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##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Tim Moore
# Contributors:
#
# MDTraj is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 2.1
# of the License, or (at your option) any later version.
#
# This library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with MDTraj. If not, see <http://www.gnu.org/licenses/>.
##############################################################################
import numpy as np
from mdtraj import load
from mdtraj.testing import eq
def test_load(get_fn):
t = load(get_fn("test_hoomdxml.dcd"), top=get_fn("well-mixed.hoomdxml"))
top = load(get_fn("well-mixed.hoomdxml")).topology
eq(t.topology, top)
eq(top.n_atoms, 6600)
eq(top.n_bonds, 3200)
eq(top.n_chains, 4000)
eq(top.n_chains, top.n_residues) # hoomdxml makes each chain 1 residue
def test_load_no_chains(get_fn):
top = load(get_fn("no_chains.hoomdxml")).topology
eq(top.n_atoms, 3)
eq(top.n_bonds, 0)
eq(top.n_chains, top.n_atoms)
eq(top.n_chains, top.n_residues)
def test_load_no_ions(get_fn):
top = load(get_fn("no_ions.hoomdxml")).topology
eq(top.n_atoms, 1296)
eq(top.n_bonds, 1152)
eq(top.n_chains, 144)
eq(top.n_chains, top.n_residues)
for bond in top.bonds: # atoms bonded to adjacent atoms by index
eq(bond[1].index - bond[0].index, 1)
def test_correct_ordering(get_fn):
traj = load(get_fn("water-box.hoomdxml"))
sodium = traj.top.select("name 'Na'")
sodium_slice = traj.atom_slice(sodium)
assert np.isclose(sodium_slice.xyz, np.array([[[30, 30, 30]]])).all()
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