pytraj
1.0.9
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Overview
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Analysis
Cookbook
Supported file formats
Topology
Trajectory
Atom mask selection
Parallel calculation
Developer guide for pytraj
Misc
API reference
What’s new?
Frequently Asked Questions
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Cookbook
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Tips »
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Tips
process many files
load from a list of files with frame stride
load specific frame numbers to memory
merge multiple trajectories to a single file
memory saving
convert trajectory
pickle data
speed up calculation with parallel: using MPI
speed up calculation with parallel: multiple cores
read cpptraj manual
Tips for out-of-core loading
Run cpptraj’s batch
Create state with existing
TrajectoryIterator
class
Create state without
TrajectoryIterator
class
Weird things in pytraj
Explicit copy
Trajectory warm up
Register to load from disk
Register to load from disk with frame stride
Register to load several files from disk
Register to load several files from disk with frame stride
Write to disk
Extract coordinates from PDB structure
Write PDB file to netcdf format (require Netcdf lib)
Fancy indexing
Iterate whole trajectory
Iterate a part of trajectory
Perform calculation
Convert data to pandas DataFrame
Convert to different file format
Combine with cpptraj command style
Convert out-of-core TrajectoryIterator to in-memory Trajectory
Parallel computing with TrajectoryIterator