Calculate protein contact order in Python

Question

Protein contact order (CO) is the locality of contacts between residues. CO also correlates with the rate of protein folding. Higher contact orders indicate longer bending times, and a lower contact order has been proposed as a predictor of potential downward folding or folding of a protein that occurs without a free energy barrier.

There is a built-in web server and perl script for calculating CO here .

Is there a way to calculate CO in python?

Answer 1

, (N,3) , np.dot, , . , abs_contact_order2:

from __future__ import print_function, division

import mdtraj as md
import numpy as np
import numba as nb

@nb.njit
def abs_contact_order(xyz, atoms_residue, cutoff_nm=.6):
    """Return the absolute contact order."""
    contact_count = 0
    seq_distance_sum = 0
    cutoff_2 = cutoff_nm*cutoff_nm
    N = len(atoms_residue)
    for i in xrange(N):
        for j in xrange(N):
            seq_dist = atoms_residue[j] - atoms_residue[i]
            if seq_dist > 0:
                d = xyz[j] - xyz[i]
                if np.dot(d, d) < cutoff_2:
                    seq_distance_sum += seq_dist 
                    contact_count += 1


    if contact_count==0.:
        return 0.

    return seq_distance_sum/float(contact_count)

@nb.njit
def abs_contact_order2(xyz, atoms_residue, cutoff_nm=.6):
    """Return the absolute contact order."""
    contact_count = 0
    seq_distance_sum = 0
    cutoff_2 = cutoff_nm*cutoff_nm
    N = len(atoms_residue)
    for i in xrange(N):
        for j in xrange(N):
            seq_dist = atoms_residue[j] - atoms_residue[i]
            if seq_dist > 0:
                d = 0.0
                for k in xrange(3):
                    d += (xyz[j,k] - xyz[i,k])**2
                if d < cutoff_2:
                    seq_distance_sum += seq_dist 
                    contact_count += 1


    if contact_count==0.:
        return 0.

    return seq_distance_sum/float(contact_count)

:

%timeit abs_co = abs_contact_order(traj.xyz[0], seq_atoms, cutoff_nm=0.60)
1 loop, best of 3: 723 ms per loop

%timeit abs_co = abs_contact_order2(traj.xyz[0], seq_atoms, cutoff_nm=0.60)
10 loops, best of 3: 28.2 ms per loop

, Numba jit nopython. , , .

, Numba "" jit, . , , , Numba jit , , , , . , , , , , .

Update:

, (i, j) (j, i) :

@nb.njit
def abs_contact_order3(xyz, atoms_residue, cutoff_nm=.6):
    """Return the absolute contact order."""
    contact_count = 0
    seq_distance_sum = 0
    cutoff_2 = cutoff_nm*cutoff_nm
    N = len(atoms_residue)
    for i in xrange(N):
        for j in xrange(i+1,N):
            seq_dist = atoms_residue[j] - atoms_residue[i]
            if seq_dist > 0:
                d = 0.0
                for k in xrange(3):
                    d += (xyz[j,k] - xyz[i,k])**2
                if d < cutoff_2:
                    seq_distance_sum += 2*seq_dist 
                    contact_count += 2


    if contact_count==0.:
        return 0.

    return seq_distance_sum/float(contact_count)

:

%timeit abs_co = abs_contact_order3(traj.xyz[0], seq_atoms, cutoff_nm=0.60)
100 loops, best of 3: 15.7 ms per loop

Answer 2

, ! MDTraj, :

import numpy as np
import mdtraj as md

@jit
def abs_contact_order(xyz, atoms_residue, cutoff_nm=.6):
    """Return the absolute contact order."""
    contact_count = 0
    seq_distance_sum = 0
    cutoff_2 = cutoff_nm*cutoff_nm
    N = len(atoms_residue)
    for i in xrange(N):
        for j in xrange(N):
            seq_dist = atoms_residue[j] - atoms_residue[i]
            if seq_dist > 0:
                d = xyz[j] - xyz[i]
                if np.dot(d, d) < cutoff_2:
                    seq_distance_sum += seq_dist 
                    contact_count += 1


    if contact_count==0.:
        print("Warning, no contacts found!")
        return 0.

    print("contact_count: ", contact_count)
    print("seq_distance_sum: ", seq_distance_sum)
    return seq_distance_sum/float(contact_count)

:

traj = md.load("test.pdb")
print("Atoms: ", traj.n_atoms)
seq_atoms = np.array([a.residue.resSeq for a in traj.top.atoms], dtype=int)

abs_co = abs_contact_order(traj.xyz[0], seq_atoms, cutoff_nm=0.60)

print("Absolute Contact Order: ", abs_co)
print("Relative Contact Order: ", abs_co/traj.n_residues)

numba 16 , @jit, ~ 1 .

perl script 8

perl contactOrder.pl -r -a -c 6 test.pdb

, jupyter .