add docs to ippidb.models

ippisite/ippidb/models.py

@@ -543,6 +543,11 @@ class PpiComplex(models.Model):
 
 
 class CompoundsManager(models.Manager):
+    """
+    Model manager for the `Compound` class
+    provides selections to `validated` or `user-visible` compounds
+    """
+
     def for_user(self, current_user):
         """
         Get compounds visible to a given user
@@ -876,7 +881,9 @@ class Compound(AutoFillableModel):
         # ]
 
     def compute_drugbank_compound_similarity(self):
-        """ compute Tanimoto similarity to existing DrugBank compounds """
+        """
+        Compute Tanimoto similarity to existing DrugBank compounds
+        """
         self.save()
         # fingerprints to compute drugbank similarities are in settings module, default FP2
         fingerprinter = FingerPrinter(getattr(settings, "DRUGBANK_FINGERPRINTS", "FP2"))
@@ -901,14 +908,14 @@ class Compound(AutoFillableModel):
     @property
     def biblio_refs(self):
         """
-        return all RefCompoundBiblio related to this compound
+        Return all RefCompoundBiblio related to this compound
         """
         return RefCompoundBiblio.objects.filter(compound=self)
 
     @property
     def pfam_ids(self):
         """
-        return all PFAM ids for the domain of the proteins of the bound
+        Return all PFAM ids for the domain of the proteins of the bound
         complexes in the PPIs this compound has an action on
         """
         pfam_ids = set()
@@ -920,6 +927,9 @@ class Compound(AutoFillableModel):
 
     @property
     def best_pXC50_compound_activity_result(self):
+        """
+        Return the best pXC50 activity
+        """
         best_pXC50_activity = self.best_activity
         if best_pXC50_activity is None:
             return None
@@ -932,7 +942,7 @@ class Compound(AutoFillableModel):
     @property
     def bioch_tests_count(self):
         """
-        return the number of associated biochemical tests
+        Return the number of associated biochemical tests
         """
         return (
             self.compoundactivityresult_set.all()
@@ -943,7 +953,7 @@ class Compound(AutoFillableModel):
     @property
     def cell_tests_count(self):
         """
-        return the number of associated cell tests
+        Return the number of associated cell tests
         """
         return (
             self.compoundactivityresult_set.all()
@@ -953,9 +963,16 @@ class Compound(AutoFillableModel):
 
     @property
     def sorted_similar_drugbank_compounds(self):
+        """
+        Return the similar Drugbank compounds,
+        sorted by decreasing similarity
+        """
         return self.drugbankcompoundtanimoto_set.order_by("-tanimoto")
 
     def is_validated(self):
+        """
+        Return the compound validation status
+        """
         # if compound is not linked to any CompoundAction this is
         # because it was dereferenced because of duplication by
         # `replace_compound_references`
@@ -969,21 +986,38 @@ class Compound(AutoFillableModel):
     is_validated.boolean = True
 
     def autofill(self):
+        """
+        Finalize the computation of the Compound
+        by computing InChi, InChiKey and Drugbank similarity  
+        """
         # compute InChi and InChiKey
         self.inchi = smi2inchi(self.canonical_smile)
         self.inchikey = smi2inchikey(self.canonical_smile)
         self.compute_drugbank_compound_similarity()
 
     def compute_fsp3(self):
+        """
+        Compute FSP3 from CSP3 and number of carbons
+        """
         self.fsp3 = self.nb_csp3 / self.nb_c
 
     def __str__(self):
+        """
+        String representation
+        """
         return "Compound #{}".format(self.id)
 
     def get_absolute_url(self):
+        """
+        Get absolute URL to the Compound page
+        """
         return reverse("compound_card", kwargs={"pk": self.pk})
 
     def clean(self):
+        """
+        Perform additional checks:
+        - check common name for the Compound is unique
+        """
         if (
             self.common_name is not None
             and self.common_name != ""
@@ -994,11 +1028,14 @@ class Compound(AutoFillableModel):
             self.add_error("common_name", "A compound with this name already exists")
 
     def get_jobs(self):
+        """
+        Retrieve the jobs for the compound
+        """
         return CompoundJob.objects.filter(compound=self)
 
     def replace_compound_references(self, replacing_compound):
         """
-        replace the references to a given compound in the data with
+        Replace the references to a given compound in the data with
         references to another new compound. used to deal with
         duplicates in the database
         """