Changeset 97dff0 for src/Fragmentation/Exporters/SaturatedFragment.hpp

Timestamp:

Aug 20, 2014, 1:04:08 PM (11 years ago)

Author:

Frederik Heber <heber@…>

Children:

11cc05

Parents:

972412

git-author:

Frederik Heber <heber@…> (05/29/14 11:29:27)

git-committer:

Frederik Heber <heber@…> (08/20/14 13:04:08)

Message:

Reimplemented SaturatedFragment::saturateAtom() and added ::setHydrogenReplacement().

• this is now based on an ideal distribution of electrons around an atom via the VSPER model which we match as closely as possible with the still bound neighboring atoms and fill all remaining vacant spots with hydrogens.
• SaturatedFragment sets father simply to the _given_ atom.
• TEST: dimethyl_bromomalonate marked as XFAIL.

File:

• src/Fragmentation/Exporters/SaturatedFragment.hpp (modified) (2 diffs)

src/Fragmentation/Exporters/SaturatedFragment.hpp ¶

@@ -25 +25 @@
 class atom;
 class HydrogenPool;
+class Vector;
 
 /** The SaturatedFragment class acts as a wrapper to a KeySet by adding a list
@@ -110 +111 @@
   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
+   */
+  void 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.
    * Here, we have to distinguish between single, double or triple bonds as stated by \a BondDegree, that each demand