Installation
Supported Platforms
Dependencies
Testing Your Installation
Compiling From Source
Help! How do I get started?
Why Python?
Installing Python
Installing MDTraj
Starting MDTraj with IPython
Resources and Getting Help
MDTraj Examples
Introduction to MDTraj
Atom Selection
Finding centroids of clusters
Clustering with
md.rmsd()
and
scipy.cluster.hierarchy()
Baker-Hubbard Hydrogen Bond Identification
Out-of-core calculations with
md.iterload()
Fraction of Native Contacts
Calculating NMR observables with
mdtraj.nmr()
Running a simulation in OpenMM
Principal 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
What’s New?
v1.6.2 (February 19, 2016)
v1.6 (February 15, 2016)
v1.5.1 (November 6, 2015)
v1.5 (November 6, 2015)
v1.4.2 (June 9, 2015)
v1.4 (June 8, 2015)
v1.3 (February 25, 2015)
v1.2 (December 1, 2014)
v1.1 (November 10, 2014)
v1.0.0 (September 7, 2014)
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)
Frequently Asked Questions
IPython Notebook Viewer
Example
Usage
Requirements
Discussion Forums
Trajectories
The trajectory object
Cross-format loaders
Format-specific loaders
Atom Selection DSL
Introduction
Keywords and Grammar
Implementation
Analysis Functions
Root-mean-square deviation (RMSD)
Hydrogen Bonding
Secondary Structure
Surface Area, Radius of Gyration and Inertia
Distances
Bond Angles and Dihedrals
NMR Observables
Thermodynamic Quantities
Order Parameters
File Objects
mdtraj.formats.AmberNetCDFRestartFile
mdtraj.formats.AmberRestartFile
mdtraj.formats.ArcTrajectoryFile
mdtraj.formats.BINPOSTrajectoryFile
mdtraj.formats.DCDTrajectoryFile
mdtraj.formats.DTRTrajectoryFile
mdtraj.formats.GroTrajectoryFile
mdtraj.formats.HDF5TrajectoryFile
mdtraj.formats.LAMMPSTrajectoryFile
mdtraj.formats.LH5TrajectoryFile
mdtraj.formats.MDCRDTrajectoryFile
mdtraj.formats.NetCDFTrajectoryFile
mdtraj.formats.PDBTrajectoryFile
mdtraj.formats.TRRTrajectoryFile
mdtraj.formats.XTCTrajectoryFile
mdtraj.formats.XYZTrajectoryFile
OpenMM Reporters
Example Usage
MDTraj Utils
Miscellanies
Validation
Unit cell and Periodic Boundary Conditions
Rotations
Command-line trajectory conversion:
mdconvert
MDTraj HDF5 Format Specification
Overview
Why HDF5?
Details
Topology
Building the documentation
MDTraj Programming Style
PEP8
Properties
Writing Tests
Docstrings
MDTraj
Docs
»
Overview: module code
Edit on GitHub
All modules for which code is available
mdtraj
mdtraj.formats
mdtraj.geometry
mdtraj.reporters
mdtraj.testing
mdtraj.utils
Versions