A command-line interface for analysis routines in Molecular Dynamics data.
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.
taurenmd’s full documentation is available at: https://taurenmd.readthedocs.io, read there:
how to install
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.
Add output dir option to fext #66
Update badges after 0.11 #65
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)
update logo link in README #63
Improved documentation for cli_rotations
Added illustration explaining the roll, pitch, and yaw angles
Add frame timestep and whole trajectory duration to report (#61)
Add support for CIF topologies in libmda using openmm.app.pdbxfile
removes the install*.yml gitactions
Updates MDAnalysis to version 2.0.0
Defines versions for all other dependencies
Corrects taking/passing of insort argument in some clients.
Upgraded roll, pitch, and yaw angle calculations with torsion angle strategy
Removed usage of PyQuaternion
improved trajectory report (#54)
Remove README badge for build: not needed.
Added some comments in the workflow files.
no changes in code, only CI.
Upgraded CI to Github Actions according to: https://github.com/joaomcteixeira/python-project-skeleton
Updated README badges
Updates documentation with JOSS citation (PR #49)
Improves CONTRIBUTION.rst guidelines (PR #46)
Client progression is now represented by a progress bar (PR #44)
Improves log in .taurenmd.cmd (PR #43)
Adds -i to every CLI interface (PR #42)
major version change because cli_imagemol lost backwards compatibility
Updates tox.ini file for Continuous Integration (PR #40)
Added support for sequence of trajectories in CLIs that use MDTraj (PR #39)
Installs taurenmd directly with Conda env
Corrected command representation in .taurenmd.cwd adding quotes when needed
Corrects incorrect usage of MDAnalysis.analysis.alignto function in trajedit.
Changed logos, PR #28
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
Added PyPI downloads badge
Improved installation instructions
Improved and clarified contributing instructions
Restructured pip deps: install_requires only takes bioplottemplates and pyquaternion
two extras_require: sup and md and all which consider both
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
Added simtk lib import check for controlled failure
added error message output for user
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
Improved CI workflow * Dropped COVERALLS * Dropped Codacy * Setup test-coverage in CodeClimate * created .codeclimate.yml with explicit configuration
Corrected version display in documentation
Code architecture improvements
Complete project main documentation
Complete library documentation
command line documented
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.
- implemented cli_rotations, calculates roll, pitch and yaw
rotation angles of selection.
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
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
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__
Created develop branch
Created client for frame extraction: cli_fext
Added option to disable export of frame0 topology in trajedit
separated lib MDAnalysis from MDTraj
libio concerns only general functions
improved imagemol I/O
trajectory loads based on MDAnalysis now read and concatenate multiple trajectories.
added interfaces: * trajedit * noSol * imagemol * rmsd * cli template
First release on PyPI.
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