Changeset 999eaf for src/Fragmentation

Timestamp:

Apr 28, 2021, 10:02:49 PM (5 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Candidate_v1.7.0, stable

Children:

6b7765

Parents:

5aa337

git-author:

Frederik Heber <frederik.heber@…> (04/18/21 08:23:36)

git-committer:

Frederik Heber <frederik.heber@…> (04/28/21 22:02:49)

Message:

Added EvaluateStabilityAction to estimate a molecule's stability.

• removes every bond and checks the energies of the products against the educt equipped with enough hydrogen molecules to compensate for the cut bond times its degree.
• outputs a CSV file with entries per bond.
• extended HomologyGraph to allow direct use of AtomIdSet, i.e. atomic ids coming from a selection in the World or from the molecule.
• DOCU: Added subsection on this action to section homology.
• TEST: Added regression test case.

Location:

src/Fragmentation

Files:

• Evaluation/StabilityEvaluator.cpp (added)
• Evaluation/StabilityEvaluator.hpp (added)
• Homology/HomologyGraph.cpp (modified) (1 diff)
• Homology/HomologyGraph.hpp (modified) (3 diffs)
• Homology/HomologyGraph_getFromKeyset.cpp (modified) (2 diffs)
• Homology/HomologyGraph_getFromKeysetStub.cpp (modified) (1 diff)
• Makefile.am (modified) (2 diffs)

src/Fragmentation/Homology/HomologyGraph.cpp

@@ -55 +55 @@
   nodes(detail::getNodesFromIndexSet(index)),
   edges(detail::getEdgesFromIndexSet(index))
+{}
+
+HomologyGraph::HomologyGraph(const AtomIdSet::atomIdSet &index) :
+  nodes(detail::getNodesFromAtomIds(index)),
+  edges(detail::getEdgesFromAtomIds(index))
 {}
 

src/Fragmentation/Homology/HomologyGraph.hpp

@@ -21 +21 @@
 #include <iosfwd>
 
+#include "AtomIdSet.hpp"
 #include "Fragmentation/Homology/FragmentEdge.hpp"
 #include "Fragmentation/Homology/FragmentNode.hpp"
@@ -79 +80 @@
   explicit HomologyGraph(const IndexSet &index);
 
+  /** Constructor for class HomologyGraph from a AtomIdSet (i.e. from atoms in the World).
+   *
+   * @param index global ids of atoms to pick
+   */
+  explicit HomologyGraph(const AtomIdSet::atomIdSet &index);
+
   /** Destructor for class HomologyGraph.
    *
@@ -200 +207 @@
   const HomologyGraph::nodes_t getNodesFromIndexSet(const IndexSet &keyset);
   const HomologyGraph::edges_t getEdgesFromIndexSet(const IndexSet &keyset);
+  const HomologyGraph::nodes_t getNodesFromAtomIds(const AtomIdSet::atomIdSet &keyset);
+  const HomologyGraph::edges_t getEdgesFromAtomIds(const AtomIdSet::atomIdSet &keyset);
 };
 

src/Fragmentation/Homology/HomologyGraph_getFromKeyset.cpp

@@ -135 +135 @@
     return getNodesFromSet<size_t>(keyset);
   }
+  const HomologyGraph::nodes_t getNodesFromAtomIds(const AtomIdSet::atomIdSet &keyset) {
+    return getNodesFromSet<atomId_t>(keyset);
+  }
   const HomologyGraph::edges_t getEdgesFromKeySet(const KeySet &keyset) {
     return getEdgesFromSet<int>(keyset);
@@ -141 +144 @@
     return getEdgesFromSet<size_t>(keyset);
   }
+  const HomologyGraph::edges_t getEdgesFromAtomIds(const AtomIdSet::atomIdSet &keyset) {
+    return getEdgesFromSet<atomId_t>(keyset);
+  }
 };  /* namespace detail */
 

src/Fragmentation/Homology/HomologyGraph_getFromKeysetStub.cpp

@@ -63 +63 @@
   }
 
+  const HomologyGraph::nodes_t getNodesFromAtomIds(const AtomIdSet::atomIdSet &keyset)
+  {
+    return HomologyGraph::nodes_t();
+  }
+
+  const HomologyGraph::edges_t getEdgesFromAtomIds(const AtomIdSet::atomIdSet &keyset)
+  {
+    return HomologyGraph::edges_t();
+  }
 };  /* namespace detail */

src/Fragmentation/Makefile.am

@@ -3 +3 @@
 
 FRAGMENTATIONSOURCE = \
+        Fragmentation/Evaluation/StabilityEvaluator.cpp \
         Fragmentation/Exporters/ExportGraph_ToAtomFragments.cpp \
         Fragmentation/Exporters/ExportGraph_ToFiles.cpp \
@@ -36 +37 @@
 
 FRAGMENTATIONHEADER = \
+        Fragmentation/Evaluation/StabilityEvaluator.hpp \
         Fragmentation/Exporters/ExportGraph_ToAtomFragments.hpp \
         Fragmentation/Exporters/ExportGraph_ToFiles.hpp \