tools-only 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')
chain = structure[0]['A']
atom1 = chain[100]['CA']
atom2 = chain[200]['CA']
# Direct subtraction gives distance
distance = atom1 - atom2
print(f'Distance: {distance:.2f} Angstroms')
# Or use numpy
import numpy as np
distance = np.linalg.norm(atom1.coord - atom2.coord)
Distance Matrix
import numpy as np
from Bio.PDB import PDBParser
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
ca_atoms = [r['CA'] for r in structure.get_residues() if r.has_id('CA') and r.id[0] == ' ']
n = len(ca_atoms)
dist_matrix = np.zeros((n, n))
for i in range(n):
for j in range(i + 1, n):
dist = ca_atoms[i] - ca_atoms[j]
dist_matrix[i, j] = dist
dist_matrix[j, i] = dist
print(f'Distance matrix shape: {dist_matrix.shape}')
Angle Between Three Atoms
from Bio.PDB import PDBParser, calc_angle
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
residue = structure[0]['A'][100]
n = residue['N']
ca = residue['CA']
c = residue['C']
# calc_angle takes Vector objects (atom.coord returns array, use atom.get_vector())
angle_rad = calc_angle(n.get_vector(), ca.get_vector(), c.get_vector())
angle_deg = np.degrees(angle_rad)
print(f'N-CA-C angle: {angle_deg:.1f} degrees')
Dihedral Angles
from Bio.PDB import PDBParser, calc_dihedral
import numpy as np
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
chain = structure[0]['A']
# Calculate phi angle (C-N-CA-C)
res_prev = chain[99]
res_curr = chain[100]
phi = calc_dihedral(
res_prev['C'].get_vector(),
res_curr['N'].get_vector(),
res_curr['CA'].get_vector(),
res_curr['C'].get_vector()
)
print(f'Phi: {np.degrees(phi):.1f} degrees')
# Calculate psi angle (N-CA-C-N)
res_next = chain[101]
psi = calc_dihedral(
res_curr['N'].get_vector(),
res_curr['CA'].get_vector(),
res_curr['C'].get_vector(),
res_next['N'].get_vector()
)
print(f'Psi: {np.degrees(psi):.1f} degrees')
Ramachandran Angles for All Residues
from Bio.PDB import PDBParser, PPBuilder, calc_dihedral
import numpy as np
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
ppb = PPBuilder()
phi_psi = []
for pp in ppb.build_peptides(structure):
angles = pp.get_phi_psi_list()
for residue, (phi, psi) in zip(pp, angles):
if phi is not None and psi is not None:
phi_psi.append((residue.resname, np.degrees(phi), np.degrees(psi)))
for name, phi, psi in phi_psi[:10]:
print(f'{name}: phi={phi:.1f}, psi={psi:.1f}')
Finding Neighbor Atoms
from Bio.PDB import PDBParser, NeighborSearch
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# Build search tree from all atoms
all_atoms = list(structure.get_atoms())
ns = NeighborSearch(all_atoms)
# Find atoms within radius of a point
center = structure[0]['A'][100]['CA'].coord
radius = 5.0 # Angstroms
neighbors = ns.search(center, radius)
print(f'Found {len(neighbors)} atoms within {radius}A')
# Find atoms within radius of another atom
ca_atom = structure[0]['A'][100]['CA']
neighbors = ns.search(ca_atom.coord, 5.0)
Finding Residue Contacts
from Bio.PDB import PDBParser, NeighborSearch
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
all_atoms = list(structure.get_atoms())
ns = NeighborSearch(all_atoms)
# Find all atom pairs within distance
contact_distance = 4.0
contacts = ns.search_all(contact_distance, level='R') # R = residue level
print(f'Found {len(contacts)} residue contacts within {contact_distance}A')
for res1, res2 in contacts[:10]:
print(f' {res1.resname}{res1.id[1]} - {res2.resname}{res2.id[1]}')
Contact Levels
from Bio.PDB import NeighborSearch
# search_all returns pairs at specified level
# Level codes: A=atom, R=residue, C=chain, M=model, S=structure
atom_contacts = ns.search_all(4.0, level='A') # Atom pairs
residue_contacts = ns.search_all(4.0, level='R') # Residue pairs
chain_contacts = ns.search_all(10.0, level='C') # Chain pairs
Superimposing Structures
from Bio.PDB import PDBParser, Superimposer
parser = PDBParser(QUIET=True)
ref_structure = parser.get_structure('ref', 'reference.pdb')
mobile_structure = parser.get_structure('mobile', 'mobile.pdb')
# Get CA atoms from both structures
ref_atoms = [r['CA'] for r in ref_structure.get_residues() if r.has_id('CA') and r.id[0] == ' ']
mobile_atoms = [r['CA'] for r in mobile_structure.get_residues() if r.has_id('CA') and r.id[0] == ' ']
# Ensure same number of atoms
n = min(len(ref_atoms), len(mobile_atoms))
ref_atoms = ref_atoms[:n]
mobile_atoms = mobile_atoms[:n]
# Superimpose
sup = Superimposer()
sup.set_atoms(ref_atoms, mobile_atoms)
print(f'RMSD before: {sup.rms:.2f} Angstroms')
# Apply transformation to all atoms in mobile structure
sup.apply(mobile_structure.get_atoms())
Calculating RMSD
from Bio.PDB import PDBParser, Superimposer
import numpy as np
parser = PDBParser(QUIET=True)
struct1 = parser.get_structure('s1', 'structure1.pdb')
struct2 = parser.get_structure('s2', 'structure2.pdb')
atoms1 = [r['CA'] for r in struct1.get_residues() if r.has_id('CA') and r.id[0] == ' ']
atoms2 = [r['CA'] for r in struct2.get_residues() if r.has_id('CA') and r.id[0] == ' ']
# Using Superimposer (with alignment)
sup = Superimposer()
