springcraft 0.3.0

Springcraft

Springcraft is a Biotite extension package, that allows the analysis of AtomArray objects via Elastic Network Models (ENMs). An ENM can be thought of as a system that connects residues via springs: Interaction of nearby residues is governed by a harmonic potential, with the native (input) conformation representing the energy minimum. Normal mode analysis allows the researcher to investigate global functional movements of a protein in a fast coarse-grained manner.

$ pip install springcraft

$ conda install -c conda-forge springcraft

$ git clone https://github.com/biotite-dev/springcraft.git
$ pip install ./springcraft

Example

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


pdbx_file = pdbx.PDBxFile.read("path/to/1l2y.cif")
atoms = pdbx.get_structure(pdbx_file, model=1)
ca = atoms[(atoms.atom_name == "CA") & (atoms.element == "C")]
ff = springcraft.InvariantForceField(cutoff_distance=7.0)
gnm = springcraft.GNM(ca, ff)
kirchhoff = gnm.kirchhoff

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

Output:

[[ 4. -1. -1. -1. -1.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.]
 [-1.  6. -1. -1. -1. -1.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0. -1.  0.]
 [-1. -1.  7. -1. -1. -1. -1.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0. -1.  0.]
 [-1. -1. -1.  7. -1. -1. -1. -1.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.]
 [-1. -1. -1. -1.  8. -1. -1. -1. -1.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.]
 [ 0. -1. -1. -1. -1.  9. -1. -1. -1.  0. -1.  0.  0.  0.  0.  0.  0. -1.  0.  0.]
 [ 0.  0. -1. -1. -1. -1.  8. -1. -1. -1. -1.  0.  0.  0.  0.  0.  0.  0.  0.  0.]
 [ 0.  0.  0. -1. -1. -1. -1.  7. -1. -1. -1.  0.  0.  0.  0.  0.  0.  0.  0.  0.]
 [ 0.  0.  0.  0. -1. -1. -1. -1.  7. -1. -1.  0.  0. -1.  0.  0.  0.  0.  0.  0.]
 [ 0.  0.  0.  0.  0.  0. -1. -1. -1.  7. -1. -1. -1. -1.  0.  0.  0.  0.  0.  0.]
 [ 0.  0.  0.  0.  0. -1. -1. -1. -1. -1.  8. -1. -1. -1.  0.  0.  0.  0.  0.  0.]
 [ 0.  0.  0.  0.  0.  0.  0.  0.  0. -1. -1.  7. -1. -1. -1. -1. -1.  0.  0.  0.]
 [ 0.  0.  0.  0.  0.  0.  0.  0.  0. -1. -1. -1.  5. -1. -1.  0.  0.  0.  0.  0.]
 [ 0.  0.  0.  0.  0.  0.  0.  0. -1. -1. -1. -1. -1.  7. -1. -1.  0.  0.  0.  0.]
 [ 0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0. -1. -1. -1.  4. -1.  0.  0.  0.  0.]
 [ 0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0. -1.  0. -1. -1.  5. -1. -1.  0.  0.]
 [ 0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0. -1.  0.  0.  0. -1.  4. -1. -1.  0.]
 [ 0.  0.  0.  0.  0. -1.  0.  0.  0.  0.  0.  0.  0.  0.  0. -1. -1.  5. -1. -1.]
 [ 0. -1. -1.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0. -1. -1.  5. -1.]
 [ 0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0.  0. -1. -1.  2.]]