code gardening in models

Former-commit-id: 1a77fa40743d91a6e6e19eea5d497cede393f08b

ippisite/ippidb/models.py

@@ -87,7 +87,7 @@ class Taxonomy(AutoFillableModel):
 
 class MolecularFunction(AutoFillableModel):
     go_id = models.CharField('Gene Ontology ID', unique=True, max_length=10)
-                             # GO term id format: 'GO:0000000'
+    # GO term id format: 'GO:0000000'
     description = models.CharField('description', max_length=500)
 
     def autofill(self):
@@ -140,8 +140,8 @@ class Domain(AutoFillableModel):
     pfam_id = models.CharField('Pfam Family Identifier', max_length=20)
     pfam_description = models.CharField('Pfam Description', max_length=100)
     domain_family = models.CharField('Domain family', max_length=25)
-                                     # TODO: what is this field? check database
-                                     # contents
+    # TODO: what is this field? check database
+    # contents
 
     def autofill(self):
         info = get_pfam_info(self.pfam_acc)
@@ -195,11 +195,12 @@ class Symmetry(models.Model):
 
 class Disease(models.Model):
     name = models.CharField('Disease', max_length=30, unique=True)
-                            # is there any database/nomenclature for diseases?
+    # is there any database/nomenclature for diseases?
 
     def __str__(self):
         return self.name
 
+
 class PpiFamily(models.Model):
     name = models.CharField('Name', max_length=30, unique=True)
 
@@ -209,6 +210,7 @@ class PpiFamily(models.Model):
     def __str__(self):
         return self.name
 
+
 class Ppi(models.Model):
     pdb_id = models.CharField('PDB ID', max_length=4, null=True)
     pockets_nb = models.IntegerField(
@@ -235,16 +237,19 @@ class Ppi(models.Model):
 
     @property
     def name(self):
-        all_protein_names = set([ppi_complex.complex.protein.short_name for ppi_complex in self.get_ppi_complexes()])
-        bound_protein_names = set([ppi_complex.complex.protein.short_name for ppi_complex in self.get_ppi_bound_complexes()])
+        all_protein_names = set(
+            [ppi_complex.complex.protein.short_name for ppi_complex in self.get_ppi_complexes()])
+        bound_protein_names = set(
+            [ppi_complex.complex.protein.short_name for ppi_complex in self.get_ppi_bound_complexes()])
         partner_protein_names = all_protein_names - bound_protein_names
         bound_str = ','.join(bound_protein_names)
         partner_str = ','.join(partner_protein_names)
         name = bound_str
-        if partner_str!='':
+        if partner_str != '':
             name += ' / ' + partner_str
         return name
 
+
 class PpiComplex(models.Model):
     ppi = models.ForeignKey(Ppi, models.CASCADE)
     complex = models.ForeignKey(ProteinDomainComplex, models.CASCADE)
@@ -257,6 +262,7 @@ class PpiComplex(models.Model):
     def __str__(self):
         return 'PPI {}, Complex {} ({})'.format(self.ppi, self.complex, self.cc_nb)
 
+
 class Compound(models.Model):
     canonical_smile = models.CharField(
         'Canonical Smile', unique=True, max_length=500)
@@ -444,7 +450,7 @@ class Compound(models.Model):
         best_pXC50_activity = self.best_pXC50_activity
         if best_pXC50_activity is None:
             return None
-        return float(best_pXC50_activity - self.a_log_p)     
+        return float(best_pXC50_activity - self.a_log_p)
 
     @property
     def best_pXC50_activity_ppi_name(self):
@@ -491,10 +497,14 @@ class Compound(models.Model):
 
 
 class PcaBiplotData(models.Model):
-    pca_biplot_data = models.CharField('PCA biplot JSON data', max_length=150000, blank=True, null=True)
+    pca_biplot_data = models.CharField(
+        'PCA biplot JSON data', max_length=150000, blank=True, null=True)
+
 
 class LeLleBiplotData(models.Model):
-    le_lle_biplot_data = models.CharField('LE-LLE biplot JSON data', max_length=150000, blank=True, null=True)
+    le_lle_biplot_data = models.CharField(
+        'LE-LLE biplot JSON data', max_length=150000, blank=True, null=True)
+
 
 class MDDRActivityClass(models.Model):
     name = models.CharField('Activity Class', max_length=100, unique=True)
@@ -581,17 +591,20 @@ class TestActivityDescription(models.Model):
         ('U', 'Unspecified')
     )
     biblio = models.ForeignKey(Bibliography, models.CASCADE)
-    protein_domain_bound_complex = models.ForeignKey(ProteinDomainBoundComplex, models.CASCADE)
+    protein_domain_bound_complex = models.ForeignKey(
+        ProteinDomainBoundComplex, models.CASCADE)
     ppi = models.ForeignKey(Ppi, models.CASCADE, blank=True, null=True)
     test_name = models.CharField('Test name', max_length=100)
     is_primary = models.BooleanField('Is primary')
-    protein_bound_construct = models.CharField('Protein bound construct', max_length=5, choices=PROTEIN_BOUND_CONSTRUCTS, blank=True, null=True)
+    protein_bound_construct = models.CharField(
+        'Protein bound construct', max_length=5, choices=PROTEIN_BOUND_CONSTRUCTS, blank=True, null=True)
     test_type = models.CharField('Test type', max_length=5, choices=TEST_TYPES)
     test_modulation_type = models.CharField(
         'Test modulation type', max_length=1, choices=TEST_MODULATION_TYPES)
     nb_active_compounds = models.IntegerField(
         'Total number of active compounds')
-    cell_line = models.ForeignKey(CellLine, models.CASCADE, blank=True, null=True)
+    cell_line = models.ForeignKey(
+        CellLine, models.CASCADE, blank=True, null=True)
 
     def get_complexes(self):
         """
@@ -606,7 +619,7 @@ class TestActivityDescription(models.Model):
     @property
     def protein_domain_partner_complex(self):
         for ppic in self.ppi.ppicomplex_set.all():
-            if hasattr(ppic.complex,'proteindomainpartnercomplex'):
+            if hasattr(ppic.complex, 'proteindomainpartnercomplex'):
                 return ppic.complex.proteindomainpartnercomplex
         return None
 
@@ -624,7 +637,8 @@ class CompoundActivityResult(models.Model):
         ('pKi', 'pKi (inhibition constant, -log10)'),
     )
     compound = models.ForeignKey(Compound, models.CASCADE)
-    test_activity_description = models.ForeignKey(TestActivityDescription, models.CASCADE)
+    test_activity_description = models.ForeignKey(
+        TestActivityDescription, models.CASCADE)
     activity_type = models.CharField(
         'Activity type', max_length=5, choices=ACTIVITY_TYPES)
     activity = models.DecimalField(
@@ -644,6 +658,7 @@ class CompoundActivityResult(models.Model):
     def is_best(self):
         return self.compound.best_pXC50_compound_activity_result.id == self.id
 
+
 class TestCytotoxDescription(models.Model):
     biblio = models.ForeignKey(Bibliography, models.CASCADE)
     test_name = models.CharField('Cytotoxicity test name', max_length=100)
@@ -654,7 +669,8 @@ class TestCytotoxDescription(models.Model):
 
 class CompoundCytotoxicityResult(models.Model):
     compound = models.ForeignKey(Compound, models.CASCADE)
-    test_cytotoxicity_description = models.ForeignKey(TestCytotoxDescription, models.CASCADE)
+    test_cytotoxicity_description = models.ForeignKey(
+        TestCytotoxDescription, models.CASCADE)
     toxicity = models.BooleanField('Toxicity', default=False)
 
     class Meta: