def run_outofplane(QCA):
pyramidquads = smiles.SmilesSearchTree("*~*(~*)~*",
QCA,
name="pyramidquads")
outofplane = geometry.ImproperTorsionOperation(pyramidquads,
name="outofplane")
outofplane.apply(targets=entries)
save(outofplane)
def run_angles( QCA):
triples = smiles.SmilesSearchTree( "*~*~*", QCA, name="triples")
angles = geometry.AngleOperation( triples, name="angles")
angles.apply( targets=entries)
save( angles)
def run_bonds( QCA):
pairs = smiles.SmilesSearchTree( "*~*", QCA, name="pairs")
bonds = geometry.BondOperation( pairs, name="bonds")
bonds.apply( targets=entries)
save( bonds)
def run_torsions( QCA):
linquads = smiles.SmilesSearchTree("*~*~*~*", QCA, name="linquads")
torsions = geometry.TorsionOperation(linquads, name="torsions")
torsions.apply( targets=entries)
save( torsions)
root_payload=client,
node_index=dict(),
db=dict())
drop = ["Intermediates", "Hessian"]
QCA.build_index(ds, drop=drop, keep_specs=["default"])
save(QCA)
entries = list(QCA.node_iter_depth_first(QCA.root(), select="Entry"))
print("There are {:d} entries total".format(len(entries)))
# The general query on the dataset.
# The results respect the key, and will only return those indices if specified
# If no key is specified, then the indices are in order as they appear in the string
query = smiles.SmilesSearchTree("[#7X3:2](~[#1:1])(~[#6])~[#6:3]=[O:4]",
QCA,
name="smiles")
query.apply(targets=entries)
if True:
# This is the torsion drive we are looking for
# For whatever reason, the mapped indices are not respected, so need the map
#
# It is possible to select just a subset of the above search.
# For example matching [2,3] will match any torsiondrive with the same
# rotatable bond
#
# This is 1-indexing
#
# This will search for the exact torsion specified above
# tmap = [1, 2, 3, 4]