taurenmd 0.6.0

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

taurenmd

Command-line and library interface for analysis routines in Molecular Dynamics. This is an experimental project.

Stable version

The stable version is hosted at the master branch.

Notes

• AppVeyor builds only for py36; see #1

• Travis is not yet configured for OSX; see #2

Development Branch

where new features are tested and code maybe broken :)

The latest development is hosted at the develop branch.

Motivation

Provide an easy interface for the most common (and not so common) routines of analysis and data representation for Molecular Dynamics.

Documentation

Read the documentation: https://taurenmd.readthedocs.io

Dependencies

taurenmd wraps around high performance Molecular Dynamics analysis libraries, such as: MDAnalysis, MDTraj, OpenMM (and implementing others…); and it contains its own routines for data representation and export, such as curated plotting templates through matplotlib and bioplottemplates.

Citing

When using and citing taurenmd, you SHOULD by all means cite the Molecular Dynamics (MD) analysis libraries upon which taurenmd wraps. Please read through each project’s documentation to understand how to cite them; these projects are linked in the Dependencies header.

Acknowledges

The concept of this project is largely inspired in the pdb-tools one script one action idea. Thanks to JoaoRodrigues for all the mentoring on MD! CI in this repository provided by cookiecutter-pylibrary with final setup by me.

Changelog

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.