Merge branch 'analysis_protocol/leaflet_to_leaflet_distance'

docs/source/ba_analyses/ac.md

@@ -1,20 +1,18 @@
 ## BilayerAnalyzer analysis: ```ac``` - Isothermal area compressibility.
-
+ 
 ## Description
-
+ 
 Estimate the isothermal area compressibility.
 
 This protocol is used to estimate the area compressibility modulus,
-
-    K_A^-1 = [(<A>kT) / var(A)]^-1 ,
-
-where A is the area in the lateral dimension of the bilayer.
+K_A^-1 = [(<A>kT) / var(A)]^-1 ,
+where A is the area in the lateal dimension of the bilayer.
 
 This protocol is identified by the analysis key: 'ac'
 
 
 #### Initiated by instance of:
-
+ 
     <class 'pybilt.bilayer_analyzer.analysis_protocols.AreaCompressibilityProtocol'>
 
 ## Syntax
@@ -24,7 +22,7 @@ ac analysis-ID keyword value
 ```
 * ac = analysis-Key - keyword/name for this analysis.
 * analysis-ID = The unique name/ID being assigned to this analysis.
-* keyword value = settings keyword value pairs
+* keyword value = settings keyword value pairs 
     * temperature (float): The absolute temperature that the simulation was run at (i.e. in Kelvin). Default: 298.15 K
 
 ### Examples
@@ -34,45 +32,45 @@ analyzer = BilayerAnalyzer(structure='name_of_structure_file',
                            trajectory='name_of_traj_file',
                            selection='resname POPC DOPC')
 ```
-
+ 
 Add by string - use default settings:
 ```python
-analyzer.add_analysis('ac ac_1')
+analyzer.add_analysis('ac ac_1') 
 ```
-
-Add by string - adjust a setting:
+ 
+Add by string - adjust a setting: 
 ```python
 analyzer.add_analysis('ac ac_1 temperature 298.15')
 ```
-
+ 
 Add by list:
 ```python
 analyzer.add_analysis(list(['ac', 'ac_1', dict({'temperature':298.15})]))
 ```
-
-Add by dict:
+ 
+Add by dict: 
 ```python
 analyzer.add_analysis(dict({'analysis_key': 'ac', 'analysis_id': 'ac_1','analysis_settings':dict({'temperature':298.15})}))
 ```
-
-To remove from analyzer:
+ 
+To remove from analyzer: 
 ```python
 analyzer.remove_analysis('ac_1')
 ```
-
+ 
 ### Output Info:
 Retrieve output after running analyses:
 ```python
 output = analyzer.get_analysis_data('ac_1')
 ```
-
-The output is type ```<class 'numpy.ndarray'>```
-
-<div class="admonition note">
-<p class="admonition-title">Note</p>
-<p> Area compressibility is the inverse of area compressibility modulus (see Ref.1).  </p>
-</div>
-
+ 
+The output is type ```<type 'numpy.ndarray'>```
+ 
+<div class="admonition note"> 
+<p class="admonition-title">Note</p> 
+<p> Area compressibility is the inverse of area compressibility modulus (see Ref.1).  </p> 
+</div> 
+ 
 ## Related analyses
 * [acm](acm.html)
 * [vcm](vcm.html)

docs/source/ba_analyses/acm.md

@@ -1,20 +1,18 @@
 ## BilayerAnalyzer analysis: ```acm``` - Area compressibility modulus.
-
+ 
 ## Description
-
+ 
 Estimate the isothermal area compressibility modulus.
 
 This protocol is used to estimate the area compressibility modulus,
-
-    K_A = (<A>kT) / var(A),
-
-where A is the area in the lateral dimension of the bilayer.
+K_A = (<A>kT) / var(A),
+where A is the area in the lateal dimension of the bilayer.
 
