source: src/Fragmentation/Fragmentation.hpp@ 99b0dc

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 99b0dc was 99b0dc, checked in by Frederik Heber <heber@…>, 13 years ago

FragmentAction now has instead of path a types parameter.

  • new output-types parameter, is a vector<string> for giving a list of desired output types similar to SetOutputFormatAction.
  • TESTFIX: as vector<string> cannot have default value, we had to adapt the two regression tests Fragmentation/FragmentMolecule.. and the fragmentation tests.
  • Property mode set to 100644
File size: 1.5 KB
Line 
1/*
2 * Fragmentation.hpp
3 *
4 * Created on: Oct 18, 2011
5 * Author: heber
6 */
7
8#ifndef FRAGMENTATION_HPP_
9#define FRAGMENTATION_HPP_
10
11
12#ifdef HAVE_CONFIG_H
13#include <config.h>
14#endif
15
16#include <string>
17
18#include "Graph/DepthFirstSearchAnalysis.hpp"
19
20#include "Fragmentation/fragmentation_helpers.hpp"
21
22#include <string>
23#include <vector>
24
25class atom;
26class Graph;
27class KeySet;
28class molecule;
29
30class Fragmentation
31{
32public:
33 Fragmentation(molecule *_mol);
34 ~Fragmentation();
35
36 int FragmentMolecule(int Order, std::string prefix, DepthFirstSearchAnalysis &DFS);
37
38 void setOutputTypes(const std::vector<std::string> &types);
39
40private:
41
42 void FragmentBOSSANOVA(molecule *mol, Graph *&FragmentList, KeyStack &RootStack);
43 int GuesstimateFragmentCount(int order);
44
45 bool CreateMappingLabelsToConfigSequence(int *&SortIndex);
46
47 // order at site
48 bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, std::string path);
49 bool StoreOrderAtSiteFile(std::string &path);
50 bool ParseOrderAtSiteFromFile(std::string &path);
51
52 // storing fragments
53 molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
54 int StoreFragmentFromKeySet_Init(molecule *mol, molecule *Leaf, KeySet &Leaflet, atom **SonList);
55 void CreateInducedSubgraphOfFragment(molecule *mol, molecule *Leaf, atom **SonList, bool IsAngstroem);
56
57private:
58 //!> pointer to molecule that is fragmented
59 molecule *mol;
60 //!> list of parser types for which a configuration file per fragment is stored
61 std::vector<std::string> typelist;
62};
63
64
65#endif /* FRAGMENTATION_HPP_ */
Note: See TracBrowser for help on using the repository browser.