source: src/Actions/GlobalListOfActions.hpp@ 5fa1e86

Candidate_v1.7.0 stable
Last change on this file since 5fa1e86 was 5fa1e86, checked in by Frederik Heber <frederik.heber@…>, 5 years ago

Added BondifyAction.

  • this allows to add non-hydrogen bonds and is complementary to saturate bonds where hydrogens are added.
  • we generate all possible candidate sets taken from non-hydrogen atoms in vicinity with hydrogens and pick one at random.
  • DOCU: added to userguide.
  • TEST: added regression test case.
  • Property mode set to 100644
File size: 5.8 KB
RevLine 
[83e90c]1/*
2 * GlobalListOfActions.hpp
3 *
4 * Created on: Sep 21, 2011
5 * Author: heber
6 */
7
8#ifndef GLOBALLISTOFACTIONS_HPP_
9#define GLOBALLISTOFACTIONS_HPP_
10
11// include config.h
12#ifdef HAVE_CONFIG_H
13#include <config.h>
14#endif
15
[004d5c]16#include <boost/preprocessor/seq/push_back.hpp>
[975b83]17#include <boost/preprocessor/seq/remove.hpp>
[004d5c]18
19// this is global list of actions valid for all cases
[442495]20// PLEASE adhere to the alphabetical ordering of the list of Actions
21// NOTE that Redo must remain at the front due to technical reasons
[004d5c]22#define GLOBALLISTOFACTIONS_initial \
23 (Redo) \
[f4b626a]24 (AnalysisAverageMoleculeForce) \
[442495]25 (AnalysisDipoleAngularCorrelation) \
26 (AnalysisDipoleCorrelation) \
27 (AnalysisMolecularVolume) \
28 (AnalysisPairCorrelation) \
29 (AnalysisPointCorrelation) \
30 (AnalysisPrincipalAxisSystem) \
31 (AnalysisSurfaceCorrelation) \
32 (AtomAdd) \
[5fa1e86]33 (AtomBondify) \
[442495]34 (AtomChangeElement) \
[bbf6dc]35 (AtomMirror) \
[310445]36 (AtomRandomPerturbation) \
[442495]37 (AtomRemove) \
38 (AtomRotateAroundOriginByAngle) \
[2fcef3]39 (AtomSaturate) \
[442495]40 (AtomSaveSelectedAtoms) \
41 (AtomTranslate) \
[c7fe90]42 (AtomTranslateToOrigin) \
[442495]43 (BondAdd) \
44 (BondRemove) \
[2d1280]45 (BondSetDegree) \
[f3db60]46 (CommandDryRun) \
[442495]47 (CommandElementDb) \
48 (CommandBondLengthTable) \
49 (CommandFastParsing) \
50 (CommandHelp) \
51 (CommandHelpRedistribute) \
[f3db60]52 (CommandNoDryRun) \
[442495]53 (CommandSetRandomNumbersEngine) \
54 (CommandSetRandomNumbersDistribution) \
55 (CommandStoreSession) \
56 (CommandVerbose) \
57 (CommandVersion) \
58 (CommandWarranty) \
59 (FillRegularGrid) \
60 (FillSurface) \
[aa55d0]61 (FillSuspendInMolecule) \
[6801f4]62 (FillVolume) \
[442495]63 (FragmentationAnalyseFragmentationResults) \
64 (FragmentationClearFragmentationResults) \
[addb51]65 (FragmentationClearFragmentationState) \
[442495]66 (FragmentationFragmentation) \
67 (FragmentationFragmentationAutomation) \
68 (FragmentationMolecularDynamics) \
69 (FragmentationParseFragmentJobs) \
[73a5f7]70 (FragmentationParseFragmentResults) \
71 (FragmentationSaveFragmentResults) \
[442495]72 (FragmentationStoreSaturatedFragment) \
[e5f61ba]73 (FragmentationStructuralOptimization) \
[987145]74 (GeometryDistanceToVector) \
75 (GeometryInputToVector) \
76 (GeometryPlaneToVector) \
77 (GeometryPositionToVector) \
[836972]78 (GeometryRemove) \
[f5ea10]79 (GraphChemicalSpaceEvaluator) \
[22b786]80 (GraphUpdateMolecules) \
[343c5a]81 (GraphCorrectBondDegree) \
[004d5c]82 (GraphCreateAdjacency) \
83 (GraphDepthFirstSearch) \
[560cbf]84 (GraphDestroyAdjacency) \
[22b786]85 (GraphSubgraphDissection) \
[442495]86 (MoleculeBondFile) \
87 (MoleculeChangeName) \
88 (MoleculeChangeBondAngle) \
[004d5c]89 (MoleculeCopy) \
[1a48d2]90 (MoleculeForceAnnealing) \
[442495]91 (MoleculeLinearInterpolationofTrajectories) \
92 (MoleculeLoad) \
[867473]93 (MoleculeRemove) \
[788dce]94 (MoleculeRotateAroundBond) \
[004d5c]95 (MoleculeRotateAroundSelfByAngle) \
[442495]96 (MoleculeRotateToPrincipalAxisSystem) \
97 (MoleculeSaveAdjacency) \
[004d5c]98 (MoleculeSaveBonds) \
[442495]99 (MoleculeSaveSelectedMolecules) \
[d40189]100 (MoleculeSaveEnergies) \
[3a51bd]101 (MoleculeStretchBond) \
