Reintroduced the Stellwagen nucleic acid model.

lewisamarshall · Jul 15, 2016 · 4938f76 · 4938f76
1 parent 721a386
commit 4938f76
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Showing 3 changed files with 34 additions and 19 deletions.
diff --git a/ionize/PolyIon/NucleicAcid.py b/ionize/PolyIon/NucleicAcid.py
@@ -38,24 +38,31 @@ def __init__(self, name=None,
     def mobility(self, pH=None, ionic_strength=None, temperature=None):
         pH, ionic_strength, temperature = \
                 self._resolve_context(pH, ionic_strength, temperature)
-        # TODO: Introduce manning condensation model
-        # mu = (3.75 - 1.8 * (self.size**-.6)) * 1e-8
-        lb = self._solvent.bjerrum(temperature)
-        k = 1./self._solvent.debye(ionic_strength, temperature)
-        mu = 6 * pi * self._solvent.viscosity(temperature) * lb / self.friction()
-        mu -= 2 * self.charge() * log(1 - exp(-k * lb / self.charge()))
+        mu = (3.75 - 1.8 * (self.size**-.6)) * 1e-8
         return mu
 
+
     def charge(self, pH=None, ionic_strength=None, temperature=None,
                moment=1):
         pH, ionic_strength, temperature = \
                 self._resolve_context(pH, ionic_strength, temperature)
 
-        return -1 * self.length() / self._solvent.bjerrum(temperature)
-
+        return -1. * self.length() / self._solvent.bjerrum(temperature)
 
     def length(self):
-        return self.size * DNA_LENGTH # TODO: Define
+        per_bp_length = 3.4e-10 # 3.4 Angstrom in meters
+        return self.size * per_bp_length
 
-    def friction(self, pH=None, ionic_strength=None, temperature=None):
+    # TODO: Finish the manning model below
+    def _friction(self, pH=None, ionic_strength=None, temperature=None):
         pass
+
+    def _manning_mobility(self, pH=None, ionic_strength=None, temperature=None):
+        pH, ionic_strength, temperature = \
+                self._resolve_context(pH, ionic_strength, temperature)
+
+        lb = self._solvent.bjerrum(temperature)
+        k = 1./self._solvent.debye(ionic_strength, temperature)
+        mu = 6 * pi * self._solvent.viscosity(temperature) * lb / self.friction()
+        mu -= 2 * self.charge() * log(1 - exp(-k * lb / self.charge()))
+        return mu
diff --git a/ionize/__version__.py b/ionize/__version__.py
@@ -1 +1 @@
-__version__ = '0.21.4'
+__version__ = '0.22.0'
diff --git a/ionize/tests.py b/ionize/tests.py
@@ -365,14 +365,22 @@ def test_moderate(self):
         self.assertFalse(sol.moderate(), 'Unbuffered acid evaluated as safe.')
         self.assertTrue(sol.titrate('tris', 8).moderate(), 'Tris buffer evaluated as unsafe.')
 
-#class TestNucleicAcid(unittest.TestCase):
-#
-#    def test_mobility(self):
-#        mu = 0
-#        for n in [10, 100, 1000, 10000, 100000, None]:
-#            mup = NucleicAcid(size=n).mobility()
-#            self.assertGreater(mup, mu, "Mobility didn't increase with size")
-#            mu = mup
+class TestNucleicAcid(unittest.TestCase):
+
+    def test_mobility(self):
+       mu = 0
+       for n in [10, 100, 1000, 10000, 100000, None]:
+           mup = NucleicAcid(size=n).mobility()
+           self.assertGreater(mup, mu, "Mobility didn't increase with size.")
+           mu = mup
+
+    def test_charge(self):
+        ch = 0
+        for n in [10, 100, 1000, 10000, 100000, None]:
+            chp = NucleicAcid(size=n).charge()
+            self.assertLess(chp, 0, "Mobility is not negative.")
+            self.assertGreater(abs(chp), abs(ch), "Mobility doesn't increase with size.")
+            ch = chp
 
 
 class TestPeptide(unittest.TestCase):