def findCellMatches(self, a, b, c, alpha, beta, gamma):
"""
TODO: docs
:param a:
:param b:
:param c:
:param alpha:
:param beta:
:param gamma:
:return:
"""
#Validate input
arguments = locals()
logger.info('The following arguments were passed: ' +
', '.join(k
for k, v in arguments.items() if v is not None))
cellAngles = crystal.CellAngles(alpha, beta, gamma)
logger.info("Created cell angles" + str(cellAngles))
cellLengths = crystal.CellLengths(a, b, c)
logger.info("Created cell lengths" + str(cellLengths))
#Tmp kept as Primitive
centring = ChemistryLib.Spacegroup_centring_text().text(1)
logger.info("Set to centering" + str(centring))
self.searchHits = self._unitCellQuery(cellAngles=cellAngles,
cellLengths=cellLengths,
centring=centring)
logger.info("Success in running request for find cell matches")
displayHits(self.searchHits)
return True
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 setLatticeParameters(self, a, b, c, alpha, beta, gamma):
"""
:param a:
:param b:
:param c:
:param alpha:
:param beta:
:param gamma:
:return:
"""
self.cellAngles = crystal.CellAngles(alpha, beta, gamma)
self.cellLengths = crystal.CellLengths(a, b, c)
#Crystal set
self.searchCrystal.cell_angles = self.cellAngles
self.searchCrystal.cell_lengths = self.cellLengths
logger.info("Set crystal: ")
logger.info(self.searchCrystal.cell_angles)
logger.info(self.searchCrystal.cell_lengths)
return True
def playgroundQuery():
query('ABEBUF')
#Just wanted a diagram genereted
#generateDiagram("ARAVIZ", "/tmp/")
pathSaved = reportGenerator("/tmp/","ARAVIZ")
print("Generated diagram for ARAVIZ :"+ pathSaved)
saveRefcodeCif("/tmp/","ARAVIZ")
cry = extractCrystalCif("/scratch/CCDC_playground/CCDCPlay/referenceCode/testsCCDC/testdata/CACDOA01");
isActive = True
#XXX: cant create own crystal so will just be settign the first entry...
firstEntry = entryReader[0]
meCrystal = firstEntry.crystal
#searchCrystal(meCrystal)
logger.info(meCrystal.formula)
#TMP JUST NEED SAMPLE DATA
a = 5.4311946
b = 5.4311946
c = 5.4311946
alp = 90
beta = 90
gamma = 90
# 11.1991
# 11.8541
# 14.0985
# 93.606
# 113.098
# 103.500
logger.info("Seraching Unit Cell")
logger.info("Lenths: " + str(a) + "," + str(b) + "," + str(c))
logger.info("Angles: " + str(alp) + "," +str(beta) + "," + str(gamma))
#logger.info("Lattice Centering: " + ChemistryLib.Spacegroup_centring_text().text(1))
#Example search
centring = ChemistryLib.Spacegroup_centring_text().text(1) #Primitive
cellAngles = crystal.CellAngles(alp,beta,gamma)
cellLengths = crystal.CellLengths(a,b,c)
displayHits(searchCellVals(a,b,c))
attemptCry = crystal.Crystal
attemptCry.lattice_centring = ChemistryLib.Spacegroup_centring_text().text(1)
attemptCry.cell_angles = cellAngles
attemptCry.cell_lengths = cellLengths
logger.info(attemptCry.cell_angles)
hits = searchCrystal(attemptCry)
displayHits(hits)
logger.info("\n\nRestraining crystal on formula");
logger.info(attemptCry.molecule)
#
mol = molecule.Molecule
mol.formula = "C1 H6 Cl1 N3 O4"
attemptCry.molecule = mol
hits = searchCrystal(attemptCry)
displayHits(hits)
#
# logger.info("\n\nRestraining crystal on spacegroup");
# attemptCry.crystal_system = "cubic"
hits = searchCrystal(attemptCry)
displayHits(hits)
logger.info("\n\nTurning tolerance off hack");
absAngleTol = 180
perLenTol = 100
hits = searchCrystalTols(attemptCry,absAngleTol,perLenTol)
displayCrystal(hits[-1].crystal)
