adding documentation

modules/mol/base/src/editor_base.hh

@@ -57,7 +57,23 @@ public:
   /// \return  The newly created chain handle
   ChainHandle InsertChain(const String& chain_name);
 
-  //ChainHandle InsertChain(ChainHandle chain, bool deep=false);
+  /// \brief create new chain
+  ///
+  /// create new chain with properties of a provided chain handle and attach it to entity.
+  ///
+  /// \param chain_name
+  ///          The chain name. Can be an arbitrary String. However, if you
+  ///          intend to use the PDB export funtionality, the \c chain_name
+  ///          should be a single letter, preferably in the range A-Z.
+  /// \param chain
+  ///          The newly created chain will take over all generic
+  ///          attached to this handle.
+  /// \param deep
+  ///          If set to true, all residues and atoms of chain will be
+  ///          completely copied into the created chain. No bonds and angles
+  ///          are added.
+  ///
+  /// \return  The newly created chain handle
   ChainHandle InsertChain(const String& chain_name, ChainHandle chain, bool deep=false);
 
   /// \name Inserting, removing and modifying order of residues
@@ -80,6 +96,21 @@ public:
   ResidueHandle AppendResidue(ChainHandle chain, const ResidueKey& k, 
                               const ResNum& num); 
 
+  /// \brief Append residue to the ent of the chain
+  ///
+  /// Append residue with all properties of provided residue into chain.
+  ///
+  /// \param residue
+  ///          All properties of this residue will be copied into the newly created
+  ///          residue. The newly created residue will not contain any atoms, except
+  ///          you set \var deep to true.
+  ///
+  /// \param deep
+  ///          if set to true, all atoms from the source residue will be copied into
+  ///          the newly created residue. No bonds and angles are added.
+  ///
+  /// \return  The newly created residue handle
+
   ResidueHandle AppendResidue(ChainHandle chain, ResidueHandle residue, bool deep=false);
 
   /// \brief  Insert residue into chain
@@ -127,6 +158,16 @@ public:
                         Real occupancy=1.0, Real b_factor=0.0, 
                         bool is_hetatm=false);
 
+  /// \brief Insert new atom
+  ///
+  /// Inserts new atom with all properties from the provided atom handle.
+  ///
+  /// \param residue is the parent residue
+  /// \param atom from which all informations will be copied over to the
+  ///        newly created atom
+  ///
+  /// \return the newly created AtomHandle
+
   AtomHandle InsertAtom(ResidueHandle residue, AtomHandle atom);
 
   /// \brief Insert new atom with alternative position indicator
@@ -136,6 +177,10 @@ public:
                            const String& ele="", Real occ=1.0,
                            Real b_factor=0.0);
 
+  /// \brief Insert new atom with alternative position indicator
+  ///
+  /// All informations will be copied over from atom, except bonds
+
   AtomHandle InsertAltAtom(ResidueHandle residue, AtomHandle atom,
                            const String& alt_group);