Getting Started
Installation
Dependencies
Testing Your Installation
MDTraj Examples
Introduction to MDTraj
Finding centroids of clusters
Clustering with
md.rmsd()
and
scipy.cluster.hierarchy()
Baker-Hubbard Hydrogen Bond Identification
Out-of-core calculations with
md.iterload()
Calculating NMR observables with
mdtraj.nmr()
Running a simulation in OpenMM
Principle components analysis (PCA) with
scikit-learn
Plotting a Ramachandran map with
matplotlib
Benchmarking MDTraj’s RMSD engine
Solvent Sccessible Surface Area (SASA) Calculation
Memory-limited two pass clustering with
scipy.cluster
Command-line trajectory conversion:
mdconvert
What’s New?
v0.9.0 (June 10, 2014)
v0.8.0 (March 10, 2014)
v0.7.0 (February 21, 2014)
v0.6.1 (February 11, 2014)
v0.6.0 (January 21, 2014)
v0.5.1 (January 4, 2014)
v0.5.0 (January 3, 2014)
Load Functions
Cross-format support
Format-specific loaders
File Objects
mdtraj.formats.ArcTrajectoryFile
mdtraj.formats.BINPOSTrajectoryFile
mdtraj.formats.DCDTrajectoryFile
mdtraj.formats.HDF5TrajectoryFile
mdtraj.formats.LH5TrajectoryFile
mdtraj.formats.MDCRDTrajectoryFile
mdtraj.formats.NetCDFTrajectoryFile
mdtraj.formats.PDBTrajectoryFile
mdtraj.formats.TRRTrajectoryFile
mdtraj.formats.XTCTrajectoryFile
Core Classes
mdtraj.Trajectory
mdtraj.Topology
Trajectory Analysis
Root-mean-square deviation (RMSD)
Hydrogen Bonding
Surface Area and Radius of Gyration
Distances
Bond Angles and Dihedrals
NMR Observables
OpenMM Reporters
Example Usage
MDTraj Utils
Miscellanies
Validation
Unit cell and Periodic Boundary Conditions
Rotations
MDTraj HDF5 Format Specification
Overview
Why HDF5?
Details
Topology
Building the documentation
MDTraj Programing Style
PEP8
Properties
Writing Tests
Docstrings
MDTraj
Docs
»
Core Classes
Edit on GitHub
Core Classes
ΒΆ
Trajectory
(xyz, topology[, time, ...])
Container object for a molecular dynamics trajectory
Topology
()
Topology stores the topological information about a system.
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