def test_atom_gro_line(self, atom_gro1: AtomGro, atom_gro3: AtomGro):
"""
Tests gro_line method.
"""
info = [
1, 'BMIM', 'N1', 1, 4.668, 3.571, 8.232, -0.2489, 0.2514, 0.1046
]
assert atom_gro1.gro_line() == info
line = ' 1BMIM N1 1 4.668 3.571 8.232 -0.2489 0.2514 0.1046'
line_compare = atom_gro1.gro_line(parsed=False)
assert isinstance(line_compare, str)
assert line_compare.strip() == line.strip()
assert len(atom_gro3.gro_line()) == 7
def test_initialization(self):
"""
Initialization test.
"""
atom = AtomGro(
(1, 'BMIM', 'N1', 1, 4.668, 3.571, 8.232, -0.2489, 0.2514, 0.1046))
assert atom.resid == 1
assert atom.resname == 'BMIM'
assert atom.name == 'N1'
assert atom.atomid == 1
assert np.isclose(atom.position, (4.668, 3.571, 8.232)).all()
assert np.isclose(atom.velocity, (-0.2489, 0.2514, 0.1046)).all()
atom = AtomGro((1, 'BMIM', 'N1', 1, 4.668, 3.571, 8.232))
assert atom.velocity is None
def residue_bmim() -> Residue:
"""
BMIM Residue instance.
"""
fname = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/BMIM_AA.gro')
with GroFile(fname) as fgro:
atoms = [AtomGro(line) for line in fgro]
return Residue(atoms)
def residue_protein() -> List[Residue]:
"""
List of Residue instances for a molecule with multiple residues.
"""
fname = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/Protein_CG.gro')
residues: List[Residue] = []
with GroFile(fname) as fgro:
atom = AtomGro(next(fgro))
residname = atom.residname
atoms = [atom]
for line in fgro:
atom = AtomGro(line)
if residname != atom.residname:
residues.append(Residue(atoms))
residname = atom.residname
atoms = [atom]
else:
atoms.append(atom)
residues.append(Residue(atoms))
return residues
def vte_aa() -> Molecule:
"""
Molecule instance of vitamin E all-atom.
"""
fgro = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/VTE_AA.gro')
with GroFile(fgro) as _file:
atoms = [AtomGro(line) for line in _file]
mgro = Residue(atoms)
fitp = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/VTE_AA.itp')
mitp = MoleculeTop(fitp)
return Molecule(mitp, [mgro])
def molecule_cg() -> Molecule:
"""
Molecule instance of curcumine coarse-grained.
"""
fgro = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/CUR_map.gro')
with GroFile(fgro) as _file:
atoms = [AtomGro(line) for line in _file]
mgro = Residue(atoms)
fitp = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/CUR_CG.itp')
mitp = MoleculeTop(fitp)
return Molecule(mitp, [mgro])
def molecule_aa() -> Molecule:
"""
Molecule instance of curcumine in all-atom resolution.
"""
fgro = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/CUR_AA.gro')
with GroFile(fgro) as _file:
atoms = [AtomGro(line) for line in _file]
mgro = Residue(atoms)
fitp = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/CUR_AA.itp')
mitp = MoleculeTop(fitp)
return Molecule(mitp, [mgro])
def vte_map_cg() -> Molecule:
"""
Molecule instance of vitamin E coarse-grained coming from the map
process.
"""
fgro = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/VTE_map.gro')
with GroFile(fgro) as _file:
atoms = [AtomGro(line) for line in _file]
mgro = Residue(atoms)
fitp = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/vitamin_E_CG.itp')
mitp = MoleculeTop(fitp)
return Molecule(mitp, [mgro])
def test_write_gro(self, molecule_protein: Molecule, tmp_path: Path):
"""
Test for writing gro files.
"""
subdir = tmp_path / "molecule_test"
subdir.mkdir()
fgrotmp = str(subdir / "test_write_gro.gro")
molecule_protein.write_gro(fgrotmp)
with GroFile(fgrotmp) as fgro:
assert fgro.natoms == 34
for line, atom in zip(fgro, molecule_protein):
atom_gro = AtomGro(line)
assert atom.atom_gro == atom_gro
def test_methods(self, atom_gro1: AtomGro, atom_gro2: AtomGro,
atom_gro3: AtomGro):
"""
Tests simple methods and magic-methods.
"""
assert atom_gro1 == atom_gro1
assert atom_gro1 != atom_gro2
assert atom_gro1 != 1
copy_1 = atom_gro1.copy()
assert copy_1 == atom_gro1
assert copy_1 is not atom_gro1
assert atom_gro1.residname == '1BMIM'
assert atom_gro2.residname == '1BMIM'
assert atom_gro3.residname == '1BF4'
assert atom_gro1.element == 'N'
assert atom_gro2.element == 'H'
assert atom_gro3.element == 'H'
atom_gro1.name = '345'
with pytest.raises(IOError):
_ = atom_gro1.element
def test_write_gro(self, residue: Residue, tmp_path: Path):
"""
Test for writing gro files.
"""
subdir = tmp_path / "residue_test"
subdir.mkdir()
fgrotmp = str(subdir / "test_write_gro.gro")
residue.write_gro(fgrotmp)
atoms = []
with GroFile(fgrotmp) as fgro:
assert fgro.natoms == 2
for line in fgro:
atoms.append(AtomGro(line))
new_residue = Residue(atoms)
assert new_residue == residue
def generate_atom_gro(resid: int = 1, resname: str = 'BMIM',
name: str = 'N1', atomid: int = 1) -> AtomGro:
info = (resid, resname, name, atomid, 4.668,
3.571, 8.232, -0.2489, 0.2514, 0.1046)
return AtomGro(info)
def atom_gro3() -> AtomGro:
info = (1, 'BF4', 'H2', 2, 5.668, 3.571, 8.232)
return AtomGro(info)
def atom_gro2() -> AtomGro:
info = (1, 'BMIM', 'H2', 2, 5.668, 3.571, 8.232, -0.2489, 0.2514, 0.1046)
return AtomGro(info)
def atom_gro1() -> AtomGro:
info = (1, 'BMIM', 'N1', 1, 4.668, 3.571, 8.232, -0.2489, 0.2514, 0.1046)
return AtomGro(info)