrapper class AgglomerativeClustering. An alias for Ward has been made available (#685).
- PCCA.trimmed_microstates_to_macrostates has been removed. This dictionary was actually keyed by untrimmed microstate labels. PCCA.transform would throw an exception when operating on a system with trimming because it was using this misleading dictionary. Please use pcca.microstate_mapping_ for this functionality (#709).
- UnionDataset has been removed after deprecation in 3.3. Please use FeatureUnion instead (#671).
- SubsetFeaturizer and ilk have been removed from the msmbuilder.featurizer namespace. Please import them from msmbuilder.featurizer.subset (#738).
- FirstSlicer has been removed. Use Slicer(first=x) for the same functionality (#738).
- msmbuilder.featurizer.load has been removed. Featurizer.save has been removed. Please use utils.load, utils.dump (#738).
- Dataset objects can call, fit_transform_with() to simplify the common pattern of applying an estimator to a dataset object to produce a new dataset object (#610).
- kinetic_mapping is a new option to tICA. It's similar to weighted_transform, but based on a better theoretical framework. weighted_transform is deprecated (#766).
- VonMisesFeaturizer uses soft bins around the unit-circle to give an alternate representation of dihedral angles (#744).
- MarkovStateModel has a partial_transform() method (#707).
- KapaAngleFeaturizer is available via the command line (#681).
- MarkovStateModel has a new attribute, percent_retained_, for ergodic trimming (#689).
- AlphaAngleFeaturizer computes the dihedral angles between alpha carbons (#691).
- FunctionFeaturizer computes features based on an arbitrary Python function or callable (#717).
- Automatic State Partitioning (APM) uses kinetic information to cluster conformations (#748).
- Consistent counts setup and ergodic cutoff across various flavors of Markov models (#718, #729, #701, #705).
- Tests no longer depend on sklearn.hmm, which has been removed (#690).
- Improvements to RSMDFeaturizer (#695, #764).
- SparseTICA is completely re-written with large performance improvements when dealing with large numbers of features (#704).
- Links for downloading example data are un-broken after figshare changed URLs (#751).
Files
msmbuilder-3.4.0.zip
Files
(1.1 MB)
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Additional details
Related works
- Is supplement to
- https://github.com/msmbuilder/msmbuilder/tree/3.4.0 (URL)