SCHWED-2440: Clarify difference between is_protein and peptide_linking.

modules/conop/doc/functions.rst

@@ -7,10 +7,10 @@ Conop Functions
               AssignBackboneTorsions(chain)
               AssignBackboneTorsions(residues)
    
-  Assigns the backbone torsions PHI, PSI and OMEGA. The backbone atoms 
-  are required to be connected for the torsions to be added. In addition, 
-  only residues for which :meth:`~ost.mol.ResidueHandle.IsPeptideLinking`
-  returns True are considered.
+  Assigns the backbone torsions PHI, PSI and OMEGA. The backbone atoms are
+  required to be connected for the torsions to be added. In addition, only
+  residues for which :attr:`~ost.mol.ResidueHandle.peptide_linking` is True are
+  considered.
 
   The first signature assigns the torsions to *res*, assuming prev is 
   the amino acid before, and *next* is the amino acid next to *res*.  

modules/mol/base/doc/entity.rst

@@ -545,7 +545,16 @@ The Handle Classes
     Whether the residue is considered to be part of a protein. This is set when
     loading a structure if the residue forms a feasible peptide bond to the
     previous or next residue (see :meth:`~ost.conop.IsBondFeasible`). Also
-    available as :meth:`IsProtein`, :meth:`SetIsProtein`.
+    available as :meth:`IsProtein`, :meth:`SetIsProtein`. In contrast to
+    :meth:`IsPeptideLinking` this excludes residues which are not connected to
+    neighbouring residues such as CA-only residues or badly positioned ones.
+
+  .. attribute:: peptide_linking
+  
+    Whether residue can form peptide bonds. This is determined based on
+    :attr:`chem_class` which is set when loading the structure.
+
+    :type: :class:`bool`
 
   .. attribute:: index
 
@@ -569,9 +578,7 @@ The Handle Classes
 
   .. method:: IsPeptideLinking()
 
-    :return: True, if residue can form peptide bonds (determined based on
-             :attr:`chem_class` set when loading the structure).
-    :rtype:  :class:`bool`
+    See :attr:`peptide_linking`
     
   .. method:: GetChain()
   

modules/mol/base/doc/query.rst

@@ -192,11 +192,11 @@ all beta sheets or "coil" for any type of coil.
 **rindex** (int): :attr:`Index<ResidueHandle.index>` of residue handle in chain.
 This index is the same for views and handles.
   
-**peptide** (bool): Whether the residue is :meth:`peptide linking
-<ResidueHandle.IsPeptideLinking>`.
+**peptide** (bool): Whether the residue is :attr:`peptide linking
+<ResidueHandle.peptide_linking>`.
 
 **protein** (bool): Whether the residue is considered to be
-:attr:`part of a protein <ResidueHandle.is_protein>`.
+:attr:`part of a connected protein <ResidueHandle.is_protein>`.
 
 **rbfac** (float): average B (temperature) factor of residue