source: src/MoleculeLeafClass.hpp@ 936a02

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
Last change on this file since 936a02 was 07a47e, checked in by Frederik Heber <heber@…>, 13 years ago

Replaced enable/disable-hydrogen by internal switch.
  • Property mode set to 100644
File size: 1.4 KB
Line 
1/*
2 * MoleculeLeafClass.hpp
3 *
4 * Created on: Oct 20, 2011
5 * Author: heber
6 */
7
8#ifndef MOLECULELEAFCLASS_HPP_
9#define MOLECULELEAFCLASS_HPP_
10
11#ifdef HAVE_CONFIG_H
12#include <config.h>
13#endif
14
15#include "Fragmentation/fragmentation_helpers.hpp"
16#include "Fragmentation/HydrogenSaturation_enum.hpp"
17
18class atom;
19class Graph;
20class molecule;
21
22
23/** A leaf for a tree of \a molecule class
24 * Wraps molecules in a tree structure
25 */
26class MoleculeLeafClass
27{
28public:
29 molecule *Leaf; //!< molecule of this leaf
30 //MoleculeLeafClass *UpLeaf; //!< Leaf one level up
31 //MoleculeLeafClass *DownLeaf; //!< First leaf one level down
32 MoleculeLeafClass *previous; //!< Previous leaf on this level
33 MoleculeLeafClass *next; //!< Next leaf on this level
34
35 //MoleculeLeafClass(MoleculeLeafClass *Up, MoleculeLeafClass *Previous);
36 MoleculeLeafClass(MoleculeLeafClass *PreviousLeaf);
37 ~MoleculeLeafClass();
38
39 bool AddLeaf(molecule *ptr, MoleculeLeafClass *Previous);
40 bool FillRootStackForSubgraphs(KeyStack *&RootStack, bool *AtomMask, int &FragmentCounter, const enum HydrogenSaturation saturation);
41 bool AssignKeySetsToFragment(molecule *reference, Graph *KeySetList, atom ***&ListOfLocalAtoms, Graph **&FragmentList, int &FragmentCounter, bool FreeList = false);
42 void TranslateIndicesToGlobalIDs(Graph **FragmentList, int &FragmentCounter, int &TotalNumberOfKeySets, Graph &TotalGraph);
43 int Count() const;
44};
45
46
47#endif /* MOLECULELEAFCLASS_HPP_ */
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