clean: make frame_slice_list private (#1258)

* clean * add pca example readme * minor
Amber-MD · May 28, 2016 · bbf3923 · bbf3923
1 parent 1f22b35
commit bbf3923
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Showing 4 changed files with 11 additions and 10 deletions.
diff --git a/README.md b/README.md
@@ -64,8 +64,9 @@ How to get started?
     ```python
     import pytraj as pt
     traj = pt.iterload("data.nc", "top.parm7")
-    pt.rmsd(traj, ref=0, mask='@CA')
-    pt.dssp(traj, ':2-16')
+    pt.rmsd(traj, mask='@CA', ref=0)
+    pt.dssp(traj, mask=':2-16')
+    pt.pca(traj, mask='!@H=', n_vecs=2)
     ```
 - check our website: [http://amber-md.github.io/pytraj] (http://amber-md.github.io/pytraj)
 

diff --git a/pytraj/core/c_core.pyx b/pytraj/core/c_core.pyx
@@ -379,7 +379,7 @@ def _load_batch(txt, traj=None):
     if traj is not None:
         lines_0 = ['parm %s' % traj.top.filename]
 
-        for fname, frame_slice in zip(traj.filelist, traj.frame_slice_list):
+        for fname, frame_slice in zip(traj.filelist, traj._frame_slice_list):
             if len(frame_slice) == 3:
                 start, stop, step = frame_slice
             elif len(frame_slice) == 2:

diff --git a/pytraj/sandbox/TrajectoryBaseIterator.py b/pytraj/sandbox/TrajectoryBaseIterator.py
@@ -60,7 +60,7 @@ def filelist(self):
 
     @property
     @abstractmethod
-    def frame_slice_list(self):
+    def _frame_slice_list(self):
         pass
 
     @abstractmethod

diff --git a/pytraj/trajectory_iterator.py b/pytraj/trajectory_iterator.py
@@ -121,7 +121,7 @@ def __init__(self, filename=None, top=None, *args, **kwd):
         else:
             raise ValueError("Topology must be None/string/Topology")
 
-        self.frame_slice_list = []
+        self._frame_slice_list = []
 
         if filename:
             if self.top.is_empty():
@@ -134,7 +134,7 @@ def __init__(self, filename=None, top=None, *args, **kwd):
         self.__dict__.update({
             '_top_filename': self.top.filename,
             'filelist': self.filelist,
-            'frame_slice_list': self.frame_slice_list,
+            '_frame_slice_list': self._frame_slice_list,
         })
 
     def __setstate__(self, state):
@@ -144,7 +144,7 @@ def __setstate__(self, state):
         else:
             # faster
             self.top = _load_Topology(state['_top_filename'])
-        self._load(state['filelist'], frame_slice=state['frame_slice_list'])
+        self._load(state['filelist'], frame_slice=state['_frame_slice_list'])
 
     def __getstate__(self):
         '''
@@ -180,7 +180,7 @@ def copy(self):
         other = self.__class__()
         other.top = self.top.copy()
 
-        for fname, frame_slice in zip(self.filelist, self.frame_slice_list):
+        for fname, frame_slice in zip(self.filelist, self._frame_slice_list):
             other._load(fname, frame_slice=frame_slice)
         return other
 
@@ -201,7 +201,7 @@ def _load(self, filename=None, top=None, frame_slice=(0, -1, 1), stride=None):
 
         if isinstance(filename, string_types) and os.path.exists(filename):
             super(TrajectoryIterator, self)._load(filename, top_, frame_slice_)
-            self.frame_slice_list.append(frame_slice_)
+            self._frame_slice_list.append(frame_slice_)
         elif isinstance(filename,
                         string_types) and not os.path.exists(filename):
 
@@ -221,7 +221,7 @@ def _load(self, filename=None, top=None, frame_slice=(0, -1, 1), stride=None):
                 full_frame_slice = [(0, -1, stride),] * len(flist)
 
             for fname, fslice in zip(flist, full_frame_slice):
-                self.frame_slice_list.append(frame_slice)
+                self._frame_slice_list.append(frame_slice)
                 super(TrajectoryIterator, self)._load(fname,
                                                       top_,
                                                       frame_slice=fslice)