more tests for the test god

Author: richardjgowers

foyer/tests/test_trappe.py

@@ -1,7 +1,7 @@
 import glob
 import itertools as it
 import os
-
+from scipy.constants import N_A, k, calorie
 import parmed as pmd
 from pkg_resources import resource_filename
 import pytest
@@ -96,6 +96,13 @@ def mol2file(request):
     )
 
 
+def parmed2trappe(val):
+    return val * calorie / (k * N_A / 1000.)
+
+def angle_parmed2trappe(val):
+    return 2 * parmed2trappe(val)
+
+
 class TestTrappeReferences(object):
     @staticmethod
     def check_atoms(ref, struc):
@@ -106,8 +113,9 @@ def check_atoms(ref, struc):
 
             assert_almost_equal(foyer_atom.charge, float(charge))
             assert_almost_equal(foyer_atom.sigma, float(sigma))
-            # TODO: figure out units here
-            #assert_almost_equal(foyer_atom.epsilon, float(epsilon))
+            assert_almost_equal(parmed2trappe(foyer_atom.epsilon),
+                                float(epsilon),
+                                decimal=3)
 
     @staticmethod
     def check_bonds(ref, struc):
@@ -122,18 +130,43 @@ def check_bonds(ref, struc):
         # lookup foyer bond and compare length
         for ref_bond in ref_bonds:
             _, desc, _, length = ref_bond.strip().split(',')
-            i, j = map(int, ref_bond.split(',')[1].strip("\"\'").split('-'))
+            i, j = map(int, desc.strip("\"\'").split('-'))
             foyer_bond = bond_dict[i, j]
 
-            assert_almost_equal(float(length), foyer_bond.type.req)
+            assert_almost_equal(foyer_bond.type.req, float(length))
             # trappe is fixed bond length, no point in K comparison
 
     @staticmethod
     def check_angles(ref, struc):
         ref_angles = ref['bend']
-
         assert len(ref_angles) == len(struc.angles)
 
+        angle_dict = {}
+        for a in struc.angles:
+            i, j, k = a.atom1.idx, a.atom2.idx, a.atom3.idx
+            if k < i:
+                i, j, k = k, j, i
+            angle_dict[i+1, j+1, k+1] = a
+
+        for ref_angle in ref_angles:
+            _, desc, _, angle, k_angle = ref_angle.strip().split(",")
+            i, j, k = map(int, desc.strip("\"\'").split('-'))
+
+            foyer_angle = angle_dict[i, j, k]
+
+            assert_almost_equal(foyer_angle.type.theteq,
+                                float(angle),
+                                decimal=4)
+            assert_almost_equal(angle_parmed2trappe(foyer_angle.type.k),
+                                float(k_angle),
+                                decimal=3)
+
+    @staticmethod
+    def check_dihedrals(ref, struc):
+        ref_dihedrals = ref['torsion']
+
+        assert len(ref_dihedrals) == len(struc.dihedrals)
+
     @pytest.mark.parametrize('trappe_ref,mol2file', [
         ('methyl_acrylate/trappe_parameters_96.csv', 'methyl_acrylate'),
     ], indirect=True)
@@ -144,6 +177,8 @@ def test_trappe_reference(self, trappe_ref, mol2file):
 
         self.check_angles(trappe_ref, mol2file)
 
+        self.check_dihedrals(trappe_ref, mol2file)
+
 
 if __name__ == '__main__':
     TestTraPPE().find_correctly_implemented()