source: src/Actions/MoleculeAction/CreateMicelleAction.cpp@ 42127c

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Last change on this file since 42127c was 42127c, checked in by Frederik Heber <heber@…>, 13 years ago

Extracted definition of MoleculeListClass and put into own header module.

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File size: 7.5 KB
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1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010 University of Bonn. All rights reserved.
5 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
6 */
7
8/*
9 * CreateMicelleAction.cpp
10 *
11 * Created on: Sept 29, 2010
12 * Author: dueck
13 */
14
15// include config.h
16#ifdef HAVE_CONFIG_H
17#include <config.h>
18#endif
19#include "CodePatterns/MemDebug.hpp"
20
21#include "Actions/ActionHistory.hpp"
22#include "Actions/ActionRegistry.hpp"
23#include "Actions/GraphAction/SubgraphDissectionAction.hpp"
24#include "Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp"
25#include "Descriptors/AtomIdDescriptor.hpp"
26#include "Descriptors/MoleculeDescriptor.hpp"
27
28#include "atom.hpp"
29#include "Bond/bond.hpp"
30#include "CodePatterns/Assert.hpp"
31#include "CodePatterns/Log.hpp"
32#include "CodePatterns/Verbose.hpp"
33#include "LinearAlgebra/Line.hpp"
34#include "molecule.hpp"
35#include "MoleculeListClass.hpp"
36#include "World.hpp"
37
38#include <iostream>
39#include <string>
40#include <vector>
41
42#include "Parser/PdbParser.hpp"
43#include "Parser/TremoloParser.hpp"
44#include "Parser/XyzParser.hpp"
45#include "Parser/FormatParserStorage.hpp"
46#include "Shapes/BaseShapes.hpp"
47#include "Shapes/ShapeOps.hpp"
48
49#include "Actions/MoleculeAction/CreateMicelleAction.hpp"
50
51#include "CreateMicelleAction.def"
52#include "Action_impl_pre.hpp"
53
54#include "UIElements/UIFactory.hpp"
55#include "UIElements/Dialog.hpp"
56#include "Actions/ValueStorage.hpp"
57
58using namespace MoleCuilder;
59
60/** =========== define the function ====================== */
61Action::state_ptr MoleculeCreateMicelleAction::performCall()
62{
63 typedef std::vector <atom *> AtomVector;
64 typedef std::vector <molecule *> MoleculeVector;
65
66 getParametersfromValueStorage();
67
68 AtomVector ever = World::getInstance().getAllAtoms();
69
70 // as all parsed atoms go into same molecule
71 // we don't need to create one and add them all to it
72 MoleculeVector all = World::getInstance().getSelectedMolecules();
73
74 // return success when none are selected
75 if (all.empty())
76 return Action::success;
77
78 // check that there is precisely one molecule
79 ASSERT(all.size() == 1,
80 "MoleculeCreateMicelleAction::performCall() - more than one molecule selected, this is not supported.");
81
82 molecule *stick = *(all.begin());
83
84
85 // create undo state for original molecule
86 std::vector<Vector> stickPositions;
87 for (molecule::const_iterator iter = stick->begin(); iter != stick->end(); ++iter)
88 stickPositions.push_back((*iter)->getPosition());
89
90 // determine principal axis system and rotate such that greatest extension is along z axis
91 if(stick->size() > 1) { // only rotate if more than one molecule present
92 Vector den(0.0,0.0,1.0);
93
94 MoleculeRotateToPrincipalAxisSystem(den);
95 }
96
97 // center molecule
98 stick->CenterOrigin();
99
100 /// Align molecule with its PAS multiple times with the some surface
101
102 // get points on surface
103
104 //double radius= 1.5*sqrt(pow(1.55, 2)*params.N);
105
106 Shape s = resize(Sphere(), params.radius);
107 std::vector<Vector> pt = s.getHomogeneousPointsOnSurface(params.N);
108
109 // mirror along x-y plane
110
111 // additionally invert molecule if desired
112 if (params.DoRotate) {
113 for (molecule::iterator it2=stick->begin();it2 !=stick->end();++it2)
114 {
115 Vector pos= (**it2).getPosition();
116 pos[2]= - pos[2];// -Min[2]
117 (**it2).setPosition(pos);
118 }
119 }
120
121 // shift molecule by its extension along z axis
122
123 for (molecule::iterator it2=stick->begin();it2 !=stick->end();++it2)
124 {
125 Vector pos= (**it2).getPosition();
126 pos[2]=pos[2]+params.radius;
127 (**it2).setPosition(pos);
128 }
129
130 // copy molecule N times and rotate it to point radially away from surface
