MSMBuilder
MSMBuilder Introduction
What’s New
2.6 Changelog
2.5.1 Changelog
2.5 Changelog
2.0.4 Changelog
2.0.3 Changelog
2.0.2 Changelog
2.0.1 Changelog
Distance Metrics:
msmbuilder.metrics
Performance Notes
Kinetic Distance Metrics
Concrete Metrics
Abstract Classes
Utility Methods
Clustering:
msmbuilder.clustering
Abstract Classes
Flat Clustering Classes
Hierarchical Clustering
Clustering Functions
Utility Functions
assigning:
msmbuilder.assigning
Functions
MSM Construction:
msmbuilder.MSMLib
Notes
Mapping
Trimming
Model Building
MSM Analysis:
msmbuilder.msm_analysis
Notes
Model Queries
Utils
Lumping:
msmbuilder.lumping
Core Lumping Routines
Private PCCA+ Implementation Code
Helper Functions
Transition Path Theory :
msmbuilder.tpt
Path Finding
MFPT & Committor Finding Functions
Hub Scores, Conditional Committors and Related Quantities
Cut Based Free Energy Profile
msmbuilder.cfep
Optimization
Example Coordinate
Container Classes:
Serializer
,
Conformation
,
Trajectory
Trajectory
arglib:
msmbuilder.arglib
Parsers
Path Manipulation
Utilities:
msmbuilder.utils
Project:
msmbuilder.Project
FahProject:
msmbuilder.FahProject
Interfacing with Folding@Home projects
Contributing
Submitting a bug report
How to contribute
MSMBuilder
Docs
»
Distance Metrics:
msmbuilder.metrics
»
msmbuilder.metrics.AtomPairs.prepare_trajectory
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msmbuilder.metrics.AtomPairs.prepare_trajectory
¶
AtomPairs.
prepare_trajectory
(
trajectory
)
¶
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