taurenmd 0.11.2

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

taurenmd

A command-line interface for analysis routines of Molecular Dynamics data.

Taurenmd provides an easy, flexible and extensible, command-line 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 perform a thorough and proficient use those libraries. But not only, taurenmd also facilitates high throughput operations, even to those proficient devs, because complex executions are reduced to single argument-rich command-lines that can be concatenated or aliased.

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. When using this software, you should cite taurenmd together with the dependencies used, please read our Citing page for a detailed explanation.

Though designed to perform as a command-line user-directed interface, all taurenmd’s core functions are openly distributed and documented. Currently, there are already several command-line interfaces available, some that perform only single tasks, while others allow complex setups, all are one-liners.

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.

Documentation

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

1. how to install

2. usage examples

3. citing

4. etc…

Versioning

This project follows strictly Semantic Versioning 2.0 for version control.

Upon release of version 1.0.0, all additions to the master branch are done by PR followed by its respective version increment and release on PyPI.

Upon version 0.8, and before version 1, SV2 major version increments are reflected in the minor version number, and minor and patch increments are reflected together in the patch version number. Everything else follows SV2 rules, in this way users can track backwards incompatibilities if they happen.

Changelog

v0.11.2 (2022-07-14)

• Add output dir option to fext #66

v0.11.1 (2022-07-14)

• Update badges after 0.11 #65

v0.11.0 (2022-07-13)

• Dropped python-bioplottemplates

• updated export statements

• Added plots to taurenmd rotations

• Added plots to taurenmd dist

• Added plots to taurenmd rmsf

• Added plots to taurenmd rmsd

• taurenmd dist now can take multiple –sel2, and all are plotted

• ParamsToDict now uses ast.literal_eval

• trajectory slice now accepts timesteps (10ns, for example)

v0.10.4 (2022-01-14)

• update logo link in README #63

v0.10.3 (2021-12-11)

• Improved documentation for cli_rotations

• Added illustration explaining the roll, pitch, and yaw angles

v0.10.2 (2021-12-03)

• Add frame timestep and whole trajectory duration to report (#61)

v0.10.1 (2021-11-24)

• Add support for CIF topologies in libmda using openmm.app.pdbxfile

• removes the install*.yml gitactions

v0.10.0 (2021-11-24)

• Updates MDAnalysis to version 2.0.0

• Defines versions for all other dependencies

• Updates CI

v0.9.9 (2021-11-22)

• Corrects taking/passing of insort argument in some clients.

v0.9.8 (2021-11-22)

• Upgraded roll, pitch, and yaw angle calculations with torsion angle strategy

• Removed usage of PyQuaternion

v0.9.7 (2021-11-20)

• improved trajectory report (#54)

v0.9.6 (2021-02-22)

• Remove README badge for build: not needed.

• Added some comments in the workflow files.

• no changes in code, only CI.

v0.9.5 (2021-02-17)

• Upgraded CI to Github Actions according to: https://github.com/joaomcteixeira/python-project-skeleton

• Updated README badges

0.9.4 (2020-06-02)

• Updates documentation with JOSS citation (PR #49)

0.9.3 (2020-05-25)

• Improves CONTRIBUTION.rst guidelines (PR #46)

0.9.2 (2020-05-17)

• Client progression is now represented by a progress bar (PR #44)

0.9.1 (2020-05-15)

• Improves log in .taurenmd.cmd (PR #43)

0.9.0 (2020-05-15)

• Adds -i to every CLI interface (PR #42)

• major version change because cli_imagemol lost backwards compatibility

0.8.14 (2020-05-12)

• Updates tox.ini file for Continuous Integration (PR #40)

0.8.13 (2020-05-12)

• Added support for sequence of trajectories in CLIs that use MDTraj (PR #39)

0.8.12 (2020-05-04)

• PR: #37

• Installs taurenmd directly with Conda env

0.8.11 (2020-04-03)

• PR: #33

• Corrected command representation in .taurenmd.cwd adding quotes when needed

0.8.10 (2020-04-02)

• PR: #32

• Corrects incorrect usage of MDAnalysis.analysis.alignto function in trajedit.

0.8.9 (2020-03-03)

• Changed logos, PR #28

0.8.8 (2020-02-03)

• PRs: #25 #26 #27

• Added taurenmd logo for readthedocs

• Added tauranmd logo in README

• Added taurenmd repository banner

• Improved details in the documentation

• Removed .ci folder, unnecessary

0.8.7 (2020-02-02)

• PR #24

• Added PyPI downloads badge

• Improved installation instructions

• Improved and clarified contributing instructions

0.8.6 (2020-01-20)

• Restructured pip deps: install_requires only takes bioplottemplates and pyquaternion

• two extras_require: sup and md and all which consider both

0.8.5 (2020-01-20)

• PR #22

• organized dependencies for PyPI

• PyPI only dependencies are referred as install_requires

• MDAnalysis and MDTraj referred in extras_require

• OpenMM left out from pip, only available in Anaconda

0.8.4 (2020-01-19)

• PR #15

• Added simtk lib import check for controlled failure

• added error message output for user

0.8.3 (2020-01-19)

• PR #16 and #19

• corrected argparse autodoc in ReadTheDocs (mock strategy)

• improved tox configuration with better env separation

• #19 reports a communication error between TravisCI and coverage servers

0.8.2 (2020-01-17)

• Improved CI workflow * Dropped COVERALLS * Dropped Codacy * Setup test-coverage in CodeClimate * created .codeclimate.yml with explicit configuration

• updated badges

0.8.1 (2020-01-15)

• PR #14

• Corrected version display in documentation

0.8.0 (2020-01-15)

• PR #13

• Code architecture improvements

• Complete project main documentation

• Complete library documentation

• command line documented

• Code clean

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.