From 87578e926f6c0f0f4e8e14a7fe7ec8dca8eea8a5 Mon Sep 17 00:00:00 2001
From: Jonathan Karr <jonrkarr@gmail.com>
Date: Wed, 14 Nov 2018 00:53:10 -0500
Subject: [PATCH] fixing translation of protein sequences, empirical formule,
 molecular weights

---
 tests/test_prokaryote_schema.py | 16 +++++++++-------
 wc_kb/prokaryote_schema.py      | 18 +++++++++---------
 2 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/tests/test_prokaryote_schema.py b/tests/test_prokaryote_schema.py
index 39650a7..6fab4f4 100644
--- a/tests/test_prokaryote_schema.py
+++ b/tests/test_prokaryote_schema.py
@@ -189,28 +189,30 @@ def test_constructor(self):
         self.assertEqual(protein.cell, None)
 
     def test_get_seq(self):
-
-        # Use table 4 since example genes are from mycoplasma genitallium
+        # Use translation table 4 since example genes are from 
+        # Mycoplasma genitallium
 
         # MPN001
         self.assertEqual(self.prot1.get_seq()[0:10], 'MKVLINKNEL')
+        self.assertEqual(self.prot1.get_seq()[-10:], 'ELKEILVPSK')
 
         # MPN011
         self.assertEqual(self.prot2.get_seq()[0:10], 'MKFKFLLTPL')
+        self.assertEqual(self.prot2.get_seq()[-10:], 'LFRYLVYLIE')
 
     def test_get_empirical_formula(self):
         # MPN001
         self.assertEqual(self.prot1.get_empirical_formula(),
-                         chem.EmpiricalFormula('C1980H3144N510O595S7'))
+                         chem.EmpiricalFormula('C1980H3146N510O596S7'))
         # MPN011
         self.assertEqual(self.prot2.get_empirical_formula(),
-                         chem.EmpiricalFormula('C1246H1926N306O351S3'))
+                         chem.EmpiricalFormula('C1246H1928N306O352S3'))
 
     def test_get_mol_wt(self):
         # MPN001
-        self.assertAlmostEqual(self.prot1.get_mol_wt(), 43838.327, delta=0.3)
+        self.assertAlmostEqual(self.prot1.get_mol_wt(), 43856.342, delta=0.3)
         # MNP011
-        self.assertAlmostEqual(self.prot2.get_mol_wt(), 26905.085, delta=0.3)
+        self.assertAlmostEqual(self.prot2.get_mol_wt(), 26923.100, delta=0.3)
 
     def test_get_charge(self):
         self.assertEqual(self.prot1.get_charge(), 1)
@@ -309,4 +311,4 @@ def test_ComplexSpeciesType(self):
         self.assertAlmostEqual(complex1.get_mol_wt(),
                                (2*prot1.get_mol_wt() + 3 * prot2.get_mol_wt()))
         self.assertEqual(complex1.get_empirical_formula(),
-                         chem.EmpiricalFormula('C7698H12066N1938O2243S23'))
+                         chem.EmpiricalFormula('C7698H12076N1938O2248S23'))
diff --git a/wc_kb/prokaryote_schema.py b/wc_kb/prokaryote_schema.py
index 4faafb5..8c75d19 100644
--- a/wc_kb/prokaryote_schema.py
+++ b/wc_kb/prokaryote_schema.py
@@ -119,22 +119,22 @@ class Meta(obj_model.Model.Meta):
         attribute_order = ('id', 'name', 'gene', 'rna', 'circular', 'double_stranded',
                            'half_life', 'comments', 'references', 'database_references')
 
-    def get_seq(self, cds=False):
+    def get_seq(self, cds=True):
         """ Get the sequence
 
         Returns:
             :obj:`Bio.Seq.Seq`: sequence
         """
-        return self.gene.get_seq().translate(table=self.cell.knowledge_base.translation_table, cds=cds)
+        seq = self.gene.get_seq().translate(table=self.cell.knowledge_base.translation_table, cds=cds)
+        return seq
 
-    def get_empirical_formula(self, cds=False):
+    def get_empirical_formula(self, cds=True):
         """ Get the empirical formula
 
         Returns:
             :obj:`chem.EmpiricalFormula`: empirical formula
         """
-
-        seq = self.get_seq(cds)
+        seq = self.get_seq(cds=cds)
         l = len(seq)
 
         n_a = seq.count('A')  # Ala: Alanine (C3 H7 N O2)
@@ -186,13 +186,13 @@ def get_empirical_formula(self, cds=False):
         formula.S = n_c + n_m
         return formula
 
-    def get_charge(self, cds=False):
+    def get_charge(self, cds=True):
         """ Get the charge at physiological pH
 
         Returns:
             :obj:`int`: charge
         """
-        seq = self.get_seq(cds)
+        seq = self.get_seq(cds=cds)
 
         n_r = seq.count('R')
         n_h = seq.count('H')
@@ -202,13 +202,13 @@ def get_charge(self, cds=False):
 
         return (n_r + n_h + n_k) - (n_d + n_e)
 
-    def get_mol_wt(self, cds=False):
+    def get_mol_wt(self, cds=True):
         """ Get the molecular weight
 
         Returns:
             :obj:`float`: molecular weight
         """
-        return self.get_empirical_formula(cds).get_molecular_weight()
+        return self.get_empirical_formula(cds=cds).get_molecular_weight()
 
 
 #####################