NMA

Install

$ git clone git@github.com:cxhernandez/nma.git && cd nma
$ python setup.py install

Usage

# Imports
import mdtraj as md
from nma import ANMA

# Load structure of choice (e.g. Water)
pdb = md.load_pdb('./examples/water.pdb')

# Initialize ANMA object
anma = ANMA(mode=0, rmsd=0.06, n_steps=50, selection='all')

# Transform the PDB into a short trajectory of a given mode
anma_traj = anma.fit_transform(pdb)

Mode 0	Mode 1	Mode 2

Complaints

Post to the issue tracker.

Shout-outs

• ProDy (for loose inspiration)