class Molecule(models.Model):
"""A Django model to hold the information for a molecule -> a 3D set of
co-ordinates"""
# Character attributes
smiles = models.CharField(max_length=255, db_index=True, null=True)
lig_id = models.CharField(max_length=5, null=True)
chain_id = models.CharField(max_length=1, null=True)
# The type of map
# Set the groups types
mol_choices, default_mol = get_mol_choices()
mol_type = models.CharField(choices=mol_choices,
default=default_mol,
max_length=2)
# Textfield
sdf_info = models.TextField(null=True)
# Float attributes
rscc = models.FloatField(null=True)
occupancy = models.FloatField(null=True)
x_com = models.FloatField(null=True)
y_com = models.FloatField(null=True)
z_com = models.FloatField(null=True)
rmsd = models.FloatField(null=True)
# Foreign key relations
prot_id = models.ForeignKey(Protein)
cmpd_id = models.ForeignKey(Compound)
# Unique constraints
class Meta:
unique_together = ("prot_id", "cmpd_id", "mol_type")
permissions = (("view_molecule", "View molecule"), )
class Molecule(models.Model):
"""Django model for holding information about a Molecule. A molecule is linked to a compound, and represents the
unique 3D coordinates for that molecule. Note a compound can be linked to multiple molecules, each with a different
3D structure, but the same 2D structure
Parameters
----------
smiles: CharField
The smiles string of the molecule. (optional) TODO: Check if this is needed...
lig_id: CharField
The ligand ID from the pdb file it originated from (e.g. LIG 1 A) (optional)
chain_id: CharField
The chain from the protein structure pdb file that this ligand is from (e.g. A) (optional)
mol_type: CharField
molecule type - from a pre-defined list and determined by file extension on upload (defined in
loader.config.get_mol_choices):
mol_choices = (
(PROASIS, "Proasis molecule", ".mol", "MOL"),
(SDF, "Sdf molecule", ".sdf", "SDF"),
(HYDROGEN, "Hydrogens added ", "_h.mol", "H_MOL"),
(
HYDROGEN_AM1_CHARGES,
"Mol2 format with Hydrogens and AM1 BCC",
".mol2",
"MOL2",
),
)
sdf_info: TextField
The 3D coordinates for the molecule in MDL (mol file) format. Taken directly from the uploaded file
rscc: FloatField
The RSCC score of the molecule 3D coordinates vs. PANDDA event map (optional)
occupancy: FloatField
The occupancy (electron density) of the molecule (optional)
x_com: FloatField
x-coordinate for centre of mass (optional)
y_com: FloatField
y-coordinate for centre of mass (optional)
z_com: FloatField
z-coordinate for centre of mass (optional)
rmsd: FloatField
RMSD of this molecule compared to ? (optional - unused)
prot_id: ForeignKey
Foreign key link to the associated protein (apo) that this ligand was pulled from
cmpd_id: ForeignKey
Foreign key link to the associated 2D compound
history: HistoricalRecords
Tracks the changes made to an instance of this model over time
"""
# Character attributes
smiles = models.CharField(max_length=255, db_index=True, null=True)
lig_id = models.CharField(max_length=5, null=True)
chain_id = models.CharField(max_length=1, null=True)
# The type of map
# Set the groups types
mol_choices, default_mol = get_mol_choices()
mol_type = models.CharField(choices=mol_choices, default=default_mol, max_length=2)
# Textfield
sdf_info = models.TextField(null=True)
# Float attributes
rscc = models.FloatField(null=True)
occupancy = models.FloatField(null=True)
x_com = models.FloatField(null=True)
y_com = models.FloatField(null=True)
z_com = models.FloatField(null=True)
rmsd = models.FloatField(null=True)
# Foreign key relations
prot_id = models.ForeignKey(Protein, on_delete=models.CASCADE)
cmpd_id = models.ForeignKey(Compound, on_delete=models.CASCADE)
history = HistoricalRecords()
# Unique constraints
class Meta:
unique_together = ("prot_id", "cmpd_id", "mol_type")