Package: taurenmd
taurenmdA command-line interface for analysis routines of Molecular Dynamics data.Taurenmdprovides an easy, flexible and extensible,command-lineinterface 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 thenon-developerusers that lack the programming skills to perform a thorough and proficient use those libraries.But not only,taurenmdalso facilitates high throughput operations, even to those proficientdevs, because complex executions are reduced to single argument-rich command-lines that can be concatenated or aliased.Taurenmdwraps around feature-rich and powerful MD analysis libraries such asMDAnalysisandMDTraj(but not only), combining them to extract the best ofthose 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, youshouldcitetaurenmdtogether with the dependencies used, please read ourCitingpage for a detailed explanation.Though designed to perform as a command-line user-directed interface, alltaurenmd’s core functions are openly distributed and documented. Currently, there are alreadyseveral command-line interfaces available, some that perform only single tasks, while others allow complex setups, all areone-liners.With this said,taurenmdaims to be a flexible and extensible peace of software, built as simple and modular as we can think of, toagilethe incorporation of new functionalities as needed.Documentationtaurenmd’s full documentation is available at:https://taurenmd.readthedocs.io, read there:how to installusage examplescitingetc…VersioningThis project follows strictlySemantic Versioning 2.0for version control.Upon release of version 1.0.0, all additions to themasterbranch are done by PR followed by its respective version increment and release onPyPI.Upon version 0.8, and before version 1, SV2 major version increments are reflected in theminorversion number, and minor and patch increments are reflected together in thepatchversion number. Everything else follows SV2 rules, in this way users can track backwards incompatibilities if they happen.Changelogv0.11.2 (2022-07-14)Add output dir option tofext#66v0.11.1 (2022-07-14)Update badges after 0.11 #65v0.11.0 (2022-07-13)Droppedpython-bioplottemplatesupdated export statementsAdded plots totaurenmd rotationsAdded plots totaurenmd distAdded plots totaurenmd rmsfAdded plots totaurenmd rmsdtaurenmd distnow can take multiple–sel2, and all are plottedParamsToDictnow usesast.literal_evaltrajectory slice now accepts timesteps (10ns, for example)v0.10.4 (2022-01-14)update logo link in README #63v0.10.3 (2021-12-11)Improved documentation forcli_rotationsAdded illustration explaining the roll, pitch, and yaw anglesv0.10.2 (2021-12-03)Add frame timestep and whole trajectory duration toreport(#61)v0.10.1 (2021-11-24)Add support for CIF topologies in libmda using openmm.app.pdbxfileremoves the install*.yml gitactionsv0.10.0 (2021-11-24)Updates MDAnalysis to version 2.0.0Defines versions for all other dependenciesUpdates CIv0.9.9 (2021-11-22)Corrects taking/passing ofinsortargument in some clients.v0.9.8 (2021-11-22)Upgraded roll, pitch, and yaw angle calculations with torsion angle strategyRemoved usage of PyQuaternionv0.9.7 (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-skeletonUpdated README badges0.9.4 (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-ito everyCLIinterface (PR #42)majorversion change becausecli_imagemollost backwards compatibility0.8.14 (2020-05-12)Updatestox.inifile for Continuous Integration (PR #40)0.8.13 (2020-05-12)Added support for sequence of trajectories in CLIs that useMDTraj(PR #39)0.8.12 (2020-05-04)PR: #37Installs taurenmd directly with Conda env0.8.11 (2020-04-03)PR: #33Corrected command representation in .taurenmd.cwd adding quotes when needed0.8.10 (2020-04-02)PR: #32Corrects incorrect usage of MDAnalysis.analysis.alignto function intrajedit.0.8.9 (2020-03-03)Changed logos, PR #280.8.8 (2020-02-03)PRs: #25 #26 #27Added taurenmd logo for readthedocsAdded tauranmd logo in READMEAdded taurenmd repository bannerImproved details in the documentationRemoved.cifolder, unnecessary0.8.7 (2020-02-02)PR #24Added PyPI downloads badgeImproved installation instructionsImproved and clarified contributing instructions0.8.6 (2020-01-20)Restructured pip deps: install_requires only takes bioplottemplates and pyquaterniontwo extras_require:supandmdandallwhich consider both0.8.5 (2020-01-20)PR #22organized dependencies for PyPIPyPI only dependencies are referred as install_requiresMDAnalysis and MDTraj referred in extras_requireOpenMM left out from pip, only available in Anaconda0.8.4 (2020-01-19)PR #15Added simtk lib import check for controlled failureadded error message output for user0.8.3 (2020-01-19)PR #16 and #19corrected argparse autodoc in ReadTheDocs (mock strategy)improved tox configuration with better env separation#19 reports a communication error between TravisCI and coverage servers0.8.2 (2020-01-17)Improved CI workflow
* Dropped COVERALLS
* Dropped Codacy
* Setup test-coverage in CodeClimate
* created.codeclimate.ymlwith explicit configurationupdated badges0.8.1 (2020-01-15)PR #14Corrected version display in documentation0.8.0 (2020-01-15)PR #13Code architecture improvementsComplete project main documentationComplete library documentationcommand line documentedCode clean0.7.2 (2019-12-25)bridged from 0.7.1Dropped 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)implementedcli_rotations, calculates roll, pitch and yawrotation angles of selection.0.6.0 (2019-12-15)implementedcli_rmsfto calculate RMSFs.0.5.1 (skipped to 0.6.0)added sort numbered trajs tocli_trajeditadded sort numbered trajectory paths in libimprovedcli_imagemolreadabilityadded selection incli_noSol0.5.0 (2019-11-24)createdcli_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 tupleadded distance calc and plot interfacecli_distancestrajeditnow saves topology unwrapped0.4.1 (2019-11-21)renumbered version to 0.4.1. from 0.3.1RMSD Cli now calculates for several selectionsParse plot vars now registers floatscorrected fext cli entry pointadded align option to trajedittopology model writen from first frame of time slicingadded unwrap() molecule method from MDAnalysis intrajeditwith respective optionstopology output now defaults to traj name +frame0.pdbadded .myparents() to Path in__init__0.3.0 (2019-11-06)CreateddevelopbranchCreated client for frame extraction:cli_fextAdded option to disable export of frame0 topology in trajedit0.2.1 (2019-10-26)dropped py35separated lib MDAnalysis from MDTrajlibioconcerns only general functionsimprovedimagemolI/O0.2.0 (2019-10-26)addedcli_report0.1.1 (2019-10-26)corrected libiotrajectory loads based on MDAnalysis now read and concatenate multiple trajectories.0.1.0 (2019-10-26)added interfaces:
*trajedit*noSol*imagemol*rmsd*cli template0.0.0 (2019-10-15)First release on PyPI.