Changes in src/Actions/FragmentationAction/FragmentationAction.cpp [bf0ff3:5d5550]

File:

• src/Actions/FragmentationAction/FragmentationAction.cpp (modified) (5 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -42 +42 @@
 #include "Fragmentation/Exporters/ExportGraph_ToFiles.hpp"
 #include "Fragmentation/Exporters/ExportGraph_ToJobs.hpp"
+#include "Fragmentation/Exporters/SaturatedBond.hpp"
+#include "Fragmentation/Exporters/SaturatedFragment.hpp"
+#include "Fragmentation/Exporters/SaturationDistanceMaximizer.hpp"
 #include "Fragmentation/Fragmentation.hpp"
 #include "Fragmentation/Graph.hpp"
@@ -87 +90 @@
   // check for selected atoms
   if (world.beginAtomSelection() == world.endAtomSelection()) {
-    ELOG(1, "There are no atoms selected for fragmentation.");
+    STATUS("There are no atoms selected for fragmentation.");
     return Action::failure;
   }
@@ -261 +264 @@
   }
 
+  // create global saturation positions map
+  SaturatedFragment::GlobalSaturationPositions_t globalsaturationpositions;
+  {
+    // go through each atom
+    for (World::AtomSelectionConstIterator iter = world.beginAtomSelection();
+        iter != world.endAtomSelection(); ++iter) {
+      const atom * const _atom = iter->second;
+
+      // skip hydrogens if treated special
+      const enum HydrogenTreatment treatment =  params.HowtoTreatHydrogen.get() ? ExcludeHydrogen : IncludeHydrogen;
+      if ((treatment == ExcludeHydrogen) && (_atom->getType()->getAtomicNumber() == 1)) {
+        LOG(4, "DEBUG: Skipping hydrogen atom " << *_atom);
+        continue;
+      }
+
+      // get the valence
+      unsigned int NumberOfPoints = _atom->getElement().getNoValenceOrbitals();
+      LOG(3, "DEBUG: There are " << NumberOfPoints
+          << " places to fill in in total for this atom " << *_atom << ".");
+
+      // check whether there are any bonds with degree larger than 1
+      unsigned int SumOfDegrees = 0;
+      bool PresentHigherBonds = false;
+      const BondList &bondlist = _atom->getListOfBonds();
+      for (BondList::const_iterator bonditer = bondlist.begin();
+          bonditer != bondlist.end(); ++bonditer) {
+        SumOfDegrees += (*bonditer)->getDegree();
+        PresentHigherBonds |= (*bonditer)->getDegree() > 1;
+      }
+
+      // check whether there are alphas to maximize the hydrogens distances
+      SaturationDistanceMaximizer::position_bins_t position_bins;
+      {
+        // gather all bonds and convert to SaturatedBonds
+        SaturationDistanceMaximizer::PositionContainers_t CutBonds;
+        for (BondList::const_iterator bonditer = bondlist.begin();
+            bonditer != bondlist.end(); ++bonditer) {
+          CutBonds.push_back(
+              SaturatedBond::ptr(new SaturatedBond(*(bonditer->get()), *_atom) )
+            );
+        }
+        SaturationDistanceMaximizer maximizer(CutBonds);
+        if (PresentHigherBonds) {
+          // then find best alphas
+          maximizer();
+        } else {
+          // if no higher order bonds, we simply gather the scaled positions
+        }
+        position_bins = maximizer.getAllPositionBins();
+        LOG(4, "DEBUG: Positions for atom " << *_atom << " are " << position_bins);
+      }
+
+      // convert into the desired entry in the map
+      SaturatedFragment::SaturationsPositionsPerNeighbor_t positions_per_neighbor;
+      {
+        BondList::const_iterator bonditer = bondlist.begin();
+        SaturationDistanceMaximizer::position_bins_t::const_iterator biniter =
+            position_bins.begin();
+
+        for (;bonditer != bondlist.end(); ++bonditer, ++biniter) {
+          const atom * const OtherAtom = (*bonditer)->GetOtherAtom(_atom);
+          std::pair<
+              SaturatedFragment::SaturationsPositionsPerNeighbor_t::iterator,
+              bool
+              > inserter;
+          // check whether we treat hydrogen special
+          if ((treatment == ExcludeHydrogen) && (OtherAtom->getType()->getAtomicNumber() == 1)) {
+            // if hydrogen, forget rescaled position and use original one
+            inserter =
+                positions_per_neighbor.insert(
+                    std::make_pair(
+                        OtherAtom->getId(),
+                        SaturatedFragment::SaturationsPositions_t(
+                            1, OtherAtom->getPosition() - _atom->getPosition())
+                    )
+                );
+          } else {
+            inserter =
+                positions_per_neighbor.insert(
+                    std::make_pair(
+                        OtherAtom->getId(),
+                        SaturatedFragment::SaturationsPositions_t(
+                            biniter->begin(),
+                            biniter->end())
+                    )
+                );
+          }
+          // if already pressent, add to this present list
+          ASSERT (inserter.second,
+              "FragmentationAction::performCall() - other atom "
+              +toString(*OtherAtom)+" already present?");
+        }
+        // bonditer follows nicely
+        ASSERT( biniter == position_bins.end(),
+            "FragmentationAction::performCall() - biniter is out of step, it still points at bond "
+            +toString(*biniter)+".");
+      }
+      // and insert
+      globalsaturationpositions.insert(
+          std::make_pair( _atom->getId(),
+              positions_per_neighbor
+          ));
+    }
+  }
+
   {
     const enum HydrogenSaturation saturation =  params.DoSaturation.get() ? DoSaturate : DontSaturate;
@@ -266 +374 @@
     if (params.types.get().size() != 0) {
       // store molecule's fragment to file
-      ExportGraph_ToFiles exporter(TotalGraph, treatment, saturation);
+      ExportGraph_ToFiles exporter(TotalGraph, treatment, saturation, globalsaturationpositions);
       exporter.setPrefix(params.prefix.get());
       exporter.setOutputTypes(params.types.get());
@@ -272 +380 @@
     } else {
       // store molecule's fragment in FragmentJobQueue
-      ExportGraph_ToJobs exporter(TotalGraph, treatment, saturation);
+      ExportGraph_ToJobs exporter(TotalGraph, treatment, saturation, globalsaturationpositions);
       exporter.setLevel(params.level.get());
       exporter();