def clean(self):
# we have to run this validator here again, because
# chemicalformula2nominalmass expects proper formulae
# django runs the validators _after_ this clean function
validate_chemical_formula(self.chemical_formula)
if self.isotope is True:
if self.mass != chemicalformula2nominalmass(self.chemical_formula):
raise ValidationError(u'Nominal mass and chemical formula are not compatible.')
#check if either inchi or inchikey are there and either complete the other one or verify
if self.inchi == '':
if self.inchikey != '':
tmpinchi = inchikey2inchi(self.inchikey)
if tmpinchi:
self.inchi = tmpinchi
else:
raise ValidationError(u'No chemical compound found for this InChI-Key.')
else:
#check if the given inchi has the InChI= in the beginning
#additionally check for Standard-InChI
if not self.inchi.startswith('InChI='):
self.inchi = 'InChI=' + self.inchi
if not self.inchi.startswith('InChI=1S'):
raise ValidationError(u'InChI %s is not a Standard-InChI (starts with 1S)' % self.inchi)
#get the rest
if self.inchikey != '':
inchikeycheck = inchi2inchikey(self.inchi)
if inchikeycheck != self.inchikey:
raise ValidationError(u'The given InChI and InChI-Key are not compatible.')
else:
tmpinchikey = inchi2inchikey(self.inchi)
if tmpinchikey:
self.inchikey = tmpinchikey
else:
raise ValidationError(u'Not a valid InChI-Key.')
if self.chemical_formula != inchi2chemicalformula(self.inchi):
raise ValidationError(u'InChI %s is not compatible with the stochiometric formula %s.' % (self.inchi, self.chemical_formula))
#we check if we already have a species with same chem formula, mass and isotope-status
sp_search = Species.objects.filter(chemical_formula__exact=self.chemical_formula).filter(mass__exact=self.mass).filter(isotope__exact=self.isotope)
#exclude this very instance
sp_search = sp_search.exclude(id__exact=self.id)
if len(sp_search) > 0:
#indeed we do
#in this case they should be isomeres and therefore have a different inchi
if self.inchi in sp_search.values_list('inchi'):
raise ValidationError(u'A species with this chemical formula and InChI already exists in the database')
if self.inchi == '':
raise ValidationError(u'Isomeres need to be distinguished via their InChI')
def clean(self):
if self.cas != u"":
validations.validate_CAS(self.cas)
if self.no_chemspider_sync is False:
if self.csid is not None:
chemobj = fitlib.chemlib.ChemicalObject(csid=self.csid)
else:
chemobj = fitlib.chemlib.ChemicalObject(
name=self.name, inchi=self.inchi, inchikey=self.inchikey, cas=self.cas
)
chemobj.complete()
if (self.inchi != "") and (self.inchi != chemobj.inchi):
raise ValidationError(
"The given InChI and the one retrieved from Chemspider do not match. %s %s"
% (self.inchi, chemobj.inchi)
)
if (self.inchikey != "") and (self.inchikey != chemobj.inchikey):
raise ValidationError(
"The given InChI-Key and the one retrieved from Chemspider do not match. %s %s"
% (self.inchikey, chemobj.inchikey)
)
if (self.csid is not None) and (self.csid != chemobj.csid):
raise ValidationError(
"The given CSID and the one retrieved from Chemspider do not match. %s %s"
% (str(self.csid), chemobj.csid)
)
self.inchi = chemobj.inchi
self.inchikey = chemobj.inchikey
self.csid = chemobj.csid
if self.inchi != "" and self.chemical_formula != "":
if self.chemical_formula != inchi2chemicalformula(self.inchi):
raise ValidationError("Chemical Formula does not match InChI")
elif self.chemical_formula == "" and self.inchi != "":
self.chemical_formula = inchi2chemicalformula(self.inchi)
def clean(self):
# we have to run this validator here again, because
# chemicalformula2nominalmass expects proper formulae
# django runs the validators _after_ this clean function
validate_chemical_formula(self.chemical_formula)
if self.isotope is True:
if self.mass != chemicalformula2nominalmass(self.chemical_formula):
raise ValidationError(
u'Nominal mass and chemical formula are not compatible.')
