Changes in src/Fragmentation/Exporters/SaturatedFragment.hpp [c39675:98a293b]

File:

• src/Fragmentation/Exporters/SaturatedFragment.hpp (modified) (6 diffs)

src/Fragmentation/Exporters/SaturatedFragment.hpp

@@ -18 +18 @@
 #include <string>
 
+#include "Atom/atom_bondedparticleinfo.hpp"
 #include "Bond/bond.hpp"
 #include "Fragmentation/KeySet.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
 #include "Parser/FormatParserStorage.hpp"
+
+#include "LinearAlgebra/Vector.hpp"
 
 class atom;
@@ -42 +45 @@
   typedef std::set<KeySet> KeySetsInUse_t;
 
+  //!> List of points giving saturation positions for a single bond neighbor
+  typedef std::list<Vector> SaturationsPositions_t;
+  //!> map for one atom, containing the saturation points for all its neighbors
+  typedef std::map<int, SaturationsPositions_t> SaturationsPositionsPerNeighbor_t;
+  //!> containing the saturation points over all desired atoms required
+  typedef std::map<int, SaturationsPositionsPerNeighbor_t> GlobalSaturationPositions_t;
+
   /** Constructor of SaturatedFragment requires \a set which we are tightly
    * associated.
@@ -48 +58 @@
    * \param _container container to add KeySet as in-use
    * \param _hydrogens pool with hydrogens for saturation
+   * \param _globalsaturationpositions saturation positions to be used
    */
   SaturatedFragment(
@@ -54 +65 @@
       HydrogenPool &_hydrogens,
       const enum HydrogenTreatment _treatment,
-      const enum HydrogenSaturation saturation);
+      const enum HydrogenSaturation saturation,
+      const GlobalSaturationPositions_t &_globalsaturationpositions);
 
   /** Destructor of class SaturatedFragment.
@@ -100 +112 @@
   /** Helper function to lease and bring in place saturation hydrogens.
    *
+   * Here, we use local information to calculate saturation positions.
+   *
    */
   void saturate();
+
+  /** Helper function to lease and bring in place saturation hydrogens.
+   *
+   * Here, saturation positions have to be calculated before and are fully
+   * stored in \a _globalsaturationpositions.
+   *
+   * \param_globalsaturationpositions
+   */
+  void saturate(const GlobalSaturationPositions_t &_globalsaturationpositions);
+
+  /** Replaces all cut bonds with respect to the given atom by hydrogens.
+   *
+   * \param _atom atom whose cut bonds to saturate
+   * \param _cutbonds list of cut bonds for \a _atom
+   * \return true - bonds saturated, false - something went wrong
+   */
+  bool saturateAtom(atom * const _atom, const BondList &_cutbonds);
 
   /** Helper function to get a hydrogen replacement for a given \a replacement.
@@ -109 +140 @@
    */
   atom * const getHydrogenReplacement(atom * const replacement);
+
+  /** Sets a saturation hydrogen at the given position in place of \a _father.
+   *
+   * \param _OwnerAtom atom "owning" the hydrogen (i.e. the one getting saturated)
+   * \param _position new position relative to \a _OwnerAtom
+   * \param _distance scale factor to the distance (default 1.)
+   * \param _father bond partner of \a _OwnerAtom that is replaced
+   */
+  const atom& setHydrogenReplacement(
+      const atom * const _OwnerAtom,
+      const Vector &_position,
+      const double _distance,
+      atom * const _father);
 
   /** Leases and adds a Hydrogen atom in replacement for the given atom \a *partner in bond with a *origin.