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

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"
@@ -90 +87 @@
   // check for selected atoms
   if (world.beginAtomSelection() == world.endAtomSelection()) {
-    STATUS("There are no atoms selected for fragmentation.");
+    ELOG(1, "There are no atoms selected for fragmentation.");
     return Action::failure;
   }
@@ -264 +261 @@
   }
 
-  // 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;
@@ -374 +266 @@
     if (params.types.get().size() != 0) {
       // store molecule's fragment to file
-      ExportGraph_ToFiles exporter(TotalGraph, treatment, saturation, globalsaturationpositions);
+      ExportGraph_ToFiles exporter(TotalGraph, treatment, saturation);
       exporter.setPrefix(params.prefix.get());
       exporter.setOutputTypes(params.types.get());
@@ -380 +272 @@
     } else {
       // store molecule's fragment in FragmentJobQueue
-      ExportGraph_ToJobs exporter(TotalGraph, treatment, saturation, globalsaturationpositions);
+      ExportGraph_ToJobs exporter(TotalGraph, treatment, saturation);
       exporter.setLevel(params.level.get());
       exporter();