def from_mol2(f):
path = str(datapath / f)
u = Universe(path)
elements = [guess_atom_element(n) for n in u.atoms.names]
u.add_TopologyAttr("elements", np.array(elements, dtype=object))
u.atoms.types = np.array([x.upper() for x in u.atoms.types], dtype=object)
return Molecule.from_mda(u, force=True)
def get_topology_cmip_elements_canonical(input_topology_filename: str) -> List:
"""
This function also accepts pdb files
Args:
input_topology_filename:
Returns:
"""
# Remove forcefield itp references from top file.
if input_topology_filename.lower().endswith('.top'):
with open(input_topology_filename) as tf:
top_lines = tf.readlines()
top_file = create_unique_file_path(
parent_dir=Path(input_topology_filename).parent.resolve(),
extension='.top')
with open(top_file, 'w') as nt:
for line in top_lines:
if re.search(r"\.ff.*\.itp", line):
continue
nt.write(line)
u = mda.Universe(top_file, topology_format="ITP")
else:
u = mda.Universe(input_topology_filename)
# mda_charges = [round(val, 4) for val in u.atoms.charges]
# mda_atom_types = list(guess_types(u.atoms.names))
mda_atom_types = []
for atom in u.atoms:
atom_element = guess_atom_element(atom.name)
if atom_element == 'H':
bonded_atom_element = guess_atom_element(atom.bonded_atoms[0].name)
if bonded_atom_element == 'O':
atom_element = 'HO'
elif bonded_atom_element in ['N', 'S']:
atom_element = 'HN'
mda_atom_types.append(atom_element)
return mda_atom_types
def test_guess_atom_element_1H(self):
assert guessers.guess_atom_element('1H') == 'H'
assert guessers.guess_atom_element('2H') == 'H'
def test_guess_atom_element_singledigit(self):
assert guessers.guess_atom_element('1') == '1'
def test_guess_atom_element_empty(self):
assert guessers.guess_atom_element('') == ''
def test_guess_atom_element(self):
assert guessers.guess_atom_element('MG2+') == 'MG'
def test_guess_element_from_name(self, name, element):
assert guessers.guess_atom_element(name) == element
def test_guess_atom_element_empty():
assert_(guessers.guess_atom_element('') == '')
def test_guess_atom_element_1H():
assert_(guessers.guess_atom_element('1H') == 'H')
assert_(guessers.guess_atom_element('2H') == 'H')
def test_guess_atom_element():
assert_(guessers.guess_atom_element('MG2+') == 'MG')
def test_guess_atom_element_1H(self):
assert guessers.guess_atom_element('1H') == 'H'
assert guessers.guess_atom_element('2H') == 'H'
def test_guess_atom_element_singledigit(self):
assert guessers.guess_atom_element('1') == '1'
def test_guess_atom_element_empty(self):
assert guessers.guess_atom_element('') == ''
def test_guess_atom_element(self):
assert guessers.guess_atom_element('MG2+') == 'MG'
