Command-line and library interface for analysis routines in Molecular Dynamics
Project description
taurenmd
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:
how to install
usage
citing
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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