import sys
from shared import timeit
from chemfiles import Selection, Trajectory
def distance(f):
ai = Selection("resid 50").evaluate(f)
bi = Selection("resid 60").evaluate(f)
min_dist = float("inf")
for i in ai:
for j in bi:
d = f.distance(i, j)
if d < min_dist:
min_dist = d
pdbfile = sys.argv[1]
repeats = int(sys.argv[2])
f = Trajectory(pdbfile).read()
print(timeit(distance, f, repeats=repeats))
import sys
from shared import timeit
import MDAnalysis as mda
from MDAnalysis.analysis.dihedrals import Ramachandran
def ramachandran(u):
Ramachandran(u.select_atoms("protein")).run()
pdbfile = sys.argv[1]
repeats = int(sys.argv[2])
u = mda.Universe(pdbfile)
print(timeit(ramachandran, u, repeats=repeats))
import sys
from shared import timeit
from chemfiles import Trajectory
def parse(filepath):
t = Trajectory(filepath)
for _ in range(t.nsteps):
t.read()
pdbfile = sys.argv[1]
repeats = int(sys.argv[2])
print(timeit(parse, pdbfile, repeats=repeats))
import sys
from shared import timeit
import mdtraj as md
def count(traj):
return sum(1 for r in traj.topology.residues if r.name == "ALA")
pdbfile = sys.argv[1]
repeats = int(sys.argv[2])
traj = md.load(pdbfile)
print(timeit(count, traj, repeats=repeats))
import sys
from shared import timeit
import mdtraj as md
def distance(traj):
da, _ = md.compute_contacts(traj, [(49, 59)], scheme="closest")
return da.min()
pdbfile = sys.argv[1]
repeats = int(sys.argv[2])
traj = md.load(pdbfile)
print(timeit(distance, traj, repeats=repeats))
import sys
from shared import timeit
from chemfiles import Selection, Trajectory
def count(f):
len(Selection("resname ALA and name CA").evaluate(f))
pdbfile = sys.argv[1]
repeats = int(sys.argv[2])
f = Trajectory(pdbfile).read()
print(timeit(count, f, repeats=repeats))
import sys
from shared import timeit
import numpy as np
import mdtraj as md
from mdtraj.geometry.dihedral import indices_phi, indices_psi
def ramachandran(traj):
md.compute_phi(traj)
md.compute_psi(traj)
pdbfile = sys.argv[1]
repeats = int(sys.argv[2])
traj = md.load(pdbfile)
print(timeit(ramachandran, traj, repeats=repeats))
