springcraft 0.1.0

Investigate molecular dynamics with elastic network models

Springcraft

The project in the CBS Hackathon to compute Elastic Network Models with Biotite.

Installation

All packages required for the development (including tests) are installed via

$ conda env create -f environment.yml

if Conda installed. The package is installed for development via

$ pip install -e .

This command requires a recent pip version.

Example

import biotite.structure.io.mmtf as mmtf
import springcraft
import numpy as np


mmtf_file = mmtf.MMTFFile.read("path/to/1l2y.mmtf")
atoms = mmtf.get_structure(mmtf_file, model=1)
ca = atoms[(atoms.atom_name == "CA") & (atoms.element == "C")]
ff = springcraft.InvariantForceField()
hessian, pairs = springcraft.compute_hessian(ca.coord, ff, 7.0)

np.set_printoptions(linewidth=100)
print(hessian)