Changeset ee4f2d for src/Fragmentation/Exporters/SaturatedFragment.hpp

Timestamp:

Aug 20, 2014, 1:09:40 PM (11 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, 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:

fc3aff

Parents:

2a03b0 (diff), 343c5a (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:

Merge branch 'EnhancingHydrogenSaturation' into stable

File:

• src/Fragmentation/Exporters/SaturatedFragment.hpp (modified) (6 diffs)

src/Fragmentation/Exporters/SaturatedFragment.hpp

@@ -18 +18 @@
 #include <string>
 
+#include "Atom/atom_bondedparticleinfo.hpp"
 #include "Bond/bond.hpp"
 #include "Fragmentation/KeySet.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
 #include "Parser/FormatParserStorage.hpp"
+
+#include "LinearAlgebra/Vector.hpp"
 
 class atom;
@@ -42 +45 @@
   typedef std::set<KeySet> KeySetsInUse_t;
 
+  //!> List of points giving saturation positions for a single bond neighbor
+  typedef std::list<Vector> SaturationsPositions_t;
+  //!> map for one atom, containing the saturation points for all its neighbors
+  typedef std::map<int, SaturationsPositions_t> SaturationsPositionsPerNeighbor_t;
+  //!> containing the saturation points over all desired atoms required
+  typedef std::map<int, SaturationsPositionsPerNeighbor_t> GlobalSaturationPositions_t;
+
   /** Constructor of SaturatedFragment requires \a set which we are tightly
    * associated.
@@ -48 +58 @@
    * \param _container container to add KeySet as in-use
    * \param _hydrogens pool with hydrogens for saturation
+   * \param _globalsaturationpositions saturation positions to be used
    */
   SaturatedFragment(
@@ -54 +65 @@
       HydrogenPool &_hydrogens,
       const enum HydrogenTreatment _treatment,
-      const enum HydrogenSaturation saturation);
+      const enum HydrogenSaturation saturation,
+      const GlobalSaturationPositions_t &_globalsaturationpositions);
 
   /** Destructor of class SaturatedFragment.
@@ -100 +112 @@
   /** Helper function to lease and bring in place saturation hydrogens.
    *
+   * Here, we use local information to calculate saturation positions.
+   *
    */
   void saturate();
+
+  /** Helper function to lease and bring in place saturation hydrogens.
+   *
+   * Here, saturation positions have to be calculated before and are fully
+   * stored in \a _globalsaturationpositions.
+   *
+   * \param_globalsaturationpositions
+   */
+  void saturate(const GlobalSaturationPositions_t &_globalsaturationpositions);
+
+  /** Replaces all cut bonds with respect to the given atom by hydrogens.
+   *
+   * \param _atom atom whose cut bonds to saturate
+   * \param _cutbonds list of cut bonds for \a _atom
+   * \return true - bonds saturated, false - something went wrong
+   */
+  bool saturateAtom(atom * const _atom, const BondList &_cutbonds);
 
   /** Helper function to get a hydrogen replacement for a given \a replacement.
@@ -109 +140 @@
    */
   atom * const getHydrogenReplacement(atom * const replacement);
+
+  /** Sets a saturation hydrogen at the given position in place of \a _father.
+   *
+   * \param _OwnerAtom atom "owning" the hydrogen (i.e. the one getting saturated)
+   * \param _position new position relative to \a _OwnerAtom
+   * \param _distance scale factor to the distance (default 1.)
+   * \param _father bond partner of \a _OwnerAtom that is replaced
+   */
+  const atom& setHydrogenReplacement(
+      const atom * const _OwnerAtom,
+      const Vector &_position,
+      const double _distance,
+      atom * const _father);
 
   /** Leases and adds a Hydrogen atom in replacement for the given atom \a *partner in bond with a *origin.