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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: Kyle A. Beauchamp
# 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 os
import pickle
import shutil
import tarfile
import numpy as np
import pytest
import scipy.sparse
import mdtraj as md
from mdtraj.formats import mol2
from mdtraj.testing import eq
def test_load_mol2(get_fn):
trj = md.load(get_fn("imatinib.mol2"))
ref_trj = md.load(get_fn("imatinib.pdb"), bond_orders=True)
eq(trj.xyz, ref_trj.xyz)
ref_top, ref_bonds = ref_trj.top.to_dataframe()
top, bonds = trj.top.to_dataframe()
# Strip bond orders from mol2 because reader does not read bond orders
ref_bonds[:, -1:] = np.zeros([ref_bonds.shape[0], 1])
# Floor bond type info since PDB does not have non-integer bond types
bonds[:, -2] = np.floor(bonds[:, -2])
eq(bonds, ref_bonds)
def test_write_from_mol2(get_fn, tmpdir):
trj = md.load(get_fn("imatinib.mol2"))
ref_trj = md.load(get_fn("imatinib.pdb"))
# Write out the mol2 as pdb
tmp_file = f"{tmpdir}/imatinib.pdb"
trj.save(tmp_file)
temp_trj = md.load(tmp_file)
# Check if xyz are the same as ref
eq(ref_trj.xyz, temp_trj.xyz)
@pytest.mark.skipif(shutil.which("obabel") is None, reason="Requires obabel")
@pytest.mark.skipif(os.environ.get("TRAVIS", None) == "true", reason="Skip on Travis.")
def test_load_freesolv_gaffmol2_vs_sybylmol2_vs_obabelpdb(get_fn, tmpdir):
tar_filename = "freesolve_v0.3.tar.bz2"
tar = tarfile.open(get_fn(tar_filename), mode="r:bz2")
os.chdir(str(tmpdir))
tar.extractall()
tar.close()
with open("./v0.3/database.pickle", "rb") as f:
database = pickle.load(f, encoding="latin-1")
for key in database:
gaff_filename = "./v0.3/mol2files_gaff/%s.mol2" % key
pdb_filename = "./v0.3/mol2files_gaff/%s.pdb" % key
sybyl_filename = "./v0.3/mol2files_sybyl/%s.mol2" % key
cmd = f"obabel -imol2 {sybyl_filename} -opdb > {pdb_filename} 2>/dev/null"
assert os.system(cmd) == 0
t_pdb = md.load(pdb_filename)
t_gaff = md.load(gaff_filename)
t_sybyl = md.load(sybyl_filename)
eq(t_pdb.n_atoms, t_gaff.n_atoms)
eq(t_pdb.n_atoms, t_sybyl.n_atoms)
eq(t_pdb.n_frames, t_gaff.n_frames)
eq(t_pdb.n_frames, t_gaff.n_frames)
eq(t_pdb.xyz, t_gaff.xyz, decimal=4)
eq(t_pdb.xyz, t_sybyl.xyz, decimal=4)
top_pdb, bonds_pdb = t_pdb.top.to_dataframe()
top_gaff, bonds_gaff = t_gaff.top.to_dataframe()
top_sybyl, bonds_sybyl = t_sybyl.top.to_dataframe()
eq(top_sybyl.name.values, top_pdb.name.values)
# eq(top_gaff.name.values, top_sybyl.name.values) # THEY CAN HAVE DIFFERENT NAMES, so this isn't TRUE!
def make_bonds_comparable(bond_array):
"""
Create a bond connectivity matrix from a numpy array of atom pairs. Avoids having to
compare the order in which bonds are listed.
"""
n_bonds = len(bond_array)
data = np.ones(n_bonds)
i = bond_array[:, 0]
j = bond_array[:, 1]
matrix = scipy.sparse.coo_matrix(
(data, (i, j)),
shape=(t_pdb.n_atoms, t_pdb.n_atoms),
).toarray()
return matrix + matrix.T # Symmetrize to account for (a ~ b) versus (b ~ a)
bond_matrix_pdb = make_bonds_comparable(bonds_pdb)
bond_matrix_gaff = make_bonds_comparable(bonds_gaff)
bond_matrix_sybyl = make_bonds_comparable(bonds_sybyl)
eq(bond_matrix_pdb, bond_matrix_gaff)
eq(bond_matrix_pdb, bond_matrix_sybyl)
# Third row from mol2 file copied below, used in testing.
# 3 N1 8.5150 -0.1620 1.3310 n3 1 LIG -0.732600
def test_mol2_dataframe(get_fn):
top, bonds = mol2.mol2_to_dataframes(get_fn("imatinib.mol2"))
eq(top.name[2], "N1")
eq(top.atype[2], "n3")
eq(top.resName[2], "LIG")
eq(float(top.charge[2]), -0.732600)
def test_mol2_dataframe_status(get_fn):
atoms, bonds = mol2.mol2_to_dataframes(get_fn("adp.mol2"))
assert atoms["charge"][1] == 1.3672
assert atoms["status"][1] == "****"
def test_mol2_warnings(get_fn):
md.load_mol2(get_fn("lysozyme-ligand-tripos.mol2"))
def test_mol2_status_bits(get_fn):
trj = md.load_mol2(get_fn("status-bits.mol2"))
eq(trj.topology.n_atoms, 18)
eq(trj.topology.n_bonds, 18)
def test_mol2_without_bonds(get_fn):
trj = md.load_mol2(get_fn("li.mol2"))
assert trj.topology.n_bonds == 0
def test_mol2_element_name(get_fn):
trj = md.load_mol2(get_fn("cl.mol2"))
top, bonds = trj.top.to_dataframe()
assert top.iloc[0]["element"] == "Cl"
@pytest.mark.parametrize(
"mol2_file",
[
("li.mol2"),
("lysozyme-ligand-tripos.mol2"),
("imatinib.mol2"),
("status-bits.mol2"),
("adp.mol2"),
("water_acn.mol2"),
],
)
def test_load_all_mol2(mol2_file, get_fn):
md.load_mol2(get_fn(mol2_file))
def test_mol2_n_residues(get_fn):
trj = md.load_mol2(get_fn("water_acn.mol2"))
assert trj.n_residues == 10
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