Changeset e6317b for src/Actions/FragmentationAction

Timestamp:

Jun 16, 2010, 12:24:21 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

492279

Parents:

f8e486 (diff), 980dd6 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Broken: Merge commit 'Gitosis/stable' into stable

Conflicts:

molecuilder/src/Actions/AnalysisAction/PairCorrelationToPointAction.cpp
molecuilder/src/Actions/AnalysisAction/PairCorrelationToSurfaceAction.cpp
molecuilder/src/Makefile.am

Location:

src/Actions/FragmentationAction

Files:

• DepthFirstSearchAction.cpp (modified) (1 diff)
• FragmentationAction.cpp (modified) (3 diffs)
• SubgraphDissectionAction.cpp (modified) (3 diffs)

src/Actions/FragmentationAction/DepthFirstSearchAction.cpp

@@ -9 +9 @@
 
 #include "Actions/FragmentationAction/DepthFirstSearchAction.hpp"
-#include "CommandLineParser.hpp"
 #include "atom.hpp"
 #include "config.hpp"

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -9 +9 @@
 
 #include "Actions/FragmentationAction/FragmentationAction.hpp"
-#include "CommandLineParser.hpp"
 #include "atom.hpp"
 #include "config.hpp"
@@ -27 +26 @@
 #include "Actions/MapOfActions.hpp"
 
-const char FragmentationFragmentationAction::NAME[] = "subspace-dissect";
+const char FragmentationFragmentationAction::NAME[] = "fragment-mol";
 
 FragmentationFragmentationAction::FragmentationFragmentationAction() :
@@ -38 +37 @@
 Action::state_ptr FragmentationFragmentationAction::performCall() {
   Dialog *dialog = UIFactory::getInstance().makeDialog();
+  clock_t start,end;
+  molecule *mol = NULL;
+  double distance = -1.;
+  int order = 0;
+  config *configuration = World::getInstance().getConfig();
+  int ExitFlag = 0;
 
-  dialog->queryEmpty(NAME, MapOfActions::getInstance().getDescription(NAME));
+  cout << "pre-dialog"<< endl;
+  dialog->queryMolecule(NAME, &mol, MapOfActions::getInstance().getDescription(NAME));
+  dialog->queryDouble("distance", &distance, MapOfActions::getInstance().getDescription("distance"));
+  dialog->queryInt("order", &order, MapOfActions::getInstance().getDescription("order"));
 
   if(dialog->display()) {
+    cout << "POST-dialog"<< endl;
+    ASSERT(mol != NULL, "No molecule has been picked for fragmentation.");
+    DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with bond distance " << distance << " angstroem, order of " << order << "." << endl);
+    DoLog(0) && (Log() << Verbose(0) << "Creating connection matrix..." << endl);
+    start = clock();
+    mol->CreateAdjacencyList(distance, configuration->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
+    DoLog(0) && (Log() << Verbose(0) << "Fragmenting molecule with current connection matrix ..." << endl);
+    if (mol->hasBondStructure()) {
+      ExitFlag = mol->FragmentMolecule(order, configuration);
+    }
+    World::getInstance().setExitFlag(ExitFlag);
+    end = clock();
+    DoLog(0) && (Log() << Verbose(0) << "Clocks for this operation: " << (end-start) << ", time: " << ((double)(end-start)/CLOCKS_PER_SEC) << "s." << endl);
     delete dialog;
     return Action::success;

src/Actions/FragmentationAction/SubgraphDissectionAction.cpp

@@ -9 +9 @@
 
 #include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
-#include "CommandLineParser.hpp"
 #include "atom.hpp"
 #include "config.hpp"
@@ -27 +26 @@
 #include "Actions/MapOfActions.hpp"
 
-const char FragmentationSubgraphDissectionAction::NAME[] = "subspace-dissect";
+const char FragmentationSubgraphDissectionAction::NAME[] = "subgraph-dissect";
 
 FragmentationSubgraphDissectionAction::FragmentationSubgraphDissectionAction() :
@@ -42 +41 @@
 
   if(dialog->display()) {
+    DoLog(1) && (Log() << Verbose(1) << "Dissecting molecular system into a set of disconnected subgraphs ... " << endl);
+    // @TODO rather do the dissection afterwards
+    MoleculeListClass *molecules = World::getInstance().getMolecules();
+    molecules->DissectMoleculeIntoConnectedSubgraphs(World::getInstance().getPeriode(), World::getInstance().getConfig());
     delete dialog;
     return Action::success;