Added documentation for mol.alg.structure_analysis

modules/mol/alg/doc/molalg.rst

@@ -873,5 +873,9 @@ used to skip frames in the analysis.
 .. automodule:: ost.mol.alg.trajectory_analysis
    :members:
 
+:mod:`mol.alg.structure_analysis <ost.mol.alg.trajectory_analysis>` -- Functions to analyze structures
+=============================================================================================================
 
+.. automodule:: ost.mol.alg.structure_analysis
+   :members:
 

modules/mol/alg/pymod/structure_analysis.py

 """
-Some functions for analyzing trajectories
+Some functions for analyzing structures
 
-Author: Niklaus Johner
+Author: Niklaus Johner (Niklaus.Johner@unibas.ch)
 """
-
 import os
 import ost
 
 def GetFrameFromEntity(eh):
   """
   This function returns a CoordFrame from an EntityHandle
-  Input:
-    eh : EntityHandle
+  
+  :param eh: 
+  :type eh: :class:`~ost.mol.EntityHandle`
+
+  :return: :class:`ost.mol.CoordFrame`
   """
   return ost.mol.CreateCoordFrame(eh.GetAtomPosList(ordered_by_index=True))
   
 def GetDistanceBetwCenterOfMass(sele1,sele2):
   """
   This function calculates the distance between the centers of mass
-  of sele1 and sele2, two selections from the same Entity.
-  Input:
-    sele1 : EntityView
-    sele2 : EntityView
+  of **sele1** and **sele2**, two selections from the same Entity.
+
+  :param sele1:
+  :param sele2:
+  :type sele1: :class:`~ost.mol.EntityView`
+  :type sele2: :class:`~ost.mol.EntityView`
+
+  :return: :class:`float`
   """
   if not sele1.IsValid() and sele2.IsValid():
     print 'invalid view'
@@ -36,10 +42,14 @@ def GetDistanceBetwCenterOfMass(sele1,sele2):
 def GetMinDistanceBetweenViews(sele1,sele2):
   """
   This function calculates the minimal distance between
-  sele1 and sele2, two selections from the same Entity.
-  Input:
-    sele1 : EntityView
-    sele2 : EntityView
+  **sele1** and **sele2**, two selections from the same Entity.
+  
+  :param sele1:
+  :param sele2:
+  :type sele1: :class:`~ost.mol.EntityView`
+  :type sele2: :class:`~ost.mol.EntityView`
+
+  :return: :class:`float`
   """
   if not sele1.IsValid() and sele2.IsValid():
     print 'invalid view'
@@ -53,11 +63,15 @@ def GetMinDistanceBetweenViews(sele1,sele2):
 
 def GetMinDistBetwCenterOfMassAndView(sele1,sele2):
   """
-  This function calculates the minimal distance between sele2 and
-  the center of mass of sele1, two selections from the same Entity.
-  Input:
-    sele1 : EntityView from which the center of mass is taken
-    sele2 : EntityView
+  This function calculates the minimal distance between **sele2** and
+  the center of mass of **sele1**, two selections from the same Entity.
+
+  :param sele1: The selection from which the center of mass is taken
+  :param sele2:
+  :type sele1: :class:`~ost.mol.EntityView`
+  :type sele2: :class:`~ost.mol.EntityView`
+
+  :return: distance (\ :class:`float`\ )
   """
   if not sele1.IsValid() and sele2.IsValid():
     print 'invalid view'
@@ -74,8 +88,11 @@ def GetAlphaHelixContent(sele1):
   """
   This function calculates the content of alpha helix in a view.
   All residues in the view have to ordered and adjacent (no gaps allowed)
-  Input:
-    sele1 : EntityView
+  
+  :param sele1:
+  :type sele1: :class:`~ost.mol.EntityView`
+
+  :return: :class:`float`
   """
   if not sele1.IsValid():
     print 'invalid view'
@@ -87,10 +104,12 @@ def GetAlphaHelixContent(sele1):
 
 def CalculateBestFitLine(sele1):
   """
-  This function calculates the best fit line to the atoms in sele1.
-  Input:
-    sele1 : EntityView
-  It returns a geom::Line3
+  This function calculates the best fit line to the atoms in **sele1**.
+  
+  :param sele1:
+  :type sele1: :class:`~ost.mol.EntityView`
+
+  :return: :class:`~ost.geom.Line3`
   """
   if not sele1.IsValid():
     print 'invalid view'
@@ -101,10 +120,12 @@ def CalculateBestFitLine(sele1):
 
 def CalculateBestFitPlane(sele1):
   """
-  This function calculates the best fit plane to the atoms in sele1.
-  Input:
-    sele1 : EntityView
-  It returns a geom::Plane
+  This function calculates the best fit plane to the atoms in **sele1**.
+  
+  :param sele1:
+  :type sele1: :class:`~ost.mol.EntityView`
+
+  :return: :class:`~ost.geom.Plane`
   """
   if not sele1.IsValid():
     print 'invalid view'
@@ -115,12 +136,14 @@ def CalculateBestFitPlane(sele1):
 
 def CalculateHelixAxis(sele1):
   """
-  This function calculates the best fit cylinder to the CA atoms in sele1,
-  and returns its axis as a Line3.  residues should be ordered correctly
-  in the EntityView.
-  Input:
-    sele1 : EntityView
-  It returns a geom::Line3
+  This function calculates the best fit cylinder to the CA atoms in **sele1**,
+  and returns its axis.  Residues should be ordered correctly
+  in **sele1**.
+  
+  :param sele1:
+  :type sele1: :class:`~ost.mol.EntityView`
+
+  :return: :class:`~ost.geom.Line3`
   """
   if not sele1.IsValid():
     print 'invalid view'
@@ -132,10 +155,17 @@ def CalculateHelixAxis(sele1):
 
 def CalculateDistanceDifferenceMatrix(sele1,sele2):
   """
-  This function calculates the pairwise distance differences between two EntityViews.
-  The two EntityViews should have the same number of atoms
+  This function calculates the pairwise distance differences between two selections (\ :class:`~ost.mol.EntityView`\ ).
+  The two selections should have the same number of atoms
   It returns an NxN DistanceDifferenceMatrix M (where N is the number of atoms in sele1)
-  where M[i,j]=(sele2.atoms[i].pos-sele2.atoms[j].pos)-(sele1.atoms[i].pos-sele1.atoms[j].pos)
+  where M[i,j]=||(sele2.atoms[i].pos-sele2.atoms[j].pos)||-||(sele1.atoms[i].pos-sele1.atoms[j].pos)||
+
+  :param sele1:
+  :param sele2:
+  :type sele1: :class:`~ost.mol.EntityView`
+  :type sele2: :class:`~ost.mol.EntityView`
+
+  :return: NxN numpy matrix
   """
   try:import numpy as npy
   except ImportError: