source: src/Actions/MoleculeAction/CreateMicelleAction.cpp@ ce7fdc

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Last change on this file since ce7fdc was ce7fdc, checked in by Frederik Heber <heber@…>, 13 years ago

HUGE: All Action-related codes resides now in namespace MoleCuilder.

  • removed all namespace std in Actions..., replaced by MoleCuilder.
  • Property mode set to 100644
File size: 7.5 KB
Line 
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 "World.hpp"
36
37#include <iostream>
38#include <string>
39#include <vector>
40
41#include "Parser/PdbParser.hpp"
42#include "Parser/TremoloParser.hpp"
43#include "Parser/XyzParser.hpp"
44#include "Parser/FormatParserStorage.hpp"
45#include "Shapes/BaseShapes.hpp"
46#include "Shapes/ShapeOps.hpp"
47
48#include "Actions/MoleculeAction/CreateMicelleAction.hpp"
49
50#include "CreateMicelleAction.def"
51#include "Action_impl_pre.hpp"
52
53#include "UIElements/UIFactory.hpp"
54#include "UIElements/Dialog.hpp"
55#include "Actions/ValueStorage.hpp"
56
57using namespace MoleCuilder;
58
59/** =========== define the function ====================== */
60Action::state_ptr MoleculeCreateMicelleAction::performCall()
61{
62 typedef std::vector <atom *> AtomVector;
63 typedef std::vector <molecule *> MoleculeVector;
64
65 getParametersfromValueStorage();
66
67 AtomVector ever = World::getInstance().getAllAtoms();
68
69 // as all parsed atoms go into same molecule
70 // we don't need to create one and add them all to it
71 MoleculeVector all = World::getInstance().getSelectedMolecules();
72
73 // return success when none are selected
74 if (all.empty())
75 return Action::success;
76
77 // check that there is precisely one molecule
78 ASSERT(all.size() == 1,
79 "MoleculeCreateMicelleAction::performCall() - more than one molecule selected, this is not supported.");
80
81 molecule *stick = *(all.begin());
82
83
84 // create undo state for original molecule
85 std::vector<Vector> stickPositions;
86 for (molecule::const_iterator iter = stick->begin(); iter != stick->end(); ++iter)
87 stickPositions.push_back((*iter)->getPosition());
88
89 // determine principal axis system and rotate such that greatest extension is along z axis
90 if(stick->size() > 1) { // only rotate if more than one molecule present
91 Vector den(0.0,0.0,1.0);
92
93 MoleculeRotateToPrincipalAxisSystem(den);
94 }
95
96 // center molecule
97 stick->CenterOrigin();
98
99 /// Align molecule with its PAS multiple times with the some surface
100
101 // get points on surface
102
103 //double radius= 1.5*sqrt(pow(1.55, 2)*params.N);
104
105 Shape s = resize(Sphere(), params.radius);
106 std::vector<Vector> pt = s.getHomogeneousPointsOnSurface(params.N);
107
108 // mirror along x-y plane
109
110 // additionally invert molecule if desired
111 if (params.DoRotate) {
112 for (molecule::iterator it2=stick->begin();it2 !=stick->end();++it2)
113 {
114 Vector pos= (**it2).getPosition();
115 pos[2]= - pos[2];// -Min[2]
116 (**it2).setPosition(pos);
117 }
118 }
119
120 // shift molecule by its extension along z axis
121
122 for (molecule::iterator it2=stick->begin();it2 !=stick->end();++it2)
123 {
124 Vector pos= (**it2).getPosition();
125 pos[2]=pos[2]+params.radius;
126 (**it2).setPosition(pos);
127 }
128
129 // copy molecule N times and rotate it to point radially away from surface
130
131 //double MYEPSILON=1e-10;
132
133 // gather created molecules for undo state
134 std::vector<molecule *> CreatedMolecules;
