{"id":15195482,"url":"https://github.com/markovmodel/molpx","last_synced_at":"2025-10-28T01:30:44.790Z","repository":{"id":60721375,"uuid":"76460348","full_name":"markovmodel/molPX","owner":"markovmodel","description":"IPython API to visualize MD-trajectories along projected trajectories inside a Jupyter notebook","archived":false,"fork":false,"pushed_at":"2019-02-14T16:40:40.000Z","size":28876,"stargazers_count":39,"open_issues_count":12,"forks_count":2,"subscribers_count":11,"default_branch":"master","last_synced_at":"2025-02-01T10:23:45.031Z","etag":null,"topics":["free-energy","ipython-notebook","jupyter-notebook","molecular-dynamics","tica","visualization","widget"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"lgpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/markovmodel.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2016-12-14T13:05:38.000Z","updated_at":"2024-04-29T16:20:11.000Z","dependencies_parsed_at":"2022-10-03T20:00:25.054Z","dependency_job_id":null,"html_url":"https://github.com/markovmodel/molPX","commit_stats":null,"previous_names":[],"tags_count":22,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markovmodel%2FmolPX","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markovmodel%2FmolPX/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markovmodel%2FmolPX/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markovmodel%2FmolPX/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/markovmodel","download_url":"https://codeload.github.com/markovmodel/molPX/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":238579176,"owners_count":19495510,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["free-energy","ipython-notebook","jupyter-notebook","molecular-dynamics","tica","visualization","widget"],"created_at":"2024-09-27T23:40:17.396Z","updated_at":"2025-10-28T01:30:38.785Z","avatar_url":"https://github.com/markovmodel.png","language":"Python","readme":"###################################################\nWelcome to molPX: The Molecular Projection Explorer\n###################################################\n|DOI| |travis_build| |appveyor_build| |coverage| |docs_build|\n\nThe Molecular Projection Explorer, molPX, is a python module that provides **interactive visualization of\nprojected coordinates of molecular dynamics (MD) trajectories** inside a `Jupyter notebook \u003chttp://jupyter.org/\u003e`_.\n\nmolPX is based on the incredibly useful  `nglview IPython/Jupyter widget \u003chttps://github.com/arose/nglview\u003e`_.\nOther libraries heavily used are  `mdtraj \u003chttp://mdtraj.org/\u003e`_ and `PyEMMA \u003chttp://www.emma-project.org/latest/\u003e`_.\nAt the moment, there is also an `sklearn \u003chttp://scikit-learn.org/stable/index.html\u003e`_ dependency that might disappear in the future.\n\n.. image:: ../images/output.gif\n   :align: center\n\nAt the moment the API consists of two subpackages:\n\n* :doc:`molpx.visualize \u003c/index_visualize\u003e`\n* :doc:`molpx.generate  \u003cindex_generate\u003e`\n\n**TL;DR**: see molPX in action through the\n\n* :doc:`Example Jupyter Notebooks \u003c/index_notebooks\u003e`\n\nFind more about the people behind molPX here:\n\n* :doc:`About \u0026 YouTube Introduction \u003c/about\u003e`\n\nDownload and Install\n=====================\n\nIf you can't wait to play around with molPX, and you have the `Anaconda scientifc python distribution\n\u003chttps://www.continuum.io/downloads\u003e`_ (which we strongly recommend), the easiest way to get molPX is to issue\nthe `conda command \u003chttps://conda.io/docs/intro.html\u003e`_:\n\n   \u003e\u003e\u003e conda install molpx -c conda-forge\n\nand jump to the Quick Start section of this document. Otherwise, check out our more exhaustive\n\n* :doc:`Installation Guide \u003c/INSTALL\u003e`\n\n\n\nQuick Start\n=============\n\nStart an ``IPython`` console\n\n    \u003e\u003e\u003e ipython\n\nImport ``molpx`` and let the example notebooks guide you\n\n    \u003e\u003e\u003e import molpx\n    \u003e\u003e\u003e molpx.example_notebooks()\n\nVoilà: you should be looking at a list of jupyter notebooks explaining the basic functionality of molPX\n\nDocumentation\n==============\n\nYou can find the latest documentation online `here \u003chttps://molpx.readthedocs.io/\u003e`_\nYou can build a local copy of the html documentation by navigating to the molPX installation\ndirectory and issuing:\n\n    \u003e\u003e\u003e cd doc\n    \u003e\u003e\u003e make html\n\nThis will generate `molPX/docs/build/html/index.html` with the html documentation. If you are missing some of\nthe requirements for the documentation , issue:\n\n    \u003e\u003e\u003e pip install -r ./source/doc_requirements.txt\n\nIf you don't know where molPX is installed, you can find out this way:\n\n    \u003e\u003e\u003e ipython\n    \u003e\u003e\u003e import molpx\n    \u003e\u003e\u003e molpx._molpxdir()\n\nThe output of the last command is one subdirectory of molPX's installation directory, so just copy it and issue:\n\n    \u003e\u003e\u003e cd the-output-of-the-molpx._molpxdir-command\n    \u003e\u003e\u003e cd ..\n\nand you are there !\n\nWarnings\n=========\n\nmolPX is currently under heavy development and the API might change rapidly. Stay tuned.\n\nData Privacy Statement\n======================\n\nWhen you import this Python package, some of your metadata is sent to our servers. These are:\n\n * molPX version\n * Python version\n * Operating System\n * Hostname/ mac address of the accessing computer\n * Time of retrieval\n\nHow to disable this feature easily:\n-----------------------------------\n\nEven before you use molPX for the first time:\n\n 1. Create a hidden folder `.molpx` in your home folder\n 2. Create a file `conf_molpx.py` inside of `.molpx` with the following line:\n    `report_status = False`\n 3. Restart your ipython/jupyter sessions\n\nHints:\n\n* This is most easily realized from terminal by issuing:\n\n        \u003e\u003e\u003e mkdir ~/.molpx\n        \u003e\u003e\u003e echo \"report_status = False\" \u003e\u003e ~/.molpx/conf_molpx.py\n\n* You can check your report status anytime by typing this line in a (i)python terminal\n\n        \u003e\u003e\u003e import molpx\n        \u003e\u003e\u003e molpx._report_status()\n\n* If you don't know where your home folder is (for whatever reason), you can find it out by typing in a (i)python terminal\n\n        \u003e\u003e\u003e import os\n        \u003e\u003e\u003e os.path.expanduser('~/.molpx')\n\n.. |DOI| image::\n   https://zenodo.org/badge/76460348.svg\n   :target: https://zenodo.org/badge/latestdoi/76460348\n   :height: 20\n   :alt: DOI\n\n.. |travis_build| image::\n   https://travis-ci.org/markovmodel/molPX.svg?branch=master\n   :height: 10\n   :target: https://travis-ci.org/markovmodel/molPX\n   :alt: Travis build status\n\n.. |appveyor_build| image::\n   https://ci.appveyor.com/api/projects/status/396ej39s3fewhwy9/branch/master?svg=true\n   :height: 10\n   :target: https://ci.appveyor.com/project/gph82/molpx\n   :alt: Appveyor build status\n\n.. |coverage| image::\n   https://codecov.io/gh/markovmodel/molPX/branch/master/graph/badge.svg\n   :height: 20\n   :target: https://codecov.io/gh/markovmodel/molPX\n   :alt: Codecov\n\n.. |docs_build| image::\n   https://readthedocs.org/projects/molpx/badge/?version=latest\n   :alt: Documentation Status\n   :height: 20\n   :target: http://molpx.readthedocs.io/en/latest/?badge=latest\n   \n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarkovmodel%2Fmolpx","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmarkovmodel%2Fmolpx","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarkovmodel%2Fmolpx/lists"}