def test_methods(self, bf4_molecule: MoleculeTop,
bmim_molecule: MoleculeTop):
"""
Tests simple methods and magic-methods.
"""
assert isinstance(bf4_molecule[0], AtomTop)
atom_compare = AtomTop('B1', 'BF4', 1, 0)
atom_compare.bonds.add(1)
atom_compare.bonds.add(2)
atom_compare.bonds.add(3)
atom_compare.bonds.add(4)
assert bf4_molecule[0] == atom_compare
assert len(bf4_molecule) == 5
assert bf4_molecule == bf4_molecule
assert bf4_molecule != 1
assert bf4_molecule != bmim_molecule
assert bf4_molecule.resname_len_list == [('BF4', 5)]
assert bmim_molecule.resname_len_list == [('BMIM', 25)]
for index, atom in enumerate(bf4_molecule):
assert bf4_molecule.index(atom) == index
# copy
copy_mol = bmim_molecule.copy()
assert copy_mol == bmim_molecule
for at1, at2 in zip(copy_mol, bmim_molecule):
assert at1 == at2
assert at1 is not at2
def test_initialization(self):
"""
Test System initialization with a system with molecules with multiple
residues.
"""
fgro = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/system_CG.gro')
fgro = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/system_CG.gro')
fitpSDS = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/SDS_AA.itp')
fitpADN = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/DNA_CG.itp')
with pytest.raises(IOError):
_ = System(fgro, fitpSDS)
empty = System(fgro)
assert not empty.different_molecules
with pytest.raises(IOError, match=r'The molecule.*'):
empty.add_molecule_top(MoleculeTop(fitpSDS))
bad_dna_top = MoleculeTop(fitpADN)
for atom in bad_dna_top[98:105]:
atom.resname = 'DA'
for atom in bad_dna_top[105:112]:
atom.resname = 'DG'
with pytest.raises(IOError, match=r'The sequence.*'):
empty.add_molecule_top(bad_dna_top)
empty.add_molecule_top(MoleculeTop(fitpADN))
def test_initialization(self, bf4_itp_fname: str):
"""
Initialization.
"""
with pytest.raises(ValueError, match=r".*txt.*"):
molecule = MoleculeTop('test.txt')
with pytest.raises(ValueError, match=r".*txt.*"):
molecule = MoleculeTop('test.itp', file_format=".txt")
# Test with fname and fopen
for i in range(2):
if not i:
molecule = MoleculeTop(bf4_itp_fname)
else:
fopen = open(bf4_itp_fname)
molecule = MoleculeTop(fopen) # type: ignore
assert molecule.ftop == bf4_itp_fname
assert molecule.name == 'BF4'
atoms_info = [('B1', 'BF4', 1), ('F2', 'BF4', 1), ('F3', 'BF4', 1),
('F4', 'BF4', 1), ('F5', 'BF4', 1)]
atoms_test = [
AtomTop(*info, i) for i, info in enumerate(atoms_info)
]
atoms_test[0].connect(atoms_test[1])
atoms_test[0].connect(atoms_test[2])
atoms_test[0].connect(atoms_test[3])
atoms_test[0].connect(atoms_test[4])
assert molecule.atoms == atoms_test
assert str(molecule) == 'MoleculeTop of BF4.'
def molecule_popc_AA() -> Molecule:
"""
Molecule instance of POPC in all-atom resolution.
"""
fitppopc = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/popc-AA.itp')
fgropopc = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/popc-AA.gro')
popcgro = SystemGro(fgropopc)[0]
popcitp = MoleculeTop(fitppopc)
return Molecule(popcitp, [popcgro])
def molecule_VTE_AA() -> Molecule:
"""
Molecule instance of E vitamin in all-atom resolution.
"""
fitpVTE = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/VTE_AA.itp')
fgroVTE = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/VTE_AA.gro')
VTEgro = SystemGro(fgroVTE)[0]
VTEitp = MoleculeTop(fitpVTE)
return Molecule(VTEitp, [VTEgro])
def test_resids(self, bf4_molecule: MoleculeTop):
"""
Resids access and setter.
"""
assert bf4_molecule.resids == [1]
with pytest.raises(ValueError, match='new_resids.*'):
bf4_molecule.resids = 1 # type: ignore
with pytest.raises(ValueError, match='Expected.*'):
bf4_molecule.resids = [0, 23]
bf4_molecule.resids = [3]
for atom in bf4_molecule:
assert atom.resid == 3
assert bf4_molecule.resids == [3]
# Multiple resids
bf4_molecule[0].resid = 8
assert bf4_molecule.resids == [8, 3]
bf4_molecule.resids = [56, 88]
assert bf4_molecule.resids == [56, 88]
def test_resnames(self, bf4_molecule: MoleculeTop):
"""
Resnames access and setter.
"""
assert bf4_molecule.resnames == ['BF4']
with pytest.raises(ValueError, match='new_resnames.*'):
bf4_molecule.resnames = 'test' # type: ignore
with pytest.raises(ValueError, match='Expected.*'):
bf4_molecule.resnames = ['test', 'test2']
bf4_molecule.resnames = ['BMIM']
for atom in bf4_molecule:
assert atom.resname == 'BMIM'
assert bf4_molecule.resnames == ['BMIM']
# Multiple resnames
bf4_molecule[0].resname = 'BF4'
assert bf4_molecule.resnames == ['BF4', 'BMIM']
bf4_molecule.resnames = ['Test', 'T2']
assert bf4_molecule.resnames == ['Test', 'T2']
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 molecule_VTE_map() -> Molecule:
"""
Molecule instance of E vitamin in coarse-grained resolution after being
mapped.
"""
fitpVTE = os.path.join(ACTUAL_PATH,
'../../gaddlemaps/data/vitamin_E_CG.itp')
fgroVTE = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/VTE_map.gro')
VTEgro = SystemGro(fgroVTE)[0]
VTEitp = MoleculeTop(fitpVTE)
return Molecule(VTEitp, [VTEgro])
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 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_update_from_top(self, molecule_bmim: Molecule):
"""
Test for update_from_molecule_top method.
"""
# Make a copy of the original top
fname = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/BMIM_AA.itp')
mol_top = MoleculeTop(fname)
for at1, at2 in zip(mol_top, molecule_bmim):
assert at1.name == at2.name
mol_top[1].name = 'test'
molecule_bmim.update_from_molecule_top(mol_top)
for at1, at2 in zip(mol_top, molecule_bmim):
assert at1.name == at2.name
assert molecule_bmim[1].name == 'test'
def molecule_top_protein() -> MoleculeTop:
"""
MoleculeTop instance for molecule with multiple residues.
"""
fname = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/Protein_CG.itp')
return MoleculeTop(fname)
def molecule_top_bmim() -> MoleculeTop:
"""
BMIM MoleculeTop instance.
"""
fname = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/BMIM_AA.itp')
return MoleculeTop(fname)
def bf4_mtop() -> MoleculeTop:
"""
A BF4 MoleculeTop.
"""
return MoleculeTop(
os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/BF4_AA.itp'))
def bmim_molecule() -> MoleculeTop:
"""
A BF4 MoleculeTop.
"""
fname = os.path.join(ACTUAL_PATH, '../../gaddlemaps/data/BMIM_AA.itp')
return MoleculeTop(fname)
def bf4_molecule(bf4_itp_fname: str) -> MoleculeTop:
"""
A BF4 MoleculeTop.
"""
return MoleculeTop(bf4_itp_fname)