vmd-python

Installable VMD as a python module

Features

All features of VMD from the 1.9.3 release, plus some optional plugins not included in binary distributions:

Read and write insertion codes in MAE files
DMS plugin for DESRES molecular file format
HOOMD plugin
Doesn't care which numpy you compile against
Support for Python 2 or Python 3

Installation

Simple binary installation with conda (currently linux-x86_64 only)

conda install -c https://conda.anaconda.org/rbetz vmd-python

Building from source

If there is no binary available for your system, you'll have to build vmd-python either with pip or setuptools. Please report any issues you have with this process, as it's still under heavy development. I am especially interested in bug reports for OSX!

First, make sure you have the following dependencies installed somehow and visible to the compiler and linker:

* netcdf >= 4.3 (on OSX: `brew install netcdf`)
* numpy
* python 2.7 or 3.6

Easy installation with pip:

pip install -i https://pypi.anaconda.org/rbetz/simple vmd-python

For the latest version:

git clone https://github.com/Eigenstate/vmd-python.git
cd vmd-python
python setup.py build
python setup.py install

Installation can take a while since it compiles VMD from source.

For Mac users

Homebrew is an easy way to get vmd-python's dependencies. brew install netcdf is the main one.

I do not have a Mac or reliable access to one. If you are sending an issue related to build errors on OSX, please be aware that I have limited ability to debug them.

I am looking for someone to contribute binaries built on osx 32 and 64 bit. Please let me know if you are willing to do this and save all the other Mac users some build time.

Included modules

The following sub-modules are part of VMD. The import system makes more sense now, so standard importing like from vmd import atomsel will work correctly.

Some of these modules don't make much sense without the graphical display window. I don't currently distribute a VMD binary with Python built in, but you can look at my build scripts and compile your own, or use the available ones from the official developers.

The following python modules are part of vmd-python. Some of these are currently not documented on the website (indicated with *).

animate
axes
atomsel (atom selection language)
color
display
evaltcl (run all your old tcl scripts)
graphics
imd
label
material
measure*
molecule (read and write all kinds of molecules)
molrep
mouse* (of limited utility in the command line...)
render
trans
topology*
vmdmenu*
vmdnumpy (very very useful!)

There are also some object oriented classes that provide a higher-level interface to the sub-modules above. Note these are case sensitive!!

Label
Material
Molecule

Usage

Here's a very simple example of using the VMD-python API to calculate the root-mean-square- fluctuation of all tyrosine residues in a loaded trajectory molid relative to some average structure molid_avg:

from vmd import molecule, vmdnumpy
import numpy as np
mask = vmdnumpy.atomselect(molid_avg, 0, "resname TYR")
ref = np.compress(mask, vmdnumpy.timestep(molid_avg, 0), axis=0)

rmsf = np.zeros(len(ref))
for frame in range(molecule.numframes(molid)):
    frame = np.compress(mask, vmdnumpy.timestep(molid, f), axis=0)
    rmsf += np.sqrt(np.sum((frame-ref)**2, axis=1))
rmsf /= float(molecule.numframes(molid)-minframe)
rmsf = np.sqrt(rmsf)

Please refer to the documentation for description of all functions. Also note that the built in help() command in Python may sometimes give you more up-to-date information than the website.

Warnings

Don't confuse the Molecule and the molecule modules. Molecule is part of the high-level Python interface, and can be pickled and have different representations. It's a class. However molecule is a module that allows loading and saving of molecules while tracking them by an integer index.

Licensing

This software is classified as a "derivative work" of the original Visual Molecular Dynamics software. It uses the main VMD source code and Python compilation options as well as code I have written for simple compilation and installation, as well as several patches I have applied.

As such, this is a MODIFIED VERSION of VMD and is not the original software distributed by Illinois.

"This software includes code developed by the Theoretical and Computational Biophysics Group at the Beckman Institute for Advanced Science and Technology at the University of Illinois at Urbana-Champaign."

Official VMD web page: http://www.ks.uiuc.edu/Research/vmd

ismaelresp/vmd-python