 This protocol is identified by the analysis key: 'acm'
 
 
 #### Initiated by instance of:
-
+ 
     <class 'pybilt.bilayer_analyzer.analysis_protocols.AreaCompressibilityModulusProtocol'>
 
 ## Syntax
@@ -24,7 +22,7 @@ acm analysis-ID keyword value
 ```
 * acm = analysis-Key - keyword/name for this analysis.
 * analysis-ID = The unique name/ID being assigned to this analysis.
-* keyword value = settings keyword value pairs
+* keyword value = settings keyword value pairs 
     * temperature (float): The absolute temperature that the simulation was run at (i.e. in Kelvin). Default: 298.15 K
 
 ### Examples
@@ -34,40 +32,40 @@ analyzer = BilayerAnalyzer(structure='name_of_structure_file',
                            trajectory='name_of_traj_file',
                            selection='resname POPC DOPC')
 ```
-
+ 
 Add by string - use default settings:
 ```python
-analyzer.add_analysis('acm acm_1')
+analyzer.add_analysis('acm acm_1') 
 ```
-
-Add by string - adjust a setting:
+ 
+Add by string - adjust a setting: 
 ```python
 analyzer.add_analysis('acm acm_1 temperature 298.15')
 ```
-
+ 
 Add by list:
 ```python
 analyzer.add_analysis(list(['acm', 'acm_1', dict({'temperature':298.15})]))
 ```
-
-Add by dict:
+ 
+Add by dict: 
 ```python
 analyzer.add_analysis(dict({'analysis_key': 'acm', 'analysis_id': 'acm_1','analysis_settings':dict({'temperature':298.15})}))
 ```
-
-To remove from analyzer:
+ 
+To remove from analyzer: 
 ```python
 analyzer.remove_analysis('acm_1')
 ```
-
+ 
 ### Output Info:
 Retrieve output after running analyses:
 ```python
 output = analyzer.get_analysis_data('acm_1')
 ```
-
-The output is type ```<class 'numpy.ndarray'>```
-
+ 
+The output is type ```<type 'numpy.ndarray'>```
+ 
 ## Related analyses
 * [ac](ac.html)
 * [vcm](vcm.html)

docs/source/ba_analyses/ald.md

@@ -61,7 +61,7 @@ Retrieve output after running analyses:
 output = analyzer.get_analysis_data('ald_1')
 ```
 
-The output is type ```<class 'numpy.ndarray'>```
+The output is type ```<type 'numpy.ndarray'>```
 
 ## Related analyses
 * [msd](msd.html)

docs/source/ba_analyses/apl_box.md

@@ -67,7 +67,7 @@ Retrieve output after running analyses:
 output = analyzer.get_analysis_data('apl_box_1')
 ```
 
-The output is type ```<class 'numpy.ndarray'>```
+The output is type ```<type 'numpy.ndarray'>```
 
 ## Related analyses
 * [apl_grid](apl_grid.html)

docs/source/ba_analyses/apl_grid.md

@@ -58,7 +58,7 @@ Retrieve output after running analyses:
 output = analyzer.get_analysis_data('apl_grid_1')
 ```
 
-The output is type ```<class 'dict'>```
+The output is type ```<type 'dict'>```
 
 ## Related analyses
 * [apl_box](apl_box.html)

docs/source/ba_analyses/area_fluctuation.md

@@ -58,7 +58,7 @@ Retrieve output after running analyses:
 output = analyzer.get_analysis_data('area_fluctuation_1')
 ```
 
-The output is type ```<class 'numpy.ndarray'>```
+The output is type ```<type 'numpy.ndarray'>```
 
 ## Related analyses
 * [acm](acm.html)

docs/source/ba_analyses/com_lateral_rdf.md

@@ -21,12 +21,12 @@ com_lateral_rdf analysis-ID keyword value
 * com_lateral_rdf = analysis-Key - keyword/name for this analysis.
 * analysis-ID = The unique name/ID being assigned to this analysis.
 * keyword value = settings keyword value pairs 
-    * leaflet (str: 'both', 'upper', or 'lower'): Specifies the bilayer leaflet to include in the estimate. Default: 'both'
-    * resname_1 (str): Specify the resname of the reference lipid type to include in this analysis. Default: 'first', the first lipid in the list pulled from the com_frame representation.
-    * resname_2 (str): Specify the resname of the target lipid type to include in this analysis. Default: 'first', the first lipid in the list pulled from the com_frame representation.
     * n_bins (int): Specifies the number of bins to use when estimating the RDF. Default: 25
-    * range_inner (float): Specify the inner distance cutoff for the RDF. Default: 0.0
     * range_outer (float): Specify the outer distance cutoff for the RDF. Default: 25.0
+    * leaflet (str: 'both', 'upper', or 'lower'): Specifies the bilayer leaflet to include in the estimate. Default: 'both'
+    * range_inner (float): Specify the inner distance cutoff for the RDF. Default: 0.0
+    * resname_2 (str): Specify the resname of the target lipid type to include in this analysis. Default: 'first', the first lipid in the list pulled from the com_frame representation.
+    * resname_1 (str): Specify the resname of the reference lipid type to include in this analysis. Default: 'first', the first lipid in the list pulled from the com_frame representation.
 
