Pairwise distance matrix

In this tutorial, we learn how to obtain pairwise distance matrix using protstruc.

In [1]:

import protstruc as ps
import matplotlib.pyplot as plt

from protstruc.general import ATOM, AA
from biopandas.pdb import PandasPdb

import protstruc as ps import matplotlib.pyplot as plt from protstruc.general import ATOM, AA from biopandas.pdb import PandasPdb

Initialize a StructureBatch instance from a PDB IDs.

In [2]:

pdb_ids = ['1REX', '4EOT']
sb = ps.StructureBatch.from_pdb_id(pdb_ids)
distmat, distmat_mask = sb.pairwise_distance_matrix()

distmat.shape

pdb_ids = ['1REX', '4EOT'] sb = ps.StructureBatch.from_pdb_id(pdb_ids) distmat, distmat_mask = sb.pairwise_distance_matrix() distmat.shape

Out[2]:

torch.Size([2, 184, 184, 15, 15])

Compute total number of residues for each protein.

In [3]:

total_lengths = sb.get_total_lengths()
total_lengths

total_lengths = sb.get_total_lengths() total_lengths

Out[3]:

tensor([130, 184])

Pairwise distance matrix between Ca atoms¶

Note that 4EOT has 2 chains, so the pairwise distance matrix shows horizontal and vertical split.

In [4]:

fig = plt.figure(figsize=(6, 3))

for i in range(2):
    pdist, mask = distmat[i, :, :, ATOM.CA, ATOM.CA], distmat_mask[i, :, :, ATOM.CA, ATOM.CA]
    total_length = total_lengths[i]

    ax = fig.add_subplot(1, 2, i+1)
    ax.matshow(pdist[:total_length, :total_length])
    ax.set_title(pdb_ids[i])

fig = plt.figure(figsize=(6, 3)) for i in range(2): pdist, mask = distmat[i, :, :, ATOM.CA, ATOM.CA], distmat_mask[i, :, :, ATOM.CA, ATOM.CA] total_length = total_lengths[i] ax = fig.add_subplot(1, 2, i+1) ax.matshow(pdist[:total_length, :total_length]) ax.set_title(pdb_ids[i])

Pairwise distance matrix between Cb atoms¶

Note that glycine residue does not have $C_{\beta}$ atom and thus the distance from/to glycine residue is not defined.

In [5]:

fig = plt.figure(figsize=(6, 3))

for i in range(2):
    pdist, mask = distmat[i, :, :, ATOM.CB, ATOM.CB], distmat_mask[i, :, :, ATOM.CB, ATOM.CB]
    total_length = total_lengths[i]

    ax = fig.add_subplot(1, 2, i+1)
    ax.matshow(pdist[:total_length, :total_length])

    ax.set_title(pdb_ids[i])

fig = plt.figure(figsize=(6, 3)) for i in range(2): pdist, mask = distmat[i, :, :, ATOM.CB, ATOM.CB], distmat_mask[i, :, :, ATOM.CB, ATOM.CB] total_length = total_lengths[i] ax = fig.add_subplot(1, 2, i+1) ax.matshow(pdist[:total_length, :total_length]) ax.set_title(pdb_ids[i])