Getting Started
Installation
Dependencies
Testing Your Installation
MDTraj Examples
Clustering with the
md.rmsd()
and
scipy.cluster.hierarchy
.
Baker-Hubbard hydrogen bond identification
Out-of-core calculations with
md.iterload()
Running a simulation in OpenMM
Principle components analysis (PCA) with
scikit-learn
Plotting a Ramachandran map with
matplotlib
Benchmarking RMSD speed
Memory-limited two pass clustering with
scipy.cluster
Command-line trajectory conversion:
mdconvert
What’s New
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.ArcTrajectoryFile
mdtraj.BINPOSTrajectoryFile
mdtraj.DCDTrajectoryFile
mdtraj.HDF5TrajectoryFile
mdtraj.LH5TrajectoryFile
mdtraj.MDCRDTrajectoryFile
mdtraj.NetCDFTrajectoryFile
mdtraj.PDBTrajectoryFile
mdtraj.TRRTrajectoryFile
mdtraj.XTCTrajectoryFile
Core Classes
mdtraj.Trajectory
mdtraj.Topology
Trajectory Analysis
mdtraj.rmsd
mdtraj.baker_hubbard
mdtraj.kabsch_sander
mdtraj.shrake_rupley
mdtraj.compute_distances
mdtraj.compute_displacements
mdtraj.compute_angles
mdtraj.compute_dihedrals
mdtraj.compute_phi
mdtraj.compute_psi
mdtraj.compute_chi1
mdtraj.compute_chi2
mdtraj.compute_chi3
mdtraj.compute_chi4
mdtraj.compute_omega
mdtraj.compute_rg
OpenMM Reporters
Example Usage
Utils
mdtraj.utils.import
mdtraj.utils.ensure_type
mdtraj.utils.ilen
mdtraj.utils.timing
mdtraj.utils.lengths_and_angles_to_box_vectors
mdtraj.utils.box_vectors_to_lengths_and_angles
MDTraj HDF5 Format Specification
Overview
Why HDF5?
Details
Topology
Building the documentation
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.
Versions