131
132 //double MYEPSILON=1e-10;
133
134 // gather created molecules for undo state
135 std::vector<molecule *> CreatedMolecules;
136
137 // TODO: remove this when we do not need MoleculeListClass anymore
138 MoleculeListClass *&molecules = World::getInstance().getMolecules();
139
140 size_t ka = 0;
141 for (; ka<pt.size()-1; ka++)
142 {
143 LOG(1, "STATUS: Creating " << ka+1 << " copy of tenside molecule 'stick' with " << stick->getAtomCount() << " atoms, ");
144 molecule *Tensid=stick->CopyMolecule();
145 molecules->insert(Tensid);
146 CreatedMolecules.push_back(Tensid);
147
148 Vector ZAxis(Vector(0.0,0.0,1.0));
149 Vector Axis(pt[ka]);
150 const double alpha = ZAxis.Angle(Axis);
151 Axis.VectorProduct(ZAxis);
152 Line RotationAxis(Vector(0.0,0.0,1.0), Axis); // pt is the current Vector of point on surface
153 LOG(2, "INFO: Rotating along axis " << RotationAxis << " by angle " << alpha << ".");
154
155 for (molecule::iterator it2=Tensid->begin();it2 !=Tensid->end();++it2)
156 {
157 (*it2)->setPosition(RotationAxis.rotateVector((*it2)->getPosition(),alpha));
158 *(*it2)+=params.center;
159 }
160
161 Tensid=NULL;
162 }
163
164 // shift molecule at given position on surface
165 {
166 LOG(1, "STATUS: Shifting " << ka+1 << " copy of tenside molecule 'stick' with " << stick->getAtomCount() << " atoms, ");
167 molecule *Tensid=stick;
168 // this molecule was present before, hence do not remove it!
169 //CreatedMolecules.push_back(Tensid);
170
171 Vector ZAxis(Vector(0.0,0.0,1.0));
172 Vector Axis(pt[pt.size()-1]);
173 const double alpha = ZAxis.Angle(Axis);
174 Axis.VectorProduct(ZAxis);
175 Line RotationAxis(Vector(0.0,0.0,1.0), Axis); // pt is the current Vector of point on surface
176 LOG(2, "INFO: Rotating along axis " << RotationAxis << " by angle " << alpha << ".");
177
178 for (molecule::iterator it2=Tensid->begin();it2 !=Tensid->end();++it2)
179 {
180 (*it2)->setPosition(RotationAxis.rotateVector((*it2)->getPosition(),alpha));
181 *(*it2)+=params.center;
182 }
183 }
184
185
186 return Action::state_ptr(new MoleculeCreateMicelleState(CreatedMolecules, stick, stickPositions, params));
187}
188
189Action::state_ptr MoleculeCreateMicelleAction::performUndo(Action::state_ptr _state)
190{
191 MoleculeCreateMicelleState *state = assert_cast<MoleculeCreateMicelleState*>(_state.get());
192
193 // removing all created molecules
194 MoleculeListClass *&molecules = World::getInstance().getMolecules();
195 LOG(0, "STATUS: Removing " << state->CreatedMolecules.size() << " molecules again.");
196 for(std::vector<molecule *>::const_iterator iter = state->CreatedMolecules.begin();
197 iter != state->CreatedMolecules.end();
198 ++iter) {
199 LOG(2, "INFO: Removing " << (*iter)->getName());
200 for(molecule::iterator AtomRunner = (*iter)->begin();
201 !(*iter)->empty();
202 AtomRunner = (*iter)->begin()) {
203 World::getInstance().destroyAtom(*AtomRunner);
204 }
205 //LOG(3, "INFO: molecules contains still " << molecules->ListOfMolecules.size() << " molecules.");
206 molecules->erase(*iter);
207 World::getInstance().destroyMolecule(*iter);
208 }
209
210 // undo changes to original molecule
211 ASSERT(state->stickPositions.size() == state->stick->size(),
212 "MoleculeCreateMicelleAction::performUndo() - number of stored positions ("
213 +toString(state->stickPositions.size())+") and number of atoms ("
214 +toString(state->stick->size())+") do not match.");
215 std::vector<Vector>::const_iterator PosIter = state->stickPositions.begin();
216 molecule::iterator iter = state->stick->begin();
217 for (; iter != state->stick->end(); ++iter, ++PosIter)
218 (*iter)->setPosition(*PosIter);
219
220 return Action::state_ptr(_state);
221}
222
223Action::state_ptr MoleculeCreateMicelleAction::performRedo(Action::state_ptr _state)
224{
225 LOG(0, "STATUS: CreateMicelleAction::performRedo() is nit implemented yet.");
226 return Action::failure;
227}
228
229
230bool MoleculeCreateMicelleAction::canUndo()
231{
232 return true;
233}
234
235bool MoleculeCreateMicelleAction::shouldUndo()
236{
237 return true;
238}
239
240/** =========== end of function ====================== */
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