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))