source: src/Fragmentation/Fragmentation.hpp@ bf42a0

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 Candidate_v1.7.0 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 bf42a0 was 2a0eb0, checked in by Frederik Heber <heber@…>, 13 years ago

FragmentationAction now works on selected atoms, split into molecules.

  • i.e. we still call Fragmentation on a specific molecule but fragmentMolecule() receives a vector of ids to use in its AtomMask. This is however not yet implemented.
  • TESTFIX: added --select-molecules-atoms to all fragmentation calls.
  • Property mode set to 100644
File size: 1.9 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 "Graph/DepthFirstSearchAnalysis.hpp"
17
18#include "Fragmentation/HydrogenSaturation_enum.hpp"
19#include "Fragmentation/fragmentation_helpers.hpp"
20#include "types.hpp"
21
22#include <map>
23#include <string>
24#include <vector>
25
26class atom;
27class AtomMask_t;
28class Graph;
29class KeySet;
30class molecule;
31
32class Fragmentation
33{
34public:
35 Fragmentation(molecule *_mol, const enum HydrogenSaturation _saturation);
36 ~Fragmentation();
37
38 int FragmentMolecule(const std::vector<atomId_t> &atomids, int Order, std::string prefix, DepthFirstSearchAnalysis &DFS);
39
40 void setOutputTypes(const std::vector<std::string> &types);
41
42private:
43
44 void FragmentBOSSANOVA(molecule *mol, Graph *&FragmentList, KeyStack &RootStack);
45 int GuesstimateFragmentCount(int order);
46
47 bool CreateMappingLabelsToConfigSequence(std::map<atomId_t, int> &SortIndex);
48
49 // order at site
50 bool CheckOrderAtSite(AtomMask_t &AtomMask, Graph *GlobalKeySetList, int Order, std::string path, bool LoopDoneAlready);
51 bool StoreOrderAtSiteFile(std::string &path);
52 bool ParseOrderAtSiteFromFile(const std::vector<atomId_t> &atomids, std::string &path);
53
54 // storing fragments
55 molecule * StoreFragmentFromKeySet(KeySet &Leaflet, bool IsAngstroem);
56 int StoreFragmentFromKeySet_Init(molecule *mol, molecule *Leaf, KeySet &Leaflet, ListOfLocalAtoms_t &SonList);
57 void CreateInducedSubgraphOfFragment(molecule *mol, molecule *Leaf, ListOfLocalAtoms_t &SonList, bool IsAngstroem);
58
59private:
60 //!> pointer to molecule that is fragmented
61 molecule *mol;
62 //!> whether to saturate dangling bonds with hydrogen and hence treat hydrogen special
63 const enum HydrogenSaturation saturation;
64 //!> list of parser types for which a configuration file per fragment is stored
65 std::vector<std::string> typelist;
66};
67
68
69#endif /* FRAGMENTATION_HPP_ */
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