[str_and_dict.get_trajectories_from_input] refactor from get_sorted_t…

…rajectories. Don't sort input lists of files. Allow mixed input, tests

mdciao/cli/cli.py

@@ -448,18 +448,18 @@ def _trajsNtop2xtcsNrefgeom(trajectories,topology):
 
     Parameters
     ----------
-    trajectories: check get_sorted_trajectories
+    trajectories: check get_trajectories_from_input
     topology : str, top
 
     Returns
     -------
     xtcs, refgeom
-    xtcs : whatever get_sorted_trajectories returns
+    xtcs : whatever get_trajectories_from_input returns
     refgeom : :obj:`mdtraj.Trajectory` object
 
     """
     # Inform about trajectories
-    xtcs = _mdcu.str_and_dict.get_sorted_trajectories(trajectories)
+    xtcs = _mdcu.str_and_dict.get_trajectories_from_input(trajectories)
     if topology is None:
         # TODO in case the xtc[0] is a pdb/grofile, it will be read one more time later
         refgeom = _load_any_geom(xtcs[0])[0]
@@ -633,16 +633,17 @@ def residue_neighborhoods(residues,
          * residues = '1,10-12,GLU*,GDP*,E30'
          Please refer to :obj:`mdciao.utils.residue_and_atom.rangeexpand_residues2residxs`
          for more info
-    trajectories : str, :obj:`mdtraj.Trajectory`, or None
+    trajectories : str, :obj:`mdtraj.Trajectory` or lists thereof
         The MD-trajectories to calculate the frequencies from.
         This input is pretty flexible. For more info check
-        :obj:`mdciao.utils.str_and_dict.get_sorted_trajectories`.
+        :obj:`mdciao.utils.str_and_dict.get_trajectories_from_input`.
         Accepted values are:
          * pattern, e.g. "*.ext"
          * one string containing a filename
          * list of filenames
          * one :obj:`mdtraj.Trajectory` object
          * list of :obj:`mdtraj.Trajectory` objects
+         * list mixing filenames and :obj:`mdtraj.Trajectory` objects
     topology : str or :obj:`~mdtraj.Trajectory`, default is None
         The topology associated with the :obj:`trajectories`
         If None, the topology of the first :obj:`trajectory` will
@@ -1150,16 +1151,17 @@ def interface(
 
     Parameters
     ----------
-    trajectories :
-        The MD-trajectories to calculate the frequencies
-        from. This input is pretty flexible. For more info check
-        :obj:`mdciao.utils.str_and_dict.get_sorted_trajectories`.
+    trajectories : str, :obj:`mdtraj.Trajectory` or lists thereof
+        The MD-trajectories to calculate the frequencies from.
+        This input is pretty flexible. For more info check
+        :obj:`mdciao.utils.str_and_dict.get_trajectories_from_input`.
         Accepted values are:
          * pattern, e.g. "*.ext"
          * one string containing a filename
          * list of filenames
-         * one :obj:`~mdtraj.Trajectory` object
-         * list of :obj:`~mdtraj.Trajectory` objects
+         * one :obj:`mdtraj.Trajectory` object
+         * list of :obj:`mdtraj.Trajectory` objects
+         * list mixing filenames and :obj:`mdtraj.Trajectory` objects
     topology : str or :obj:`~mdtraj.Trajectory`, default is None
         The topology associated with the :obj:`trajectories`
         If None, the topology of the first :obj:`trajectory` will
@@ -1670,16 +1672,17 @@ def sites(site_inputs,
         found in the topology will be discarded.
         See :obj:`mdciao.sites` for more info on
         the site format.
-    trajectories :
-        The MD-trajectories to calculate the frequencies
-        from. This input is pretty flexible. For more info check
-        :obj:`mdciao.utils.str_and_dict.get_sorted_trajectories`.
+    trajectories : str, :obj:`mdtraj.Trajectory` or lists thereof
+        The MD-trajectories to calculate the frequencies from.
+        This input is pretty flexible. For more info check
+        :obj:`mdciao.utils.str_and_dict.get_trajectories_from_input`.
         Accepted values are:
          * pattern, e.g. "*.ext"
          * one string containing a filename
          * list of filenames
-         * one :obj:`~mdtraj.Trajectory` object
-         * list of :obj:`~mdtraj.Trajectory` objects
+         * one :obj:`mdtraj.Trajectory` object
+         * list of :obj:`mdtraj.Trajectory` objects
+         * list mixing filenames and :obj:`mdtraj.Trajectory` objects
     topology : str or :obj:`~mdtraj.Trajectory`, default is None
         The topology associated with the :obj:`trajectories`
         If None, the topology of the first :obj:`trajectory` will

mdciao/utils/str_and_dict.py

@@ -99,31 +99,33 @@ def _kwargs_subs(funct_or_method, exclude=None):
     return _mpldocstring.Substitution(
         substitute_kwargs=_kwargs_docstring(funct_or_method, exclude=exclude))
 
