def unitCellQuerySettings(cellLengths, cellAngles, centring, absAngTol,
percentLenTol):
"""
:param cellLengths: float
:param cellAngles: float
:param centring: float
:param absAngTol: float
:param percentLenTol: float
:return: ccdc.search.SearchHit
"""
logger.info("Created cell angles" + str(cellAngles))
logger.info("Created cell lengths" + str(cellLengths))
logger.info("Set to centering" + str(centring))
query = ReducedCellSearch.Query(angles=cellAngles,
lengths=cellLengths,
lattice_centring=centring)
searcher = ReducedCellSearch(query)
if (percentLenTol != None):
searcher.settings.percent_length_tolerance = percentLenTol
if (absAngTol != None):
searcher.settings.absolute_angle_tolerance = absAngTol
return retrieveHits(searcher)
def searchCellAngles(alpha, beta, gamma):
"""
@deprecated:
:param alpha: float
:param beta: float
:param gamma: float
:return: ccdc.search.SearchHit
"""
cellAngles = crystal.CellAngles(alpha, beta, gamma)
query = ReducedCellSearch.Query(angles=cellAngles)
searcher = ReducedCellSearch(query)
return retrieveHits(searcher)
def searchCellVals(a, b, c):
"""
The generic lattice centering does not work...
@deprecated: need to set crystal system
:param a: float
:param b: float
:param c: float
:return: ccdc.search.SearchHit
"""
cellLen = crystal.CellLengths(a, b, c)
query = ReducedCellSearch.Query(lengths=cellLen)
specifics = query._get_query()
searcher = ReducedCellSearch(query)
return retrieveHits(searcher)
def unitCellQuery(cellLengths, cellAngles, centring):
"""
:param cellLengths: float
:param cellAngles: float
:param centring: ChemLin.Spacegroupcentering TODO: validation?
:return: ccdc.search.SearchHit
"""
logger.info("Created cell angles"+ str(cellAngles))
logger.info("Created cell lengths" + str(cellLengths))
logger.info("Set to centering" + str(centring))
query = ReducedCellSearch.Query(angles=cellAngles, lengths=cellLengths, lattice_centring=centring)
searcher = ReducedCellSearch(query)
return retrieveHits(searcher)
def search(self):
# searches the csd data base for a crystal with known parameters returns best result
cellA = namedtuple('CellAngles', ['alpha', 'beta', 'gamma']) # create a named tuple for ccdc module
angles = list(self.angles) # make a list of angles
more_angles = cellA(angles[0],angles[1],angles[2]) # append angles to the tuple
cellL = namedtuple('CellLengths',['a','b','c'])
cell_lengths = self.cell_lengths
more_lengths = cellL(cell_lengths[0],cell_lengths[1],cell_lengths[2])
query = ReducedCellSearch.Query(lengths = more_lengths,angles = more_angles ,lattice_centring = 'primitive' )
searcher = ReducedCellSearch(query)
hits = searcher.search() # search for all hits
h = hits[0] # top hit
print h.identifier, h.crystal.cell_lengths, h.crystal.cell_angles, h.crystal.lattice_centring # print the best result
def my_reduced_cell_search(
user_a,
user_b,
user_c,
user_alpha,
user_beta,
user_gamma,
user_centring,
database=csdsql_database_path,
filename=json_search_results_path,
length_tolerance=1.5,
angle_tolerance=2.0,
):
# lattice_centring_dict = {
# 'P':'primitive','C':'C-centred','F':'F-centred','I':'I-centred',
# 'R':'R-obverse','?':'unknown centring','B':'B-centred','A':'A-centred'}
# build the search
query = ReducedCellSearch.Query(
CellLengths(a=user_a, b=user_b, c=user_c),
CellAngles(alpha=user_alpha, beta=user_beta, gamma=user_gamma),
user_centring,
)
searcher = ReducedCellSearch(query=query, )
searcher.settings.absolute_angle_tolerance = float(length_tolerance)
searcher.settings.percent_length_tolerance = float(angle_tolerance)
hits = searcher.search(database=database) # /inhouse.csdsql
# load in the cif database as a list of dictionaries
with open(json_database_path, "r") as filehandle:
data = filehandle.read()
data = json.loads(data)
search_results = [] # the list of dicts to export as json
for h in hits:
for i in data:
if i["hash"] == h.identifier:
print(i["hash"])
search_results.append(i)
elif i["_database_code_CSD"] == h.identifier:
print(h.identifier)
search_results.append(i)
parsed_cifs_2_json(search_results,
filename="../database_files/search_results.json")
print(str(len(hits)) + " hits found.")
def search(self):
# searches the csd data base for a crystal with known parameters returns best result
cellA = namedtuple('CellAngles', ['alpha', 'beta', 'gamma']) # create a named tuple for ccdc module
angles = list(self.angles) # make a list of angles
more_angles = cellA(float(angles[0]),float(angles[1]),float(angles[2])) # append angles to the tuple
cellL = namedtuple('CellLengths',['a','b','c'])
cell_lengths = self.cell_lengths
more_lengths = cellL(float(cell_lengths[0]),float(cell_lengths[1]),float(cell_lengths[2]))
query = ReducedCellSearch.Query(lengths = more_lengths,angles = more_angles ,lattice_centring = 'primitive' )
searcher = ReducedCellSearch(query)
hits = searcher.search() # search for all hits
i = 0
while i < float(self.numhits):
h = hits[i]
print h.identifier, h.crystal.cell_lengths, h.crystal.cell_angles, h.crystal.lattice_centring # print the best result
i += 1