source: src/Fragmentation/fragmentation_helpers.hpp@ 23fb72

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 23fb72 was a03d25, checked in by Frederik Heber <heber@…>, 14 years ago

Placed all routines working on UniqueFragments struct inside this class.

  • changed struct to class.
  • Property mode set to 100644
File size: 2.3 KB
RevLine 
[ba1823]1/*
2 * fragmentation_helpers.hpp
3 *
4 * Created on: Oct 18, 2011
5 * Author: heber
6 */
7
8#ifndef FRAGMENTATION_HELPERS_HPP_
9#define FRAGMENTATION_HELPERS_HPP_
10
11
12#ifdef HAVE_CONFIG_H
13#include <config.h>
14#endif
15
16#include <list>
17#include <map>
18#include <string>
19#include <vector>
20
21#include "graph.hpp"
22
23class bond;
24class molecule;
25
26bool ScanBufferIntoKeySet(char *buffer, KeySet &CurrentSet);
27bool ParseKeySetFile(std::string &path, Graph *&FragmentList);
28bool ParseTEFactorsFile(char *path, Graph *FragmentList);
29bool StoreKeySetFile(Graph &KeySetList, std::string &path);
30bool StoreTEFactorsFile(Graph &KeySetList, char *path);
31std::map<int,KeySet> * GraphToIndexedKeySet(Graph *GlobalKeySetList);
32void InsertIntoAdaptiveCriteriaList(std::map<int, std::pair<double,int> > *AdaptiveCriteriaList, std::map<int,KeySet> &IndexKeySetList, int FragOrder, int No, double Value);
33int CountLinesinFile(std::ifstream &InputFile);
34std::map<int, std::pair<double,int> > * ScanAdaptiveFileIntoMap(std::string &path, std::map<int,KeySet> &IndexKeySetList);
35std::map<double, std::pair<int,int> > * ReMapAdaptiveCriteriaListToValue(std::map<int, std::pair<double,int> > *AdaptiveCriteriaList, molecule *mol);
36bool MarkUpdateCandidates(bool *AtomMask, std::map<double, std::pair<int,int> > &FinalRootCandidates, int Order, molecule *mol);
37void PrintAtomMask(bool *AtomMask, int AtomCount);
38void SPFragmentGenerator_ClearingTouched(int verbosity, int *&TouchedList, int SubOrder, int &TouchedIndex);
39int AddPowersetToSnakeStack(int verbosity, int CurrentCombination, int SetDimension, KeySet *FragmentSet, std::vector<bond *> &BondsSet, int *&TouchedList, int &TouchedIndex);
40int CountSetMembers(std::list<bond *>::const_iterator SetFirst, std::list<bond *>::const_iterator SetLast, int *&TouchedList, int TouchedIndex);
41int FillBondsList(std::vector<bond *> &BondsList, std::list<bond *>::const_iterator SetFirst, std::list<bond *>::const_iterator SetLast, int *&TouchedList, int TouchedIndex);
42void RemoveAllTouchedFromSnakeStack(int verbosity, KeySet *FragmentSet, int *&TouchedList, int &TouchedIndex);
[a03d25]43
[ba1823]44int CombineAllOrderListIntoOne(Graph *&FragmentList, Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol);
45void FreeAllOrdersList(Graph ***FragmentLowerOrdersList, KeyStack &RootStack, molecule *mol);
46
47#endif /* FRAGMENTATION_HELPERS_HPP_ */
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