sup.set_atoms(atoms1, atoms2)
rmsd_aligned = sup.rms
print(f'RMSD (aligned): {rmsd_aligned:.2f} A')
# Raw RMSD (no alignment)
coords1 = np.array([a.coord for a in atoms1])
coords2 = np.array([a.coord for a in atoms2])
rmsd_raw = np.sqrt(np.mean(np.sum((coords1 - coords2) ** 2, axis=1)))
print(f'RMSD (raw): {rmsd_raw:.2f} A')
CEAligner for Dissimilar Structures
from Bio.PDB import PDBParser, CEAligner
parser = PDBParser(QUIET=True)
ref = parser.get_structure('ref', 'reference.pdb')
mobile = parser.get_structure('mobile', 'query.pdb')
# CE alignment works for structures with different sequences
aligner = CEAligner()
aligner.set_reference(ref)
aligner.align(mobile)
print(f'RMSD: {aligner.rms:.2f} A')
# CEAligner automatically modifies mobile structure coordinates
Center of Mass
from Bio.PDB import PDBParser
import numpy as np
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# Unweighted center (geometric center)
coords = np.array([a.coord for a in structure.get_atoms()])
center = coords.mean(axis=0)
print(f'Geometric center: {center}')
# Mass-weighted center (approximate - uses atom count)
# For accurate mass-weighted, use element masses
atoms = list(structure.get_atoms())
masses = {'C': 12.0, 'N': 14.0, 'O': 16.0, 'S': 32.0, 'H': 1.0}
total_mass = 0
weighted_sum = np.zeros(3)
for atom in atoms:
mass = masses.get(atom.element, 12.0)
weighted_sum += mass * atom.coord
total_mass += mass
center_of_mass = weighted_sum / total_mass
print(f'Center of mass: {center_of_mass}')
Radius of Gyration
import numpy as np
from Bio.PDB import PDBParser
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
coords = np.array([a.coord for a in structure.get_atoms()])
center = coords.mean(axis=0)
# Radius of gyration
rg = np.sqrt(np.mean(np.sum((coords - center) ** 2, axis=1)))
print(f'Radius of gyration: {rg:.2f} A')
Finding Surface Residues
from Bio.PDB import PDBParser, NeighborSearch
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# Simple approach: residues with few neighbors
all_atoms = list(structure.get_atoms())
ns = NeighborSearch(all_atoms)
surface_residues = []
for residue in structure.get_residues():
if residue.id[0] != ' ':
continue
if not residue.has_id('CA'):
continue
ca = residue['CA']
neighbors = ns.search(ca.coord, 10.0, level='R')
if len(neighbors) < 15: # Threshold for surface
surface_residues.append(residue)
print(f'Surface residues: {len(surface_residues)}')
Vector Operations
from Bio.PDB import PDBParser
from Bio.PDB.vectors import Vector, rotaxis
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# Get vectors from atoms
atom1 = structure[0]['A'][100]['CA']
atom2 = structure[0]['A'][101]['CA']
v1 = atom1.get_vector()
v2 = atom2.get_vector()
# Vector operations
diff = v2 - v1
print(f'Distance vector: {diff}')
print(f'Length: {diff.norm():.2f}')
# Normalize
unit = diff.normalized()
# Cross product
cross = v1 ** v2
# Dot product
dot = v1 * v2
Chi Angles (Sidechain Dihedrals)
from Bio.PDB import PDBParser, calc_dihedral
import numpy as np
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# Chi1 angle for a residue (N-CA-CB-CG)
residue = structure[0]['A'][100]
if residue.has_id('CB') and residue.has_id('CG'):
chi1 = calc_dihedral(
residue['N'].get_vector(),
residue['CA'].get_vector(),
residue['CB'].get_vector(),
residue['CG'].get_vector()
)
print(f'Chi1: {np.degrees(chi1):.1f} degrees')
Solvent Accessible Surface Area (SASA)
from Bio.PDB import PDBParser
from Bio.PDB.SASA import ShrakeRupley
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# Calculate SASA using Shrake-Rupley algorithm
sr = ShrakeRupley()
sr.compute(structure, level='S') # S=structure, M=model, C=chain, R=residue, A=atom
# Access total SASA
print(f'Total SASA: {structure.sasa:.2f} A^2')
# Access per-residue SASA
for residue in structure.get_residues():
if hasattr(residue, 'sasa'):
print(f'{residue.resname}{residue.id[1]}: {residue.sasa:.2f} A^2')
SASA with Custom Parameters
from Bio.PDB import PDBParser
from Bio.PDB.SASA import ShrakeRupley
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
# Higher precision (more points = slower but more accurate)
sr = ShrakeRupley(probe_radius=1.4, n_points=960)
sr.compute(structure, level='R')
# Per-atom SASA
for atom in structure.get_atoms():
print(f'{atom.name}: {atom.sasa:.2f} A^2')
Identifying Buried vs Exposed Residues
from Bio.PDB import PDBParser
from Bio.PDB.SASA import ShrakeRupley
parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')
sr = ShrakeRupley()
sr.compute(structure, level='R')
buried = []
exposed = []
for residue in structure.get_residues():
if residue.id[0] != ' ':
continue
if hasattr(residue, 'sasa'):
if residue.sasa < 10.0: # Threshold in A^2
buried.append(residue)
else:
exposed.append(residue)
print(f'Buried: {len(buried)}, Exposed: {len(exposed)}')
Related Skills
- structure-io - Parse and write structure files
- structure-navigation - Access chains, residues, atoms
- structure-modification - Transform coordinates, modify structures
- alignment/pairwise-alignment - Sequence alignment for structure comparison