Geometric Analysis

Measure distances, angles, and dihedrals. Superimpose structures and calculate RMSD. Find neighbor atoms and contacts.

Required Imports

from Bio.PDB import PDBParser, NeighborSearch, Superimposer
from Bio.PDB import calc_angle, calc_dihedral
import numpy as np

Distance Between Atoms

from Bio.PDB import PDBParser

parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')