Merge pull request #34 from martimunicoy/torsions_fix

Improve dihedral compatibility

docs/releasehistory.rst

@@ -22,11 +22,12 @@ Bugfixes
 """"""""
 - `PR #22 <https://github.com/martimunicoy/offpele/pull/22>`_: Fixes many bugs. For example, the default output name of the solvent parameters template is changed to `ligandParams.txt`, which is the name that PELE expects.
 - `PR #32 <https://github.com/martimunicoy/offpele/pull/32>`_: Minor fixes in ToolkitWrapper classes.
+- `PR #34 https://github.com/martimunicoy/offpele/pull/34: Improves the translation of dihedrals coming from the Open Force Fielf Toolkit and corrects the lack of exclusions in PELE 1-4 list that result from Impact's dihedral definitions.
 
 Tests added
 """""""""""
 - `PR #31 <https://github.com/martimunicoy/offpele/pull/31>`_: Adds tests to validate some functions of the new SchrodingerToolkitWrapper.
-
+- `PR #34 https://github.com/martimunicoy/offpele/pull/34: Adds tests to further validate the assignment of parameters from the Open Force Field Toolkit.
 
 0.2.1
 -----

offpele/template/impact.py

@@ -251,8 +251,8 @@ def _write_bond(self, file):
             # Atom 2 id
             file.write('{:5d}'.format(idx2))
             file.write(' ')
-            # Spring constant (PELE works with half of the OFF's spring)
-            file.write('{: 9.3f}'.format(spring / 2.0))
+            # Spring constant
+            file.write('{: 9.3f}'.format(spring))
             file.write(' ')
             # Equilibrium distance
             file.write('{: 6.3f}\n'.format(eq_dist))
@@ -283,8 +283,8 @@ def _write_thet(self, file):
             # Atom 3 id
             file.write('{:5d}'.format(idx3))
             file.write(' ')
-            # Spring constant (PELE works with half of the OFF's spring)
-            file.write('{: 11.5f}'.format(spring / 2.0))
+            # Spring constant
+            file.write('{: 11.5f}'.format(spring))
             # Equilibrium angle
             file.write('{: 11.5f}\n'.format(eq_angl))
 
@@ -973,6 +973,8 @@ def __init__(self, proper):
                          prefactor=proper.prefactor,
                          constant=proper.constant)
 
+        self.exclude = proper.exclude
+
     @property
     def atom1_idx(self):
         """
@@ -1007,7 +1009,10 @@ def atom3_idx(self):
         atom3_idx : int
             The index of the third atom involved in this Proper object
         """
-        return super().atom3_idx + 1
+        if self.exclude:
+            return (super().atom3_idx + 1) * -1
+        else:
+            return super().atom3_idx + 1
 
     @property
     def atom4_idx(self):