class Protein(models.Model):
"""A Django model to hold the information for a given protein, unique set of coords"""
# code for this protein (e.g. NUDT5A-x0001_1)
code = models.CharField(max_length=50, db_index=True)
target_id = models.ForeignKey(Target)
apo_holo = models.NullBooleanField()
# Set the groups types
prot_choices, default_prot = get_prot_choices()
prot_type = models.CharField(choices=prot_choices,
default=default_prot,
max_length=2)
pdb_info = models.FileField(upload_to="pdbs/", null=True, max_length=255)
bound_info = models.FileField(upload_to="bound/",
null=True,
max_length=255)
cif_info = models.FileField(upload_to="cifs/", null=True, max_length=255)
mtz_info = models.FileField(upload_to="mtzs/", null=True, max_length=255)
map_info = models.FileField(upload_to="maps/", null=True, max_length=255)
aligned = models.NullBooleanField()
aligned_to = models.ForeignKey("self", null=True)
has_eds = models.NullBooleanField()
class Meta:
unique_together = ("code", "prot_type")
permissions = (("view_protein", "View protein"), )
class Protein(models.Model):
"""Django model for holding information about a protein. A protein is a protein structure which has a unique set of
3D coordinates, rather than a target, which is a set of protein objects of the same protein. A Molecule object is
also linked to a protein, so that a complete structure is comprised of the molecule and protein in separate parts in
fragalysis.
Parameters
----------
code: CharField
A unique name for the protein (e.g. NUDT5A-x0001_1)
target_id: ForeignKey
Foreign key linking the protein to it's target
apo_holo: NullBooleanField
0 for apo (ligand removed), 1 for holo (ligand in tact)
prot_type: CharField
protein type - from a pre-defined list and determined by file extension on upload (defined in
loader.config.get_prot_choices):
prot_choices = (
(APO, "Apo", "_apo.pdb", "APO"),
(STRIPPED, "Stripped", "_no_buffer_altlocs.pdb", "STRIPPED"),
(TLEAPED, "Tleaped", "_tleap.pdb", "TLEAP"),
(CHUNKED, "Chunked", "_chunk.pdb", "CHUNK"),
(BOUND, "Bound", '_bound.pdb', "BOUND")
)
pdb_info: FileField
File link to apo pdb structure - pdb file with ligand removed
bound_info: FileField
File link to bound state structure - same as apo pdb but with ligand in-tact
cif_info: FileField
File link to cif file for ligand restraints (optional)
mtz_info: FileField
File link to uploaded mtz file (optional)
map_info: FileField
File link to uploaded map file (optional)
aligned: NullBooleanField
Bool - 1 if aligned, 0 if not
aligned_to: ForeignKey (self)
Foreign key to another instance of a protein to which this protein is aligned (optional)
has_eds: NullBooleanField
Bool - 1 if has ED, 0 it not (optional)
"""
# code for this protein (e.g. NUDT5A-x0001_1A)
code = models.CharField(max_length=50, db_index=True)
target_id = models.ForeignKey(Target, on_delete=models.CASCADE)
apo_holo = models.NullBooleanField()
# Set the groups types
prot_choices, default_prot = get_prot_choices()
prot_type = models.CharField(
choices=prot_choices, default=default_prot, max_length=2
)
pdb_info = models.FileField(upload_to="pdbs/", null=True, max_length=255)
bound_info = models.FileField(upload_to="bound/", null=True, max_length=255)
cif_info = models.FileField(upload_to="cifs/", null=True, max_length=255)
mtz_info = models.FileField(upload_to="mtzs/", null=True, max_length=255)
map_info = models.FileField(upload_to="maps/", null=True, max_length=255)
sigmaa_info = models.FileField(upload_to="maps/", null=True, max_length=255)
diff_info = models.FileField(upload_to="maps/", null=True, max_length=255)
event_info = models.FileField(upload_to="maps/", null=True, max_length=255)
aligned = models.NullBooleanField()
aligned_to = models.ForeignKey("self", null=True, on_delete=models.CASCADE)
has_eds = models.NullBooleanField()
class Meta:
unique_together = ("code", "prot_type")