Changeset c39675 for src/Fragmentation/Exporters/SaturatedFragment.hpp

Timestamp:

Apr 8, 2013, 11:56:08 AM (12 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:

7cdf58

Parents:

6cabaac

git-author:

Frederik Heber <heber@…> (03/03/13 21:15:14)

git-committer:

Frederik Heber <heber@…> (04/08/13 11:56:08)

Message:

Added saturate() to SaturatedFragment.

• basically, this is AddHydrogenReplacementAtom() but stripped down a bit as we use hydrogens from the pool and as atoms for the fragment need not be copied anymore, we don't need all the father mambo jumbo.
• SaturatedFragment additionally now needs to know about how hydrogens are treated and whether we actually saturate.
• SaturatedFragmentUnitTest requires libLinearAlgebra.

File:

• src/Fragmentation/Exporters/SaturatedFragment.hpp (modified) (4 diffs)

src/Fragmentation/Exporters/SaturatedFragment.hpp

@@ -14 +14 @@
 #endif
 
+#include <iosfwd>
 #include <set>
+#include <string>
 
+#include "Bond/bond.hpp"
 #include "Fragmentation/KeySet.hpp"
+#include "Fragmentation/HydrogenSaturation_enum.hpp"
+#include "Parser/FormatParserStorage.hpp"
 
+class atom;
 class HydrogenPool;
 
@@ -46 +52 @@
       const KeySet &_set,
       KeySetsInUse_t &_container,
-      HydrogenPool &_hydrogens);
+      HydrogenPool &_hydrogens,
+      const enum HydrogenTreatment _treatment,
+      const enum HydrogenSaturation saturation);
 
   /** Destructor of class SaturatedFragment.
@@ -62 +70 @@
   }
 
+  /** Getter for the FullMolecule this instance is associated with.
+   *
+   * \return const ref to FullMolecule
+   */
+  const KeySet & getFullMolecule() const
+  {
+    return FullMolecule;
+  }
+
+  /** Getter for the SaturationHydrogens this instance is associated with.
+   *
+   * \return const ref to SaturationHydrogens
+   */
+  const KeySet & getSaturationHydrogens() const
+  {
+    return SaturationHydrogens;
+  }
+
+  /** Prints the config of the fragment of \a _type to \a out.
+   *
+   * \param out output stream to write to
+   * \param _type parser type to write config
+   */
+  bool OutputConfig(
+      std::ostream &out,
+      const ParserTypes _type) const;
+
+private:
+  /** Helper function to lease and bring in place saturation hydrogens.
+   *
+   */
+  void saturate();
+
+  /** Helper function to get a hydrogen replacement for a given \a replacement.
+   *
+   * \param replacement atom to "replace" with hydrogen in a fragment.
+   * \return ref to leased hydrogen atom
+   */
+  atom * const getHydrogenReplacement(atom * const replacement);
+
+  /** Leases and adds a Hydrogen atom in replacement for the given atom \a *partner in bond with a *origin.
+   * Here, we have to distinguish between single, double or triple bonds as stated by \a BondDegree, that each demand
+   * a different scheme when adding \a *replacement atom for the given one.
+   * -# Single Bond: Simply add new atom with bond distance rescaled to typical hydrogen one
+   * -# Double Bond: Here, we need the **BondList of the \a *origin atom, by scanning for the other bonds instead of
+   *    *Bond, we use the through these connected atoms to determine the plane they lie in, vector::MakeNormalvector().
+   *    The orthonormal vector to this plane along with the vector in *Bond direction determines the plane the two
+   *    replacing hydrogens shall lie in. Now, all remains to do is take the usual hydrogen double bond angle for the
+   *    element of *origin and form the sin/cos admixture of both plane vectors for the new coordinates of the two
+   *    hydrogens forming this angle with *origin.
+   * -# Triple Bond: The idea is to set up a tetraoid (C1-H1-H2-H3) (however the lengths \f$b\f$ of the sides of the base
+   *    triangle formed by the to be added hydrogens are not equal to the typical bond distance \f$l\f$ but have to be
+   *    determined from the typical angle \f$\alpha\f$ for a hydrogen triple connected to the element of *origin):
+   *    We have the height \f$d\f$ as the vector in *Bond direction (from triangle C1-H1-H2).
+   *    \f[ h = l \cdot \cos{\left (\frac{\alpha}{2} \right )} \qquad b = 2l \cdot \sin{\left (\frac{\alpha}{2} \right)} \quad \rightarrow \quad d = l \cdot \sqrt{\cos^2{\left (\frac{\alpha}{2} \right)}-\frac{1}{3}\cdot\sin^2{\left (\frac{\alpha}{2}\right )}}
+   *    \f]
+   *    vector::GetNormalvector() creates one orthonormal vector from this *Bond vector and vector::MakeNormalvector creates
+   *    the third one from the former two vectors. The latter ones form the plane of the base triangle mentioned above.
+   *    The lengths for these are \f$f\f$ and \f$g\f$ (from triangle H1-H2-(center of H1-H2-H3)) with knowledge that
+   *    the median lines in an isosceles triangle meet in the center point with a ratio 2:1.
+   *    \f[ f = \frac{b}{\sqrt{3}} \qquad g = \frac{b}{2}
+   *    \f]
+   *    as the coordination of all three atoms in the coordinate system of these three vectors:
+   *    \f$\pmatrix{d & f & 0}\f$, \f$\pmatrix{d & -0.5 \cdot f & g}\f$ and \f$\pmatrix{d & -0.5 \cdot f & -g}\f$.
+   *
+   * \param TopBond pointer to bond between \a *origin and \a *replacement
+   * \param Origin atom that is actually contained in the fragment
+   * \param Replacement pointer to the atom which shall be copied as a hydrogen atom in this molecule
+   * \param isAngstroem whether the coordination of the given atoms is in AtomicLength (false) or Angstrom(true)
+   * \return number of atoms added, if < bond::BondDegree then something went wrong
+   */
+  bool AddHydrogenReplacementAtom(
+      bond::ptr TopBond,
+      atom *Origin,
+      atom *Replacement,
+      bool IsAngstroem);
+
 private:
   //!> container to mark ourselves RAII-style
@@ -73 +158 @@
   //!> key set containing the ids of all hydrogens added for saturation
   KeySet SaturationHydrogens;
+  //!> whether hydrogens are generally contained in set or not
+  const enum HydrogenTreatment treatment;
+  //!> whether to actually saturate or not
+  const enum HydrogenSaturation saturation;
 };