def __textSearch(self, aMol):
search = TextNumericSearch()
search.add_compound_name(aMol.identifier,
mode="anywhere",
ignore_non_alpha_num=True)
# search.add_synonym(m.identifier) - no need to add synonym separate (should automatically search both name and synonym)
textHits = search.search(max_hits_per_structure=1)
return textHits
def searchName(name):
"""
:param name:
:return: ccdc.search.SearchHit
"""
searcher = TextNumericSearch()
searcher.add_synonym(name)
return retrieveHits(searcher)
def searchName(name):
"""
:param name:
:return: ccdc.search.SearchHit
"""
searcher = TextNumericSearch()
searcher.add_synonym(name)
return retrieveHits(searcher)
def get_csd_entries_by_author(author):
"""
Uses the default csd databases based on the version of the python API this is being used
conducts a search
returns list of refcodes
"""
query = TextNumericSearch()
query.add_author(author)
return [h.identifier for h in query.search()]
def searchCCDCNumber(num):
"""
TODO: look at email reply got
:param num:
:return: ccdc.search.SearchHit
"""
searcher = TextNumericSearch()
searcher.add_ccdc_number(num)
return retrieveHits(searcher)
def searchCCDCNumber(num):
"""
TODO: look at email reply got
:param num:
:return: ccdc.search.SearchHit
"""
searcher = TextNumericSearch()
searcher.add_ccdc_number(num)
return retrieveHits(searcher)
def searchRefcode(refCode):
"""
TODO: validation refcode
:param refCode: refcode format of six letters + digits ... n
:return: ccdc.search.SearchHit
"""
query = TextNumericSearch()
query.add_all_identifiers(refCode)
hits = query.search()
return hits
def searchRefcode(refCode):
"""
TODO: validation refcode
:param refCode: refcode format of six letters + digits ... n
:return: ccdc.search.SearchHit
"""
query = TextNumericSearch()
query.add_all_identifiers(refCode)
hits = query.search()
return hits
def cacl_density(doi):
print doi
query = TextNumericSearch()
query.add_doi(doi)
hits = query.search()
ref_codes = []
for hit in hits:
ref_codes.append(hit.identifier)
csd_crystal_reader = CrystalReader('CSD')
if len(ref_codes) == 0:
density = 1
else:
crystal = csd_crystal_reader.crystal(ref_codes[0])
density = crystal.calculated_density
return "%.3f" % density
def searchCSD(self):
query = TextNumericSearch()
for doi in self.doiList:
# Return any dois which have any structures associated with them:
refCodes = []
query.add_doi(doi, mode='anywhere', ignore_non_alpha_num=False)
searchResults = query.search()
n = int(len(searchResults))
for i in searchResults:
refCodes.append(i.identifier)
query.clear()
if n != 0:
print 'Hit: ' + str(n) + ' in ' + str(doi)
for i in refCodes:
print str(i)
self.doiHits.append(doi)
self.nDoiStructures.append(n)
print str(len(self.doiHits)) + ' Hits found.'