minor reformats for models

ippisite/ippidb/models.py

@@ -76,9 +76,9 @@ class Bibliography(AutoFillableModel):
     source = models.CharField(
         'Bibliographic type', max_length=2, choices=SOURCES, default=SOURCES[0][0])
     id_source = models.CharField('Bibliographic ID', max_length=25)
-    title = models.CharField('Title', max_length=300)
-    journal_name = models.CharField('Journal name', max_length=50, null=True, blank=True)
-    authors_list = models.CharField('Authors list', max_length=500)
+    title = models.TextField('Title')
+    journal_name = models.TextField('Journal name', null=True, blank=True)
+    authors_list = models.TextField('Authors list')
     biblio_year = models.PositiveSmallIntegerField('Year')
     cytotox = models.BooleanField('Cytotoxicity data', default=False)
     in_silico = models.BooleanField('in silico study', default=False)
@@ -162,7 +162,7 @@ class Bibliography(AutoFillableModel):
 
 class Taxonomy(AutoFillableModel):
     """
-    Taxonomy IDs (from NCBI Taxonomy) 
+    Taxonomy IDs (from NCBI Taxonomy)
     and the corresponding human-readable name
     """
     taxonomy_id = models.DecimalField(
@@ -186,7 +186,7 @@ class Taxonomy(AutoFillableModel):
 
 class MolecularFunction(AutoFillableModel):
     """
-    Molecular functions (from Gene Ontology) 
+    Molecular functions (from Gene Ontology)
     and the corresponding human-readable description
     """
     go_id = models.CharField('Gene Ontology ID', unique=True, max_length=10)
@@ -214,7 +214,7 @@ class MolecularFunction(AutoFillableModel):
 
 class Protein(AutoFillableModel):
     """
-    Protein information (from Uniprot) 
+    Protein information (from Uniprot)
     and the corresponding human-readable name
     """
     uniprot_id = models.CharField('Uniprot ID', unique=True, max_length=10)
@@ -275,7 +275,7 @@ class Protein(AutoFillableModel):
 
 class Domain(AutoFillableModel):
     """
-    Domain (i.e. Protein domain) information (from PFAM) 
+    Domain (i.e. Protein domain) information (from PFAM)
     """
     pfam_acc = models.CharField('Pfam Accession', max_length=10, unique=True)
     pfam_id = models.CharField('Pfam Family Identifier', max_length=20)
@@ -470,8 +470,8 @@ class CompoundManager(models.Manager):
         # Lipinsky a_log_p (<5)
         qs = qs.annotate(lipinsky_a_log_p=Case(When(a_log_p__lte=5, then=True), default=False, output_field=BooleanField()))
         # Lipinsky global
-        qs = qs.annotate(lipinsky_score=Cast(F('lipinsky_mw'), IntegerField())+Cast(F('lipinsky_hba'), IntegerField())+ \
-            Cast(F('lipinsky_hbd'), IntegerField()) + Cast(F('lipinsky_a_log_p'), IntegerField()))
+        qs = qs.annotate(lipinsky_score=Cast(F('lipinsky_mw'), IntegerField()) + Cast(F('lipinsky_hba'), IntegerField()) +
+                         Cast(F('lipinsky_hbd'), IntegerField()) + Cast(F('lipinsky_a_log_p'), IntegerField()))
         qs = qs.annotate(lipinsky=Case(When(lipinsky_score__gte=3, then=True), default=False, output_field=BooleanField()))
         # Veber hba_hbd (<=12)
         qs = qs.annotate(hba_hbd=F('nb_acceptor_h')+F('nb_donor_h'))
@@ -481,14 +481,12 @@ class CompoundManager(models.Manager):
         # Veber Rotatable Bonds (<=10)
         qs = qs.annotate(veber_rb=Case(When(nb_rotatable_bonds__lte=10, then=True), default=False, output_field=BooleanField()))
         # Veber global (Rotatable bonds and (hba_hbd or tpsa))
-        #qs = qs.annotate(veber=F('veber_rb').bitand(F('veber_hba_hbd').bitor(F('veber_tpsa'))))
         qs = qs.annotate(veber=Case(When(Q(Q(nb_rotatable_bonds__lte=10) & (Q(hba_hbd__lte=12) | Q(tpsa__lte=140))), then=True), default=False, output_field=BooleanField()))
         # Pfizer AlogP (<=3)
         qs = qs.annotate(pfizer_a_log_p=Case(When(a_log_p__lte=3, then=True), default=False, output_field=BooleanField()))
         # Pfizer TPSA (>=75)
         qs = qs.annotate(pfizer_tpsa=Case(When(tpsa__gte=75, then=True), default=False, output_field=BooleanField()))
         # Pfizer global (AlogP and TPSA)
-        #qs = qs.annotate(pfizer=F('pfizer_a_log_p').bitand(F('pfizer_tpsa')))
         qs = qs.annotate(pfizer=Case(When(Q(Q(a_log_p__lte=3) & Q(tpsa__gte=75)), then=True), default=False, output_field=BooleanField()))
         # PDB ligand available
         qs = qs.annotate(pdb_ligand_av=Cast(Max(Case(When(compoundaction__ligand_id__isnull=False, then=1), default=0, output_field=IntegerField())), BooleanField()))
@@ -514,7 +512,7 @@ class CompoundManager(models.Manager):
         qs = qs.annotate(insilico_av=Cast(Max(Case(When(refcompoundbiblio__bibliography__in_silico=True, then=1), default=0, output_field=IntegerField())), BooleanField()))
         # number of tests available
         qs = qs.annotate(tests_av=Count('compoundactivityresult', distinct=True))
-        #@formatter:on
+        # @formatter:on
         return qs