Welcome to molPX: The Molecular Projection Explorer

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The Molecular Projection Explorer, molPX, is a python module that provides interactive visualization of projected coordinates of molecular dynamics (MD) trajectories inside a Jupyter notebook.

molPX is based on the incredibly useful nglview IPython/Jupyter widget. Other libraries heavily used are mdtraj and PyEMMA. At the moment, there is also an sklearn dependency that might disappear in the future.

_images/output.gif

At the moment the API consists of two subpackages:

TL;DR: see molPX in action through the

Find more about the people behind molPX here:

Download and Install

If you can’t wait to play around with molPX, and you have the Anaconda scientifc python distribution (which we strongly recommend), the easiest way to get molPX is to issue the conda command:

>>> conda install molPX -c omnia

and jump to the Quick Start section of this document. Otherwise, check out our more exhaustive

Quick Start

Start an IPython console

>>> ipython

Import molpx and let the example notebook guide you

>>> import molpx
>>> molpx.example_notebook()

Voilà: you should be looking at a jupyter notebook explaining the basic functionality of molPX

Documentation

You can find the latest documentation online here You can build a local copy of the html documentation by navigating to the molPX installation directory and issuing:

>>> cd doc
>>> make html

This will generate molPX/docs/build/html/index.html with the html documentation. If you are missing some of the requirements for the documentation , issue:

>>> pip install -r ./source/doc_requirements.txt

If you don’t know where molPX is installed, you can find out this way:

>>> ipython
>>> import molpx
>>> molpx._molpxdir()

The output of the last command is one subdirectory of molPX’s installation directory, so just copy it and issue:

>>> cd the-output-of-the-molpx._molpxdir-command
>>> cd ..

and you are there !

Warnings

molPX is currently under heavy development and the API might change rapidly. Stay tuned.

Data Privacy Statement

When you import this Python package, some of your metadata is sent to our servers. These are:

  • molPX version
  • Python version
  • Operating System
  • Hostname/ mac address of the accessing computer
  • Time of retrieval

How to disable this feature easily:

Even before you use molPX for the first time:

  1. Create a hidden folder .molpx in your home folder
  2. Create a file conf_molpx.py inside of .molpx with the following line: report_status = False
  3. Restart your ipython/jupyter sessions

Hints:

  • You can check your report status anytime by typing this line in a (i)python terminal

    >>> import molpx
    >>> molpx._report_status()
    
  • 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

    >>> import os
    >>> os.path.expanduser('~/.molpx')
    

Known Issues

  • The installation of nglview might give a SandboxViolation error. Until we figure this out,

try to install nglview externally issuing:

>>> conda install nglview -c bioconda

or, alternatively

>>> pip install nglview
  • Note that molPX only works with nglview versions >=0.6.2.1.
  • The interplay between some modules (nglview, nbextensions, ipywidgets) might limit you to use python3.X on some platforms. Sorry about that.

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