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Command-line and library interface for analysis routines in Molecular Dynamics

Project description

taurenmd

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A command-line interface for analysis routines in Molecular Dynamics.

Taurenmd provides an easy, flexible and extensible, interface for the most common (and not so common) routines of analysis and representation of Molecular Dynamics (MD) data.

It bridges the gap between the highly complex (and powerful) Python libraries available for analysis of MD data and the non-developer users that lack the programming skills to use those libraries thoroughly. But not only, taurenmd also facilitates high throughput operations, even to those proficient devs, because complex executions are reduced to a single argument-rich command line.

Taurenmd wraps around feature-rich and powerful MD analysis libraries such as MDAnalysis and MDTraj (but not only), combining them to extract the best of those worlds. We use these libraries to access and extract MD data and calculate observables, and we have also added our own routines of analysis when needed.

With this said, taurenmd aims to be a flexible and extensible peace of software, built as simple and modular as we can think of, to agile the incorporation of new functionalities as needed.

taurenmd aims to be a command-line user-directed interface, but its core functions are openly available and distributed in the library architecture. Currently, there are already several commands available, some that perform only single tasks, while others allow complex setups, all are one-liners.

Documentation

taurenmd full documentation is available at: https://taurenmd.readthedocs.io, read there:

  1. how to install

  2. usage

  3. citing

  4. etc…

Changelog

0.7.2 (2019-12-25)

  • bridged from 0.7.1

  • Dropped Appveyor and EXPLICIT Windows support because of #1.

  • restructured project GitHub layout. Deprecated develop branch.

  • Readthedocs documentation improvements in structure and content.

0.7.0 (2019-12-23)

  • implemented cli_rotations, calculates roll, pitch and yaw

    rotation angles of selection.

0.6.0 (2019-12-15)

  • implemented cli_rmsf to calculate RMSFs.

0.5.1 (skipped to 0.6.0)

  • added sort numbered trajs to cli_trajedit

  • added sort numbered trajectory paths in lib

  • improved cli_imagemol readability

  • added selection in cli_noSol

0.5.0 (2019-11-24)

  • created cli_angle. Calculates angles between a plane along the trajectory. Plane is given by the three centre_of_geometries of three selections.

  • args to plot passed as list are transformed to tuple

  • added distance calc and plot interface cli_distances

  • trajedit now saves topology unwrapped

0.4.1 (2019-11-21)

  • renumbered version to 0.4.1. from 0.3.1

  • RMSD Cli now calculates for several selections

  • Parse plot vars now registers floats

  • corrected fext cli entry point

  • added align option to trajedit

  • topology model writen from first frame of time slicing

  • added unwrap() molecule method from MDAnalysis in trajedit with respective options

  • topology output now defaults to traj name + frame0.pdb

  • added .myparents() to Path in __init__

0.3.0 (2019-11-06)

  • Created develop branch

  • Created client for frame extraction: cli_fext

  • Added option to disable export of frame0 topology in trajedit

0.2.1 (2019-10-26)

  • dropped py35

  • separated lib MDAnalysis from MDTraj

  • libio concerns only general functions

  • improved imagemol I/O

0.2.0 (2019-10-26)

  • added cli_report

0.1.1 (2019-10-26)

  • corrected libio

  • trajectory loads based on MDAnalysis now read and concatenate multiple trajectories.

0.1.0 (2019-10-26)

  • added interfaces: * trajedit * noSol * imagemol * rmsd * cli template

0.0.0 (2019-10-15)

  • First release on PyPI.

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