class Compound(models.Model):
name = models.CharField(max_length=256)
molecule = models.MolField()
torsionbv = models.BfpField(null=True)
mfp2 = models.BfpField(null=True)
ffp2 = models.BfpField(null=True)
class Compound(models.Model):
unique_id = models.CharField(max_length=13, unique=True, blank=False)
description = models.TextField(blank=True)
smiles = models.CharField(max_length=4096, blank=False, unique=True)
inchi = models.CharField(max_length=4096, blank=False, unique=True)
inchi_key = models.CharField(max_length=27, blank=False, unique=True)
mol_weight_exact = models.FloatField(blank=False)
heavy_atoms_count = models.IntegerField(blank=False)
ring_count = models.IntegerField(blank=False)
mol = models.MolField()
torsionbv = models.BfpField(null=True)
mfp2 = models.BfpField(null=True)
ffp2 = models.BfpField(null=True)
class MoleculeAlreadyExists(Exception):
pass
def _generate_id(self):
number = datetime.now().timestamp()
number=int(number * 10e6) # get seconds
random_data = number.to_bytes(8, byteorder='big')
return 'MI-M-' + hashlib.md5(random_data).hexdigest()[:8]
def __init__(self, *args, **kwargs):
if len(args) > 2:
super(Compound, self).__init__(*args, **kwargs)
return
mol_as_RDmol = args[0] if len(args) > 0 else None
if not mol_as_RDmol:
mol_as_RDmol = kwargs['mol_as_RDmol'] if 'mol_as_RDmol' in kwargs else None
if not mol_as_RDmol:
raise RuntimeError("No RDMol specified")
description = args[1] if len(args) > 1 else None
if not description:
description = kwargs['description'] if 'description' in kwargs else ''
new_kwargs = dict()
new_kwargs['unique_id'] = self._generate_id()
new_kwargs['smiles'] = Chem.MolToSmiles(mol_as_RDmol, isomericSmiles=True, canonical=True)
new_kwargs['inchi'] = Chem.MolToInchi(mol_as_RDmol)
new_kwargs['inchi_key'] = Chem.InchiToInchiKey(new_kwargs['inchi'])
new_kwargs['mol_weight_exact'] = Descriptors.ExactMolWt(mol_as_RDmol)
new_kwargs['heavy_atoms_count'] = Lipinski.HeavyAtomCount(mol_as_RDmol)
new_kwargs['ring_count'] = Lipinski.RingCount(mol_as_RDmol)
new_kwargs['mol'] = mol_as_RDmol
super(Compound, self).__init__(description=description, **new_kwargs)
def save(self, *args, **kwargs):
if Compound.objects.filter(inchi_key=self.inchi_key).exists():
raise Compound.MoleculeAlreadyExists("Molecule with the same InchiKey was found. Cannot save.")
super(Compound, self).save(*args, **kwargs)
def __str__(self):
return self.unique_id
class Fingerprint(rdkit_models.Model):
bfp = rdkit_models.BfpField(null=True, verbose_name="Binary Fingerprint")
class Meta:
db_table = 'compound_fingerprint'
verbose_name = 'Compound Fingerprint'
verbose_name_plural = 'Compound Fingerprints'
def __unicode__(self):
return u"Compound Fingerprint with ID {}".format(self.id)
class ChemicalEntity(models.Model):
canonicalSMILES = models.CharField(max_length=65536, unique=True, blank=False)
inchi = models.CharField(max_length=65536, unique=True, blank=False)
inchiKey = models.CharField(max_length=65536, unique=True, blank=False)
# from django-rdkit
rdMol = models.MolField()
morganFP = models.BfpField(null=True)
class Meta:
unique_together = ('canonicalSMILES', 'inchiKey')
def __str__(self):
return '%s object <%s>' % (self.__class__.__name__, self.inchiKey)
@property
def fingerprint(self):
if not self.morganFP:
self.morganFP = AllChem.GetMorganFingerprintAsBitVect(self.rdMol, radius=2, nBits=512)
return self.morganFP
class BfpModel(models.Model):
bfp = models.BfpField(null=True)