 ### Examples
 Construct analyzer:
@@ -43,17 +43,17 @@ analyzer.add_analysis('com_lateral_rdf com_lateral_rdf_1')
 
 Add by string - adjust a setting: 
 ```python
-analyzer.add_analysis('com_lateral_rdf com_lateral_rdf_1 leaflet both')
+analyzer.add_analysis('com_lateral_rdf com_lateral_rdf_1 n_bins 25')
 ```
 
 Add by list:
 ```python
-analyzer.add_analysis(list(['com_lateral_rdf', 'com_lateral_rdf_1', dict({'leaflet':'both'})]))
+analyzer.add_analysis(list(['com_lateral_rdf', 'com_lateral_rdf_1', dict({'n_bins':25})]))
 ```
 
 Add by dict: 
 ```python
-analyzer.add_analysis(dict({'analysis_key': 'com_lateral_rdf', 'analysis_id': 'com_lateral_rdf_1','analysis_settings':dict({'leaflet':'both'})}))
+analyzer.add_analysis(dict({'analysis_key': 'com_lateral_rdf', 'analysis_id': 'com_lateral_rdf_1','analysis_settings':dict({'n_bins':25})}))
 ```
 
 To remove from analyzer: 
@@ -67,7 +67,7 @@ Retrieve output after running analyses:
 output = analyzer.get_analysis_data('com_lateral_rdf_1')
 ```
 
-The output is type ```<class 'tuple'>```
+The output is type ```<type 'tuple'>```
 
 ## Related analyses
 * [nnf](nnf.html)

docs/source/ba_analyses/dc_cluster.md

@@ -66,7 +66,7 @@ Retrieve output after running analyses:
 output = analyzer.get_analysis_data('dc_cluster_1')
 ```
 
-The output is type ```<class 'dict'>```
+The output is type ```<type 'dict'>```
 
 <div class="admonition note"> 
 <p class="admonition-title">Note</p> 

docs/source/ba_analyses/disp_vec.md

@@ -20,11 +20,11 @@ disp_vec analysis-ID keyword value
 * disp_vec = analysis-Key - keyword/name for this analysis.
 * analysis-ID = The unique name/ID being assigned to this analysis.
 * keyword value = settings keyword value pairs 
+    * scale (bool): Specify whether to scale the coordinates by the box dimensions of the reference frame. Default: False
+    * interval (int): Sets the frame interval over which to compute the displacement vectors.
     * leaflet (str: 'both', 'upper', or 'lower'): Specifies the bilayer leaflet to include in the estimate. Default: 'both'
-    * resname (str): Specify the resname of the lipid type to include in this analysis. Default: 'all', includes all lipid types.
     * wrapped (bool): Specify whether to use the wrapped ('True') or un-wrapped ('False') coordintes for the base of the vectors. Default: False
-    * interval (int): Sets the frame interval over which to compute the displacement vectors.
-    * scale (bool): Specify whether to scale the coordinates by the box dimensions of the reference frame. Default: False
+    * resname (str): Specify the resname of the lipid type to include in this analysis. Default: 'all', includes all lipid types.
     * scale_to_max (bool): Specify whether to scale the coordinates by the box dimensions of the maximum box size in the anlysis. Default: False.
 