#check if either inchi or inchikey are there and either complete the other one or verify
if self.inchi == '':
if self.inchikey != '':
tmpinchi = inchikey2inchi(self.inchikey)
if tmpinchi:
self.inchi = tmpinchi
else:
raise ValidationError(
u'No chemical compound found for this InChI-Key.')
else:
#check if the given inchi has the InChI= in the beginning
#additionally check for Standard-InChI
if not self.inchi.startswith('InChI='):
self.inchi = 'InChI=' + self.inchi
if not self.inchi.startswith('InChI=1S'):
raise ValidationError(
u'InChI %s is not a Standard-InChI (starts with 1S)' %
self.inchi)
#get the rest
if self.inchikey != '':
inchikeycheck = inchi2inchikey(self.inchi)
if inchikeycheck != self.inchikey:
raise ValidationError(
u'The given InChI and InChI-Key are not compatible.')
else:
tmpinchikey = inchi2inchikey(self.inchi)
if tmpinchikey:
self.inchikey = tmpinchikey
else:
raise ValidationError(u'Not a valid InChI-Key.')
if self.chemical_formula != inchi2chemicalformula(self.inchi):
raise ValidationError(
u'InChI %s is not compatible with the stochiometric formula %s.'
% (self.inchi, self.chemical_formula))
def clean(self):
# we have to run this validator here again, because
# chemicalformula2nominalmass expects proper formulae
# django runs the validators _after_ this clean function
validate_chemical_formula(self.chemical_formula)
if self.isotope is True:
if self.mass != chemicalformula2nominalmass(self.chemical_formula):
raise ValidationError(u'Nominal mass and chemical formula are not compatible.')
#check if either inchi or inchikey are there and either complete the other one or verify
if self.inchi == '':
if self.inchikey != '':
tmpinchi = inchikey2inchi(self.inchikey)
if tmpinchi:
self.inchi = tmpinchi
else:
raise ValidationError(u'No chemical compound found for this InChI-Key.')
else:
#check if the given inchi has the InChI= in the beginning
#additionally check for Standard-InChI
if not self.inchi.startswith('InChI='):
self.inchi = 'InChI=' + self.inchi
if not self.inchi.startswith('InChI=1S'):
raise ValidationError(u'InChI %s is not a Standard-InChI (starts with 1S)' % self.inchi)
#get the rest
if self.inchikey != '':
inchikeycheck = inchi2inchikey(self.inchi)
if inchikeycheck != self.inchikey:
raise ValidationError(u'The given InChI and InChI-Key are not compatible.')
else:
tmpinchikey = inchi2inchikey(self.inchi)
if tmpinchikey:
self.inchikey = tmpinchikey
else:
raise ValidationError(u'Not a valid InChI-Key.')
if self.chemical_formula != inchi2chemicalformula(self.inchi):
raise ValidationError(u'InChI %s is not compatible with the stochiometric formula %s.' % (self.inchi, self.chemical_formula))
def clean(self):
# we have to run this validator here again, because
# chemicalformula2nominalmass expects proper formulae
# django runs the validators _after_ this clean function
validate_chemical_formula(self.chemical_formula)
if self.isotope is True:
if self.mass != chemicalformula2nominalmass(self.chemical_formula):
raise ValidationError(
u'Nominal mass and chemical formula are not compatible.')
#check if either inchi or inchikey are there and either complete the other one or verify
if self.inchi == '':
if self.inchikey != '':
tmpinchi = inchikey2inchi(self.inchikey)
if tmpinchi:
self.inchi = tmpinchi
else:
raise ValidationError(
u'No chemical compound found for this InChI-Key.')
else:
#check if the given inchi has the InChI= in the beginning
#additionally check for Standard-InChI
if not self.inchi.startswith('InChI='):
self.inchi = 'InChI=' + self.inchi
if not self.inchi.startswith('InChI=1S'):
raise ValidationError(
u'InChI %s is not a Standard-InChI (starts with 1S)' %
self.inchi)
#get the rest
if self.inchikey != '':
inchikeycheck = inchi2inchikey(self.inchi)
if inchikeycheck != self.inchikey:
raise ValidationError(
u'The given InChI and InChI-Key are not compatible.')
else:
tmpinchikey = inchi2inchikey(self.inchi)
if tmpinchikey:
self.inchikey = tmpinchikey
else:
raise ValidationError(u'Not a valid InChI-Key.')
if self.chemical_formula != inchi2chemicalformula(self.inchi):
raise ValidationError(
u'InChI %s is not compatible with the stochiometric formula %s.'
% (self.inchi, self.chemical_formula))
#we check if we already have a species with same chem formula, mass and isotope-status
sp_search = Species.objects.filter(
chemical_formula__exact=self.chemical_formula).filter(
mass__exact=self.mass).filter(isotope__exact=self.isotope)
#exclude this very instance
sp_search = sp_search.exclude(id__exact=self.id)
if len(sp_search) > 0:
#indeed we do
#in this case they should be isomeres and therefore have a different inchi
if self.inchi in sp_search.values_list('inchi'):
raise ValidationError(
u'A species with this chemical formula and InChI already exists in the database'
)
if self.inchi == '':
raise ValidationError(
u'Isomeres need to be distinguished via their InChI')