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##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2025 Stanford University and the Authors
#
# Authors: Lee-Ping Wang
# Contributors: Robert McGibbon, Jeremy M. G. Leung
#
# 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
import mdtraj as md
from mdtraj.formats import ArcTrajectoryFile, PDBTrajectoryFile
from mdtraj.formats.arc import load_arc
from mdtraj.testing import eq
def test_read_0(get_fn):
"""Check if .arc positions are read correctly"""
with ArcTrajectoryFile(get_fn("4waters.arc")) as f:
xyz, leng, ang = f.read()
with PDBTrajectoryFile(get_fn("4waters.pdb")) as f:
xyz2 = f.positions
eq(xyz, xyz2, decimal=3)
def test_read_arctraj(get_fn):
traj = md.load(get_fn("nitrogen.arc"), top=get_fn("nitrogen.pdb"))
owntop = md.load(get_fn("nitrogen.arc"))
eq(traj.xyz, owntop.xyz)
def test_read_arctraj_top(get_fn):
"""Check if anything other than residues differ between loading
a ``.arc`` file with two different topologies"""
pdbtop = load_arc(get_fn("4waters.arc"), top=get_fn("4waters.pdb"))
arctop = load_arc(get_fn("4waters.arc"))
eq(pdbtop.n_atoms, arctop.n_atoms)
eq(pdbtop.xyz, arctop.xyz)
# Only the residues should differ
assert pdbtop.n_residues == 4
assert arctop.n_residues == 1
for ipdb, iarc in zip(pdbtop.top._atoms, arctop.top._atoms):
# check if atoms are in the same order with same element identity
eq(ipdb.name, iarc.name)
eq(ipdb.element, iarc.element)
for ipdb, iarc in zip(pdbtop.top._bonds, arctop.top._bonds):
# Check if connectivity is the same, based on index, which is
# implicitly checked in the for loop above
eq(ipdb.atom1.index, iarc.atom1.index)
eq(ipdb.atom2.index, iarc.atom2.index)
def test_read_pbc(get_fn):
with ArcTrajectoryFile(get_fn("thf200.arc")) as f:
xyz, leng, ang = f.read()
eq(xyz[0, 0], np.array([21.231166, 32.549819, 8.278454]), decimal=3)
eq(xyz[0, -1], np.array([29.013880, 6.255754, 44.074519]), decimal=3)
eq(leng, np.array([[45.119376, 45.119376, 45.119376]]), decimal=3)
eq(ang, np.array([[90.0, 90.0, 90.0]]), decimal=3)
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