-def get_sorted_trajectories(trajectories):
+def get_trajectories_from_input(trajectories):
     r"""
     Common parser for something that can be interpreted as a trajectory
 
     Parameters
     ----------
     trajectories: can be one of these things:
-        - pattern, e.g. "*.ext"
-        - one string containing a filename
-        - list of filenames
-        - one :obj:`mdtraj.Trajectory` object
-        - list of :obj:`mdtraj.Trajectory` objects
+        * pattern, e.g. "*.ext"
+        * one single string containing a filename
+        * one single :obj:`mdtraj.Trajectory` object
+        * one list containing
+         * just filenames
+         * just :obj:`mdtraj.Trajectory` objects
+         * a mix of filenames and :obj:`mdtraj.Trajectory` objects
 
     Returns
     -------
-        - for an input pattern, sorted trajectory filenames that match that pattern
-        - for filename, one list containing that filename
-        - for a list of filenames, a sorted list of filenames
-        - for one :obj:`mdtraj.Trajectory` object, a list containing that object
-        - list of :obj:`mdtraj.Trajectory` objects (i.e. does nothing)
-
+    outtrajs : list
+        A list of trajectories. This list can be, depending on the input:
+        * for an input pattern: sorted trajectory filenames that match that pattern
+        * for filename or an :obj:`mdtraj.Trajectory`:
+        one list containing that filename or :obj:`mdtraj.Trajectory` object
+        * for a list, that same list (i.e. nothing happens)
 
     """
     if isinstance(trajectories,str):
-        _trajectories = _glob(trajectories)
+        _trajectories = _natsorted(_glob(trajectories))
         if len(_trajectories)==0:
             raise FileNotFoundError("Couldn't find (or pattern-match) anything to '%s'.\n"
                                     "ls $CWD[%s]:\n%s:"%(trajectories,
@@ -132,15 +134,13 @@ def get_sorted_trajectories(trajectories):
         else:
             trajectories=_trajectories
 
-    if isinstance(trajectories[0],str):
-        xtcs = _natsorted(trajectories)
-    elif isinstance(trajectories, _md.Trajectory):
-        xtcs = [trajectories]
+    if type(trajectories) in [_md.Trajectory, str]:
+        outtrajs = [trajectories]
     else:
-        assert all([isinstance(itraj, _md.Trajectory) for itraj in trajectories])
-        xtcs = trajectories
+        assert all([type(itraj) in [_md.Trajectory, str] for itraj in trajectories])
+        outtrajs = trajectories
 
-    return xtcs
+    return outtrajs
 
 def inform_about_trajectories(trajectories, only_show_first_and_last=False):
     r"""

tests/test_str_and_dict_utils.py

@@ -24,29 +24,29 @@ def setUp(self):
         self.traj_reverse = md.load(test_filenames.traj_xtc_stride_20, top=self.geom.top)[::-1]
 
     def test_glob_with_pattern(self):
-        str_and_dict.get_sorted_trajectories(path.join(test_filenames.example_path,"*.xtc"))
+        str_and_dict.get_trajectories_from_input(path.join(test_filenames.example_path, "*.xtc"))
 
     def test_glob_with_filename(self):
-        str_and_dict.get_sorted_trajectories(test_filenames.traj_xtc_stride_20)
+        str_and_dict.get_trajectories_from_input(test_filenames.traj_xtc_stride_20)
 
     def test_with_one_trajectory_object(self):
-        list_out = str_and_dict.get_sorted_trajectories(self.traj)
+        list_out = str_and_dict.get_trajectories_from_input(self.traj)
         assert len(list_out)==1
         assert isinstance(list_out[0], md.Trajectory)
 
     def test_with_trajectory_objects(self):
-        str_and_dict.get_sorted_trajectories([self.traj,
-                                 self.traj_reverse])
+        str_and_dict.get_trajectories_from_input([self.traj,
+                                                  self.traj_reverse])
 
 
     def test_fails_if_not_traj_at_all(self):
         with pytest.raises(FileNotFoundError):
-            str_and_dict.get_sorted_trajectories("bogus.xtc")
+            str_and_dict.get_trajectories_from_input("bogus.xtc")
 
     def test_fails_if_not_trajs(self):
         with pytest.raises(AssertionError):
-            str_and_dict.get_sorted_trajectories([self.traj,
-                                     1])
+            str_and_dict.get_trajectories_from_input([self.traj,
+                                                      1])
 
 
 class Test_inform_about_trajectories(unittest.TestCase):