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 2affd1 was 343c5a, checked in by Frederik Heber <heber@…>, 10 years ago |
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Added CorrectBondDegreeAction and fixed Calculation tests.
- pdb files do have bond graph but not the right degrees.
- there also lies some ambiguity in here as double bonds depend on the chosen
matching.
|
-
Property mode
set to
100644
|
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File size:
1.0 KB
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| 1 | /*
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| 2 | * CorrectBondDegreeAction.def
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| 3 | *
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| 4 | * Created on: Jul 31, 2014
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| 5 | * Author: heber
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| 6 | */
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| 7 |
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| 8 | // all includes and forward declarations necessary for non-integral types below
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| 9 | #include <vector>
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| 10 | #include "types.hpp"
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| 11 |
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| 12 | struct BondInfo_t;
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| 13 |
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| 14 | // i.e. there is an integer with variable name Z that can be found in
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| 15 | // ValueStorage by the token "Z" -> first column: int, Z, "Z"
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| 16 | // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
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| 17 | #undef paramtypes
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| 18 | #undef paramtokens
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| 19 | #undef paramdescriptions
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| 20 | #undef paramdefaults
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| 21 | #undef paramreferences
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| 22 | #undef paramvalids
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| 23 |
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| 24 | #define statetypes (std::vector<BondInfo_t>)
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| 25 | #define statereferences (bonds)
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| 26 |
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| 27 | // some defines for all the names, you may use ACTION, STATE and PARAMS
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| 28 | #define CATEGORY Graph
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| 29 | #define MENUNAME "graph"
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| 30 | #define MENUPOSITION 1
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| 31 | #define ACTIONNAME CorrectBondDegree
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| 32 | #define TOKEN "correct-bonddegree"
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| 33 |
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| 34 |
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| 35 | // finally the information stored in the ActionTrait specialization
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| 36 | #define DESCRIPTION "correct a present bond graph with respect to the valency of the involved atoms"
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| 37 | #undef SHORTFORM
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