Changeset 73916f for src/Parser/FormatParserStorage.cpp

Timestamp:

Dec 16, 2010, 5:32:22 PM (15 years ago)

Author:

Frederik Heber <heber@…>

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, Candidate_v1.7.0, 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:

fc5c3a

Parents:

512f85

git-author:

Frederik Heber <heber@…> (12/11/10 15:57:00)

git-committer:

Frederik Heber <heber@…> (12/16/10 17:32:22)

Message:

Extended FormatParser::save() to use vector<atom *> to save.

• This is needed to make the save functions also work on selected atoms or molecules only.
• Within ParserCommonUnitTest, ParserTremoloUnitTest we create the vector by calling World's getAllAtoms() (which would have been done before in the specialized save() functions).
• new functions in FormatParserStorage:
  • saveSelectedAtoms().
  • saveSelectedMolecules().
  • saveWorld().
• renamed ::get() and ::put() to ::load() and ::save() to have it more consistent with underlying FormatParser functions and also to avoid misinterpretation with all ::get...() functions.

File:

• src/Parser/FormatParserStorage.cpp (modified) (4 diffs)

src/Parser/FormatParserStorage.cpp

@@ -36 +36 @@
 
 #include "Helpers/Assert.hpp"
+
+#include "molecule.hpp"
 
 #include "Patterns/Singleton_impl.hpp"
@@ -224 +226 @@
  * \return true - parsing ok, false - suffix unknown
  */
-bool FormatParserStorage::get(std::istream &input, std::string suffix)
+bool FormatParserStorage::load(std::istream &input, std::string suffix)
 {
   if (suffix == ParserSuffixes[mpqc]) {
@@ -243 +245 @@
 }
 
+/** Stores all selected atoms in an ostream depending on its suffix
+ * \param &output output stream
+ * \param suffix
+ * \return true - storing ok, false - suffix unknown
+ */
+bool FormatParserStorage::saveSelectedAtoms(std::ostream &output, std::string suffix)
+{
+  std::vector<atom *> atoms = World::getInstance().getSelectedAtoms();
+  return save(output, suffix, atoms);
+}
+
+/** Stores all selected atoms in an ostream depending on its suffix
+ * We store in the order of the atomic ids, not in the order they appear in the molecules.
+ * Hence, we first create a vector from all selected molecules' atoms.
+ * \param &output output stream
+ * \param suffix
+ * \return true - storing ok, false - suffix unknown
+ */
+bool FormatParserStorage::saveSelectedMolecules(std::ostream &output, std::string suffix)
+{
+  std::vector<molecule *> molecules = World::getInstance().getSelectedMolecules();
+  std::map<size_t, atom *> IdAtoms;
+  for (std::vector<molecule *>::const_iterator MolIter = molecules.begin();
+      MolIter != molecules.end();
+      ++MolIter) {
+    for(molecule::atomSet::const_iterator AtomIter = (*MolIter)->begin();
+        AtomIter != (*MolIter)->end();
+        ++AtomIter) {
+      IdAtoms.insert( make_pair((*AtomIter)->getId(), (*AtomIter)) );
+    }
+  }
+  std::vector<atom *> atoms;
+  atoms.reserve(IdAtoms.size());
+  for (std::map<size_t, atom *>::const_iterator iter = IdAtoms.begin();
+      iter != IdAtoms.end();
+      ++iter) {
+    atoms.push_back(iter->second);
+  }
+  return save(output, suffix, atoms);
+}
 
 /** Stores world in an ostream depending on its suffix
@@ -249 +291 @@
  * \return true - storing ok, false - suffix unknown
  */
-bool FormatParserStorage::put(std::ostream &output, std::string suffix)
+bool FormatParserStorage::saveWorld(std::ostream &output, std::string suffix)
+{
+  std::vector<atom *> atoms = World::getInstance().getAllAtoms();
+  return save(output, suffix, atoms);
+}
+
+/** Stores a given vector of \a atoms in an ostream depending on its suffix
+ * \param &output output stream
+ * \param suffix
+ * \return true - storing ok, false - suffix unknown
+ */
+bool FormatParserStorage::save(std::ostream &output, std::string suffix, const std::vector<atom *> &atoms)
 {
   if (suffix == ParserSuffixes[mpqc]) {
-    getMpqc().save(&output);
+    getMpqc().save(&output, atoms);
   } else if (suffix == ParserSuffixes[pcp]) {
-    getPcp().save(&output);
+    getPcp().save(&output, atoms);
   } else if (suffix == ParserSuffixes[pdb]) {
-    getPdb().save(&output);
+    getPdb().save(&output, atoms);
   } else if (suffix == ParserSuffixes[tremolo]) {
-    getTremolo().save(&output);
+    getTremolo().save(&output, atoms);
   } else if (suffix == ParserSuffixes[xyz]) {
-    getXyz().save(&output);
+    getXyz().save(&output, atoms);
   } else {
     DoeLog(1) && (eLog() << Verbose(1) << "Unknown suffix " << suffix << " to for FormatParserStorage::put()." << endl);