Changeset f5fa48 for src/Fragmentation/Exporters/SaturatedFragment.hpp

Timestamp:

Aug 20, 2014, 1:06:47 PM (11 years ago)

Author:

Frederik Heber <heber@…>

Children:

d635829

Parents:

ce0ca4

git-author:

Frederik Heber <heber@…> (07/18/14 17:08:09)

git-committer:

Frederik Heber <heber@…> (08/20/14 13:06:47)

Message:

SaturatedFragment can deal with a global saturation position map.

• so far, we create an empty one in FragmentationAction such that nothing's changed for the moment.
• similarly in StoreSaturatedFragmentAction. However, there this is intended as only local information is required (it's only a single fragment).

File:

• src/Fragmentation/Exporters/SaturatedFragment.hpp (modified) (5 diffs)

src/Fragmentation/Exporters/SaturatedFragment.hpp

@@ -23 +23 @@
 #include "Parser/FormatParserStorage.hpp"
 
+#include "LinearAlgebra/Vector.hpp"
+
 class atom;
 class HydrogenPool;
-class Vector;
 
 /** The SaturatedFragment class acts as a wrapper to a KeySet by adding a list
@@ -43 +44 @@
   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.
@@ -49 +57 @@
    * \param _container container to add KeySet as in-use
    * \param _hydrogens pool with hydrogens for saturation
+   * \param _globalsaturationpositions saturation positions to be used
    */
   SaturatedFragment(
@@ -55 +64 @@
       HydrogenPool &_hydrogens,
       const enum HydrogenTreatment _treatment,
-      const enum HydrogenSaturation saturation);
+      const enum HydrogenSaturation saturation,
+      const GlobalSaturationPositions_t &_globalsaturationpositions);
 
   /** Destructor of class SaturatedFragment.
@@ -101 +111 @@
   /** 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.