little updates

dwhswenson · Aug 23, 2016 · Aug 13, 2016 · Aug 13, 2016 · Aug 13, 2016 · Aug 14, 2016
commit d2cdd58d5e72309599bb998666a752ae37bed94a
diff --git a/openpathsampling/analysis/move_scheme.py b/openpathsampling/analysis/move_scheme.py
@@ -358,6 +358,19 @@ def initial_conditions_from_trajectories(self, trajectories,
         strategies : dict
             a dict that specifies the options used when ensemble functions
             are used to create a new sample.
+        preconditions : list of str
+            a list of possible steps to modify the initial list of trajectories.
+            possible choices are
+
+                1.  `sort-shortest` - sorting by shortest first,
+                2.  `sort_median` - sorting by the middle one first and then in
+                    move away from the median length
+                3.  `sort-longest` - sorting by the longest first
+                4.  `reverse` - reverse the order and
+                5.  `mirror` which will add the reversed trajectories to the
+                    list in the same order
+
+            Default is `None` which means to do nothing.
         reuse_strategy : str
             if `avoid` then reusing the same same trajectory twice is avoided.
             `avoid-symmetric` will also remove reversed copies
@@ -383,8 +396,10 @@ def initial_conditions_from_trajectories(self, trajectories,
         if sample_set is None:
             sample_set = paths.SampleSet([])
 
+        ensembles = self.list_initial_ensembles()
+
         return sample_set.generate_from_trajectories(
-            self.list_initial_ensembles(),
+            ensembles,
             trajectories,
             preconditions,
             strategies,

diff --git a/openpathsampling/sample.py b/openpathsampling/sample.py
@@ -415,7 +415,6 @@ def generate_from_trajectories(
                     list in the same order
 
             Default is `None` which means to do nothing.
-
         strategies : dict
             a dict that specifies the options used when ensemble functions
             are used to create a new sample.

diff --git a/openpathsampling/tests/testmovescheme.py b/openpathsampling/tests/testmovescheme.py
@@ -604,6 +604,14 @@ def assert_init_cond(sample_set, ensembles, expected):
             strategies=['get']
         )
 
+        # for t1 in map(lambda x: init_cond[x].trajectory, ensembles):
+        #     for i, t2 in enumerate([traj1, traj2, traj3, traj1r, traj2r, traj3r]):
+        #         print i,
+        #         if t1 == t2:
+        #             print '=='
+        #         else:
+        #             print '!='
+
         assert_init_cond(
             init_cond, ensembles,
             [traj1, traj2, traj3] + [traj3] + [traj3r] * 3