def load_atoms(cid=None, smiles=None) -> Atoms:
inputs = [cid, smiles]
input_check = [a is not None for a in inputs]
if input_check.count(True) == 1:
index = input_check.index(True)
if index == 0:
compounds = pubchem_conformer_search(cid=cid)
else:
compounds = pubchem_conformer_search(smiles=smiles)
else:
return Atoms()
return compounds[0].atoms
def test_pubchem():
from ase.data.pubchem import pubchem_search, pubchem_conformer_search
from ase.data.pubchem import pubchem_atoms_search
from ase.data.pubchem import pubchem_atoms_conformer_search
# check class functionality
data = pubchem_search('ammonia', mock_test=True)
data.get_atoms()
data.get_pubchem_data()
# XXX maybe verify some of this data?
# check the various entry styles and the functions that return atoms
pubchem_search(cid=241, mock_test=True).get_atoms()
pubchem_atoms_search(smiles='CCOH', mock_test=True)
pubchem_atoms_conformer_search('octane', mock_test=True)
# (maybe test something about some of the returned atoms)
# check conformer searching
confs = pubchem_conformer_search('octane', mock_test=True)
for conf in confs:
pass
try: # check that you can't pass in two args
pubchem_search(name='octane', cid=222, mock_test=True)
raise Exception('Test Failed')
except ValueError:
pass
try: # check that you must pass at least one arg
pubchem_search(mock_test=True)
raise Exception('Test Failed')
except ValueError:
pass
def main():
try:
compounds = pubchem_conformer_search(cid=31525001)
for conformer in compounds:
# print(conformer.data)
atoms = conformer.atoms
print(atoms.symbols)
print(atoms.positions)
print(atoms.numbers)
points = []
for step, number in enumerate(atoms.numbers):
point = {number: atoms.positions[step]}
points.append(point)
print(points)
except ValueError:
print('The compound is not found in PubChem!')
def main():
try:
compounds = pubchem_conformer_search(smiles='C=CC=C=CNO')
for conformer in compounds:
# print(conformer.data)
atoms = conformer.atoms
# print(points.symbols)
# print(points.positions)
# print(points.numbers)
points = []
for step, number in enumerate(atoms.numbers):
point = list(atoms.positions[step]).copy()
point.append(colors[number])
points.append(point)
# 平滑操作
# smoothing(point)
# print(points)
draw(points)
except ValueError as e:
print(str(e))
print('The compound is not found in PubChem!')
from ase.data.pubchem import pubchem_search, pubchem_conformer_search
from ase.data.pubchem import pubchem_atoms_search
from ase.data.pubchem import pubchem_atoms_conformer_search
# check class functionality
data = pubchem_search('ammonia', mock_test=True)
atoms = data.get_atoms()
entry_data = data.get_pubchem_data()
# check the various entry styles and the functions that return atoms
atoms = pubchem_search(cid=241, mock_test=True).get_atoms()
atoms = pubchem_atoms_search(smiles='CCOH', mock_test=True)
atoms = pubchem_atoms_conformer_search('octane', mock_test=True)
# check conformer searching
confs = pubchem_conformer_search('octane', mock_test=True)
for conf in confs:
pass
try: # check that you can't pass in two args
atoms = pubchem_search(name='octane', cid=222, mock_test=True)
raise Exception('Test Failed')
except ValueError:
pass
try: # check that you must pass at least one arg
atoms = pubchem_search(mock_test=True)
raise Exception('Test Failed')
except ValueError:
pass