[066442]102 (MoleculeTranslate) \
[442495]103 (MoleculeVerletIntegration) \
[50d49d]104 (PotentialFitPartialCharges) \
[78202b]105 (PotentialParseAtomFragments) \
[442495]106 (PotentialParseHomologies) \
[2082637]107 (PotentialParseParticleParameters) \
[f1eabd]108 (PotentialParsePotentials) \
[78202b]109 (PotentialSaveAtomFragments) \
[442495]110 (PotentialSaveHomologies) \
[2082637]111 (PotentialSaveParticleParameters) \
[0ea063]112 (PotentialSavePotentials) \
[004d5c]113 (ParserSaveSelectedAtomsAsExtTypes) \
114 (ParserSetParserParameters) \
115 (ParserSetOutputFormats) \
[442495]116 (ParserSetTremoloAtomdata) \
[004d5c]117 (Undo) \
[442495]118 (SelectionAllAtoms) \
119 (SelectionAllAtomsInsideVolume) \
120 (SelectionAllAtomsOfMolecule) \
[004d5c]121 (SelectionAllMolecules) \
[442495]122 (SelectionAllShapes) \
[4de4f6]123 (SelectionAtomBondNeighbors) \
[442495]124 (SelectionAtomByElement) \
125 (SelectionAtomById) \
[3f6aac]126 (SelectionAtomByName) \
[442495]127 (SelectionAtomByOrder) \
[0ad4781]128 (SelectionAtomByRandom) \
[442495]129 (SelectionClearAllAtoms) \
[004d5c]130 (SelectionClearAllMolecules) \
[442495]131 (SelectionInvertAtoms) \
[ebc499]132 (SelectionInvertMolecules) \
[442495]133 (SelectionMoleculeOfAtom) \
[004d5c]134 (SelectionMoleculeByFormula) \
[442495]135 (SelectionMoleculeById) \
136 (SelectionMoleculeByName) \
137 (SelectionMoleculeByOrder) \
[004d5c]138 (SelectionNotAllAtoms) \
[eff536]139 (SelectionNotAllAtomsInsideVolume) \
[004d5c]140 (SelectionNotAllAtomsOfMolecule) \
[442495]141 (SelectionNotAllMolecules) \
[a27dcb]142 (SelectionNotAllShapes) \
[442495]143 (SelectionNotAtomByElement) \
[3f6aac]144 (SelectionNotAtomById) \
145 (SelectionNotAtomByName) \
[442495]146 (SelectionNotAtomByOrder) \
147 (SelectionNotMoleculeOfAtom) \
148 (SelectionNotMoleculeByFormula) \
149 (SelectionNotMoleculeById) \
150 (SelectionNotMoleculeByName) \
151 (SelectionNotMoleculeByOrder) \
[2c004d]152 (SelectionNotShapeByName) \
[3213f2]153 (SelectionPopAtoms) \
154 (SelectionPushAtoms) \
[a84e8d]155 (SelectionPopMolecules) \
156 (SelectionPushMolecules) \
[442495]157 (SelectionShapeByName) \
[d475a6]158 (ShapeCombineShapes) \
[f20da5]159 (ShapeCreateShape) \
[0b5057]160 (ShapeRemoveShape) \
[a2bbb1]161 (ShapeRotateShape) \
[29ea65]162 (ShapeStretchShape) \
[442495]163 (ShapeTranslateShape) \
164 (TesselationConvexEnvelope) \
165 (TesselationNonConvexEnvelope) \
166 (WorldAddEmptyBoundary) \
167 (WorldBoundInBox) \
168 (WorldCenterInBox) \
169 (WorldCenterOnEdge) \
170 (WorldChangeBox) \
171 (WorldInput) \
172 (WorldOutput) \
173 (WorldOutputAs) \
174 (WorldRepeatBox) \
175 (WorldScaleBox) \
176 (WorldSetBoundaryConditions) \
177 (WorldSetDefaultName) \
[72e40d0]178 (WorldSetWorldTime) \
179 (WorldStepWorldTime)
[004d5c]180
[786d28]181// extend list of actions in case levmar is available
[48d20d]182#ifdef HAVE_LEVMAR
183#define GLOBALLISTOFACTIONS_LEVMAR \
184 BOOST_PP_SEQ_PUSH_BACK( \
[98d166]185 BOOST_PP_SEQ_PUSH_BACK( \
186 GLOBALLISTOFACTIONS_initial, \
187 PotentialFitPotential \
188 ), \
189 PotentialFitCompoundPotential \
[48d20d]190 )
191#else
192#define GLOBALLISTOFACTIONS_LEVMAR \
[786d28]193 GLOBALLISTOFACTIONS_initial
[48d20d]194#endif /* HAVE_LEVMAR */
195
196// define final list
[0d4168]197#ifdef HAVE_PYTHON
198#define GLOBALLISTOFACTIONS_PYTHON \
199 BOOST_PP_SEQ_PUSH_BACK( \
200 GLOBALLISTOFACTIONS_LEVMAR, \
201 CommandLoadSession \
202 )
203#else
204#define GLOBALLISTOFACTIONS_PYTHON \
205 GLOBALLISTOFACTIONS_LEVMAR
206#endif
207
208#define GLOBALLISTOFACTIONS GLOBALLISTOFACTIONS_PYTHON
209
210// define python list
211// skips CommandLoadSession as this causes dangerous infinite loops
212#define GLOBALLISTOFPYTHONACTIONS \
213 GLOBALLISTOFACTIONS_LEVMAR
[48d20d]214
[83e90c]215#endif /* GLOBALLISTOFACTIONS_HPP_ */
216
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