Update documentation and README according to auto LeafletFinder updates

Author: yusuferentunc

README.md

@@ -23,7 +23,7 @@ With DomHMM you can:
 
 - Calculate the area per lipid for each lipid in every leaflet.
 - Compute the average S<sub>CC</sub> parameter for each acyl chain of every lipid.
-- Easily identify lateral nano- and microdomains in your membrane simulations.
+- Identify lateral nano- and microdomains in your membrane simulations.
 
 Documentation
 --------------
@@ -157,7 +157,6 @@ tails = {"DPPC": [["C1B", "C2B", "C3B", "C4B"], ["C1A", "C2A", "C3A", "C4A"]],
 sterol_heads = {"CHOL": "ROH"}
 sterol_tails = {"CHOL": ["ROH", "C1"]}
 model = domhmm.PropertyCalculation(universe_or_atomgroup=uni,
-                                       leaflet_kwargs={"select": "name PO4", "pbc": True},
                                        membrane_select=membrane_select,
                                        leaflet_select="auto",
                                        heads=heads,

docs/source/how-to-run.rst

@@ -14,7 +14,6 @@ DomHMM's main class is ``PropertyCalculation``. In a basic example, it is initia
 .. code-block::
 
     model = domhmm.PropertyCalculation(universe_or_atomgroup=universe,
-                                       leaflet_kwargs=leaflet_kwargs,
                                        membrane_select=membrane_select,
                                        leaflet_select="auto",
                                        heads=heads,
@@ -42,21 +41,14 @@ Let's dive into each parameter's details.
     path2tpr = "YOUR_TPR_FILE.tpr"
     universe = mda.Universe(path2tpr, path2xtc)
 
-* ``leaflet_kwargs`` parameter stands for MDAnalysis ``LeafletFinder`` function's arguments. It is used to determine each leaflet's lipids. ``leaflet_kwargs`` requires head groups of lipids but not sterols.
-
-.. code-block::
-
-    # An example where all lipids head group is PO4
-    leaflet_kwargs={"select": "name PO4", "pbc": True}
-
 * ``membrane_select`` argument is for atom group selection of universe. It is useful for simulations that contain non-membrane residues/molecules inside. If the universe contains only membrane elements, the parameter can be left in the default option which is ``all``
 
 .. code-block::
 
     # An example where simulation contains DPPC and DIPC lipids, and CHOL sterol
     membrane_select = "resname DPPC DIPC CHOL"
 
-* ``leaflet_select`` argument is a selection option for lipids which can be a list of atom groups, a list of string queries, or automatic via LeafletFinder.
+* ``leaflet_select`` argument is a selection option for lipids which can be a list of atom groups, a list of string queries, or automatic via LeafletFinder. In automatic option, lipid head groups from ``heads`` parameter will be used for leaflet identification or user can setup with ``leaflet_kwargs`` optional parameter.
 
 .. code-block::
 
@@ -143,6 +135,13 @@ Option for saving result plots in pdf format.
 
 Verbose option for debugging. It shows which steps are done in the analysis.
 
+* ``leaflet_kwargs`` parameter stands for MDAnalysis ``LeafletFinder`` function's arguments and used with ``leaflet_select="auto"`` option. It is used to determine each leaflet's lipids. ``leaflet_kwargs`` requires head groups of lipids but not sterols.
+
+.. code-block::
+
+    # An example where all lipids head group is PO4
+    leaflet_kwargs={"select": "name PO4", "pbc": True}
+
 * ``lipid_leaflet_rate``
 
 The frame rate for checking lipids leaflet assignments via LeafletFinder. In the default option, it is equal to 0 which means leaflet assignment is only done at the beginning of the analysis.

docs/source/post-analysis.rst

@@ -73,6 +73,6 @@ Users can save and reload the model itself or required data via `pickle`_.
 
 
 .. note::
-    When loading the full model, the MDAnalysis universe will load the trajectory and topology file from the same directory that was given in the analysis run. Therefore, full-model saving can't be loaded if files do not exist.
+    When loading the full model, the MDAnalysis universe will load the trajectory and topology file from the same directory that was given in the analysis run. Therefore, full-model saving may not be loaded from outside of analysis directory.
 
 .. _pickle: https://www.mdanalysis.org/pages/mdakits/