Doc update for Select queries.

modules/mol/base/doc/entity.rst

@@ -508,15 +508,16 @@ The Handle Classes
   
   .. attribute:: chem_class
   
-    The chemical class of a residue is used to broadly categorize residues based 
-    on their chemical properties. For example, peptides belong  to the 
+    The chemical class of a residue is used to broadly categorize residues based
+    on their chemical properties. For example, peptides belong to the
     `L_PEPTIDE_LINKING` or `D_PEPTIDE_LINKING` classes.
 
   .. attribute:: chem_type
 
     The chemical type of a residue is a classification of all compounds
     obtained from the PDB component dictionary. For example, ions belong to the
-    class `ChemType::IONS`, amino acids to `ChemType::AMINOACIDS`.
+    class `ChemType::IONS`, amino acids to `ChemType::AMINOACIDS`. The type is
+    only properly set if a compund library is used.
   
   .. attribute:: sec_structure
   
@@ -529,6 +530,10 @@ The Handle Classes
     most likely not be set properly for all except PDB files coming from 
     pdb.org.
 
+  .. attribute:: index
+
+    Residue index (starting at 0) within chain.
+
   .. method:: FindAtom(atom_name)
 
     Get atom by atom name. See also :attr:`atoms`
@@ -544,6 +549,12 @@ The Handle Classes
 
     Get list of all atoms of this residue. To access a single atom, use
     :meth:`FindAtom`.
+
+  .. method:: IsPeptideLinking()
+
+    :return: True, if residue can form peptide bonds (determined based on
+             :attr:`chem_class` set when loading the structure).
+    :rtype:  :class:`bool`
     
   .. method:: GetChain()
   
@@ -568,6 +579,10 @@ The Handle Classes
   .. method:: GetChemType()
     
     See :attr:`chem_type`
+
+  .. method:: GetIndex()
+    
+    See :attr:`index`
   
 
 .. class:: AtomHandle
@@ -668,6 +683,10 @@ The Handle Classes
     
     :type: list of :class:`bond handles<BondHandle>`
   
+  .. attribute:: index
+
+    Atom index (starting at 0) within entity.
+
   .. method:: FindBondToAtom(other_atom)
 
     Finds and returns the bond formed between this atom and `other_atom`. If no 
@@ -731,7 +750,7 @@ The Handle Classes
 
   .. method:: GetIndex()
     
-    Returns the index of the atom.
+    See :attr:`index`
     
     :rtype: int
 
@@ -1444,6 +1463,10 @@ The View Classes
 
     :type: :class:`AtomViewList`
 
+  .. attribute:: index
+
+    Residue index (starting at 0) within chain view.
+
   .. method:: RemoveAtom(atom_view)
   
     Remove atom from residue and all associated bonds. If the atom is not part 

modules/mol/base/doc/query.rst

@@ -175,36 +175,40 @@ The following properties may be used in predicates. The type is given for each p
 Properties of Chains
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-
 **cname/chain** (str) :attr:`Chain name<ChainHandle.name>` 
   
 Properties of Residues
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-
 **rname** (str): :attr:`Residue name<ResidueHandle.name>`
  
-**rnum** (int): :attr:`Residue number<ResidueHandle.number>`. Currently only the numeric part is honored.
+**rnum** (int): :attr:`Residue number<ResidueHandle.number>`. Currently only the
+numeric part is honored.
  
-**rtype** (str): Residue type as given by the DSSP code, i.e. H for helix, E for extended.
-  
-**rindex** (int): :attr:`Index<ResidueHandle.index>` of residue in chain. This 
-index is the same for views and handles.
+**rtype** (str): Residue type as given by the DSSP code (e.g. "H" for alpha
+helix, "E" for extended), "helix" for all helix types, "ext" or "strand" for
+all beta sheets or "coil" for any type of coil.
   
-**ishetatm** (bool): Whether the atom is a :attr:`heterogenous<AtomHandle.is_hetatm>` atom.
+**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 a :meth:`peptide <ResidueHandle.IsPeptideLinking>`.
+**peptide** (bool): Whether the residue is :meth:`peptide linking
+<ResidueHandle.IsPeptideLinking>`.
+
+**protein** (bool): 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.
 
 **rbfac** (float): average B (temperature) factor of residue
 
-**ligand** (bool) Whether the residue is a ligand. For official PDB files, the ligand property is set based on HET records.
+**ligand** (bool) Whether the residue is a :meth:`ligand
+<ResidueHandle.is_ligand>`.
 
 **water** (bool) Whether the residue is water.
 
 Properties of Atoms
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-
 **aname** (str): :attr:`Atom name<AtomHandle.name>`
   
 **ele** (str): :attr:`Atom element<AtomHandle.element>`
@@ -219,6 +223,14 @@ Properties of Atoms
 
 **z** (float): :attr:`Z<AtomHandle.pos>` coordinate of atom.
 
+**aindex** (int): :attr:`Atom index<AtomHandle.index>`
+
+**ishetatm** (bool): Whether the atom is a :attr:`heterogenous
+atom<AtomHandle.is_hetatom>`.
+
+**acharge** (float): :attr:`Atom charge<AtomHandle.charge>`
+
+
 Query API documentation
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