documented trappe test methods a bit more

Author: richardjgowers

foyer/tests/test_trappe.py

@@ -97,25 +97,31 @@ def mol2file(request):
 
 
 def parmed2trappe(val):
+    # convert kcal/mol (parmed units) to K/k_B (trappe units)
     return val * calorie / (k * N_A / 1000.)
 
 def angle_parmed2trappe(val):
+    # trappe angle units need doubling
     return 2 * parmed2trappe(val)
 
 def assert_dihedrals_match(foyer_d, reference_params):
+    # Check that a dihedral from foyer matches the text in the csv file
+    # foyer_d - parmed rb_torsion
+    # reference_params - dihedral parameters from trappe csv file
     def conv1(t):
-        # convert RB to Trappe#1
-        raise ValueError
+        # convert RB to original Trappe dihedral form:
+        # V = c0 + c1(1 + cos phi) + c1(1 - cos 2phi) + c3(1 + cos 3phi)
         R0, R1, R2, R3 = t.c0, t.c1, t.c2, t.c3
-        c0 = R0 - R1 + R2 - R3
-        c1 = R1 + 3/4. * R3
-        c2 = -0.5 * R2
-        c3 = 1/4. * R3
+        c0 = - R0 + R1 + R2 + R3
+        c1 = - R1 - 3/4. * R3
+        c2 = - 0.5 * R2
+        c3 = - 1/4. * R3
 
         return c0, c1, c2, c3
 
     def conv2(t):
-        # convert RB to Trappe#2
+        # convert RB to second Trappe dihedral form:
+        # V = c0 + c1 cos phi + c2 cos 2phi + c3 cos 3phi + c4 cos 4phi
         R0, R1, R2, R3, R4 = t.c0, t.c1, t.c2, t.c3, t.c4
         print(list(map(lambda x: x * calorie, [R0, R1, R2, R3, R4])))
         c0 = - R0 + 0.5 * R2 + 3/8. * R4
@@ -130,9 +136,9 @@ def conv2(t):
     # check parameters in *foyer_d* match the raw text from trappe
     # trappe's params are in one of two functional forms.....
     if len(reference_params) == 5:
-        # using later form
+        # using later form, has an extra column
         foyer_params = conv2(foyer_d.type)
-    else:
+    elif len(reference_params) == 4:
         # using original dihedral form
         foyer_params = conv1(foyer_d.type)