This repo is a fork from https://github.com/arose/mdsrv, mostly to be used with pytraj.

Install

git clone https://github.com/Amber-MD/mdsrv
cd mdsrv
python setup.py install

# or do the shortcut without git cloning
pip install git+https://github.com/Amber-MD/mdsrv

# AMBER users
amber.pip install git+https://github.com/Amber-MD/mdsrv --prefix=$AMBERHOME

Require

• pytraj
• A modern web browser
• flask

Usage

In your shell terminal

mdsrv my.parm7 my.nc

How does the UI look like? http://arose.github.io/ngl/

Interested in using NGL in Jupyter notebook? Please visit https://github.com/arose/nglview

Original README.md

MDsrv is a simple server that enables remote access to coordinate trajectories from molecular dynamics simulations. It can be used together with the NGL Viewer (http://github.com/arose/ngl) to interactively view trajectories of molecular complexes in a web-browser, either within a local network or from anywhere over the internet.

Formats supported are:

• xtc/trr
• nc, netcdf
• dcd

Thanks to code from MDAnalysis (http://www.mdanalysis.org/) there is random access to xtc/trr trajectory files via indexing and seeking capabilities added to the libxdrfile2 library.

Table of contents

• Installation
• Running
• [RESTful API](#restful api)
• Deployment
• Changelog
• License

Installation

From PyPI:

pip install mdsrv

Configuration file

Optional. Copy/rename the sample app.cfg file. It allows e.g. setting data_dir data directories that will be accessible through the web server and to define access restrictions.

Running

The mdsrv command starts a local server and opens a browser window with the web application.

To use a custom configuration file

mdsrv --cfg my_conf.cfg

Load a topology and trajectory at startup

mdsrv struc.gro traj.xtc

RESTful API

The RESTful API is the interface through which the web application gets all data but it may be also used to access the served trajectory data from other applications.

File content

To retrieve a file from data_dir <root> with file path <filename> call:

/file/<root>/<filename>

Directory content description

To get a JSON description of available data_dir directories call:

/dir/

To get a JSON description of the directory content in data_dir <root> call:

/dir/<root>/

To get a JSON description of the directory content in data_dir <root> at path <path> call:

/dir/<root>/<path>

The JSON description is a list of file or sub-directory entries:

[
    {
        "name": "name of sub-directory",
        "path": "path relative to `<root>`",
        "dir": "`true` if entry is a directory",
        "restricted": "`true` if access is restricted"
    },
    {
        "name": "name of the file",
        "path": "path relative to `<root>`",
        "size": "file size in bytes"
    },
    {
        ...
    }
]

Frame count

To get the number of frames the trajectory in data_dir <root> with file path <filename> has call:

/traj/numframes/<root>/<filename>

Frame coordinates

To get the coordinates of frame number <frame> of the trajectory in data_dir <root> with file path <filename> call:

/traj/frame/<frame>/<root>/<filename>

The set of atoms for which coordinates should be returned can be restricted by POSTing an atomIndices parameter with the following format. A list of index ranges is defined by pairs of integers separated by semi-colons (;) where the two integers within a pair are separated by a comma (,). To select atoms with indices (starting at zero) 5 to 10 and 22 to 30 send:

5,10;22,30

The coordinate frame is returned in binary format and also contains the frame number, the simulation time (when available) and the box vectors.

Offset	Size	Type	Description
0	4	int	frame number
4	4	float	simulation time
8	4	float	X coordinate of box vector A
12	4	float	Y
16	4	float	Z
20	4	float	X coordinate of box vector B
24	4	float	Y
28	4	float	Z
32	4	float	X coordinate of box vector C
36	4	float	Y
40	4	float	Z
44	4	float	X coordinate of first atom
48	4	float	Y
52	4	float	Z
...	...	...	...

Deployment

The Apache Webserver can used to run the server via mod_wsgi. First make sure you have everything required installed:

sudo apt-get install git apache2 libapache2-mod-wsgi

Then you need to create a wsgi configuration file to be referenced in the Apache configuration. There is an example named mdsrv.wsgi.sample in the root directory of this package. Also, a snippet showing how the configuration for Apache should look like can be found in the apache.config.sample file.

Finally, to restart apache issue

sudo /etc/init.d/apache2 restart

Changelog

Version 0.2

• DOC: described arguments of the comand line tool
• ADD: --host and --port arguments

Version 0.1.1

Initial release

License

Generally MIT, see the LICENSE file for details.