 ### Examples
@@ -42,17 +42,17 @@ analyzer.add_analysis('disp_vec disp_vec_1')
 
 Add by string - adjust a setting: 
 ```python
-analyzer.add_analysis('disp_vec disp_vec_1 leaflet both')
+analyzer.add_analysis('disp_vec disp_vec_1 scale False')
 ```
 
 Add by list:
 ```python
-analyzer.add_analysis(list(['disp_vec', 'disp_vec_1', dict({'leaflet':'both'})]))
+analyzer.add_analysis(list(['disp_vec', 'disp_vec_1', dict({'scale':False})]))
 ```
 
 Add by dict: 
 ```python
-analyzer.add_analysis(dict({'analysis_key': 'disp_vec', 'analysis_id': 'disp_vec_1','analysis_settings':dict({'leaflet':'both'})}))
+analyzer.add_analysis(dict({'analysis_key': 'disp_vec', 'analysis_id': 'disp_vec_1','analysis_settings':dict({'scale':False})}))
 ```
 
 To remove from analyzer: 
@@ -66,7 +66,7 @@ Retrieve output after running analyses:
 output = analyzer.get_analysis_data('disp_vec_1')
 ```
 
-The output is type ```<class 'list'>```
+The output is type ```<type 'list'>```
 
 <div class="admonition note"> 
 <p class="admonition-title">Note</p> 

docs/source/ba_analyses/disp_vec_corr.md

@@ -26,8 +26,8 @@ disp_vec_corr analysis-ID keyword value
 * keyword value = settings keyword value pairs 
     * leaflet (str: 'both', 'upper', or 'lower'): Specifies the bilayer leaflet to include in the estimate. Default: 'both'
     * resname (str): Specify the resname of the lipid type to include in this analysis. Default: 'all', includes all lipid types.
-    * wrapped (bool): Specify whether to use the wrapped ('True') or un-wrapped ('False') coordintes for the base of the vectors. Default: False
     * interval (int): Sets the frame interval over which to compute the displacement vectors. f
+    * wrapped (bool): Specify whether to use the wrapped ('True') or un-wrapped ('False') coordintes for the base of the vectors. Default: False
 
 ### Examples
 Construct analyzer:
@@ -68,7 +68,7 @@ Retrieve output after running analyses:
 output = analyzer.get_analysis_data('disp_vec_corr_1')
 ```
 
-The output is type ```<class 'list'>```
+The output is type ```<type 'list'>```
 
 ## Related analyses
 * [disp_vec](disp_vec.html)

docs/source/ba_analyses/disp_vec_corr_avg.md

@@ -27,8 +27,8 @@ disp_vec_corr_avg analysis-ID keyword value
 * keyword value = settings keyword value pairs 
     * leaflet (str: 'both', 'upper', or 'lower'): Specifies the bilayer leaflet to include in the estimate. Default: 'both'
     * resname (str): Specify the resname of the lipid type to include in this analysis. Default: 'all', includes all lipid types.
-    * wrapped (bool): Specify whether to use the wrapped ('True') or un-wrapped ('False') coordintes for the base of the vectors. Default: False
     * interval (int): Sets the frame interval over which to compute the displacement vectors.
+    * wrapped (bool): Specify whether to use the wrapped ('True') or un-wrapped ('False') coordintes for the base of the vectors. Default: False
 
 ### Examples
 Construct analyzer:
@@ -69,7 +69,7 @@ Retrieve output after running analyses:
 output = analyzer.get_analysis_data('disp_vec_corr_avg_1')
 ```
 
-The output is type ```<class 'numpy.ndarray'>```
+The output is type ```<type 'numpy.ndarray'>```
 
 ## Related analyses
 * [disp_vec](disp_vec.html)

docs/source/ba_analyses/disp_vec_nncorr.md

@@ -26,8 +26,8 @@ disp_vec_nncorr analysis-ID keyword value
 * keyword value = settings keyword value pairs 
     * leaflet (str: 'both', 'upper', or 'lower'): Specifies the bilayer leaflet to include in the estimate. Default: 'both'
     * resname (str): Specify the resname of the lipid type to include in this analysis. Default: 'all', includes all lipid types.
-    * wrapped (bool): Specify whether to use the wrapped ('True') or un-wrapped ('False') coordintes for the base of the vectors. Default: False
     * interval (int): Sets the frame interval over which to compute the displacement vectors. f
+    * wrapped (bool): Specify whether to use the wrapped ('True') or un-wrapped ('False') coordintes for the base of the vectors. Default: False
 
 ### Examples
 Construct analyzer:
@@ -68,7 +68,7 @@ Retrieve output after running analyses:
 output = analyzer.get_analysis_data('disp_vec_nncorr_1')
 ```
 
-The output is type ```<class 'list'>```
+The output is type ```<type 'list'>```
 
 ## Related analyses
 * [disp_vec](disp_vec.html)