PyEMMA
1.2.1
  • Installation
  • Runtime Configuration
  • PyEMMA API
    • Coordinates package (pyemma.coordinates)
    • Markov State Models package (pyemma.msm)
      • User API
      • MSM functions (low-level API)
        • io - Input and output for MSM related files (pyemma.msm.io)
        • generation - MSM generation tools (pyemma.msm.generation)
        • estimation - MSM estimation from data (pyemma.msm.estimation)
        • analysis - MSM analysis functions (pyemma.msm.analysis)
        • flux - Reactive flux an transition pathways (pyemma.msm.flux)
    • Plotting API
  • IPython Notebook Tutorials
  • Changelog
  • Developer’s Guide
 
PyEMMA
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  • PyEMMA API »
  • Markov State Models package (pyemma.msm) »
  • io - Input and output for MSM related files (pyemma.msm.io)
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io - Input and output for MSM related files (pyemma.msm.io)¶

Discrete trajectory io¶

read_discrete_trajectory(filename) Read discrete trajectory from ascii file.
read_dtraj(filename) Read discrete trajectory from ascii file.
write_discrete_trajectory(filename, dtraj) Write discrete trajectory to ascii file.
write_dtraj(filename, dtraj) Write discrete trajectory to ascii file.
load_discrete_trajectory(filename) Read discrete trajectory form binary file.
load_dtraj(filename) Read discrete trajectory form binary file.
save_discrete_trajectory(filename, dtraj) Write discrete trajectory to binary file.
save_dtraj(filename, dtraj) Write discrete trajectory to binary file.

Dense and sparse matrix io¶

read_matrix(filename[, mode, dtype, comments]) Read matrix from ascii file.
write_matrix(filename, A[, mode, fmt, ...]) Write matrix to ascii file.
load_matrix(filename[, mode]) Read matrix from binary file.
save_matrix(filename, A[, mode]) Save matrix as binary file.
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