135
136 // TODO: remove this when we do not need MoleculeListClass anymore
137 MoleculeListClass *&molecules = World::getInstance().getMolecules();
138
139 size_t ka = 0;
140 for (; ka<pt.size()-1; ka++)
141 {
142 LOG(1, "STATUS: Creating " << ka+1 << " copy of tenside molecule 'stick' with " << stick->getAtomCount() << " atoms, ");
143 molecule *Tensid=stick->CopyMolecule();
144 molecules->insert(Tensid);
145 CreatedMolecules.push_back(Tensid);
146
147 Vector ZAxis(Vector(0.0,0.0,1.0));
148 Vector Axis(pt[ka]);
149 const double alpha = ZAxis.Angle(Axis);
150 Axis.VectorProduct(ZAxis);
151 Line RotationAxis(Vector(0.0,0.0,1.0), Axis); // pt is the current Vector of point on surface
152 LOG(2, "INFO: Rotating along axis " << RotationAxis << " by angle " << alpha << ".");
153
154 for (molecule::iterator it2=Tensid->begin();it2 !=Tensid->end();++it2)
155 {
156 (*it2)->setPosition(RotationAxis.rotateVector((*it2)->getPosition(),alpha));
157 *(*it2)+=params.center;
158 }
159
160 Tensid=NULL;
161 }
162
163 // shift molecule at given position on surface
164 {
165 LOG(1, "STATUS: Shifting " << ka+1 << " copy of tenside molecule 'stick' with " << stick->getAtomCount() << " atoms, ");
166 molecule *Tensid=stick;
167 // this molecule was present before, hence do not remove it!
168 //CreatedMolecules.push_back(Tensid);
169
170 Vector ZAxis(Vector(0.0,0.0,1.0));
171 Vector Axis(pt[pt.size()-1]);
172 const double alpha = ZAxis.Angle(Axis);
173 Axis.VectorProduct(ZAxis);
174 Line RotationAxis(Vector(0.0,0.0,1.0), Axis); // pt is the current Vector of point on surface
175 LOG(2, "INFO: Rotating along axis " << RotationAxis << " by angle " << alpha << ".");
176
177 for (molecule::iterator it2=Tensid->begin();it2 !=Tensid->end();++it2)
178 {
179 (*it2)->setPosition(RotationAxis.rotateVector((*it2)->getPosition(),alpha));
180 *(*it2)+=params.center;
181 }
182 }
183
184
185 return Action::state_ptr(new MoleculeCreateMicelleState(CreatedMolecules, stick, stickPositions, params));
186}
187
188Action::state_ptr MoleculeCreateMicelleAction::performUndo(Action::state_ptr _state)
189{
190 MoleculeCreateMicelleState *state = assert_cast<MoleculeCreateMicelleState*>(_state.get());
191
192 // removing all created molecules
193 MoleculeListClass *&molecules = World::getInstance().getMolecules();
194 LOG(0, "STATUS: Removing " << state->CreatedMolecules.size() << " molecules again.");
195 for(std::vector<molecule *>::const_iterator iter = state->CreatedMolecules.begin();
196 iter != state->CreatedMolecules.end();
197 ++iter) {
198 LOG(2, "INFO: Removing " << (*iter)->getName());
199 for(molecule::iterator AtomRunner = (*iter)->begin();
200 !(*iter)->empty();
201 AtomRunner = (*iter)->begin()) {
202 World::getInstance().destroyAtom(*AtomRunner);
203 }
204 //LOG(3, "INFO: molecules contains still " << molecules->ListOfMolecules.size() << " molecules.");
205 molecules->erase(*iter);
206 World::getInstance().destroyMolecule(*iter);
207 }
208
209 // undo changes to original molecule
210 ASSERT(state->stickPositions.size() == state->stick->size(),
211 "MoleculeCreateMicelleAction::performUndo() - number of stored positions ("
212 +toString(state->stickPositions.size())+") and number of atoms ("
213 +toString(state->stick->size())+") do not match.");
214 std::vector<Vector>::const_iterator PosIter = state->stickPositions.begin();
215 molecule::iterator iter = state->stick->begin();
216 for (; iter != state->stick->end(); ++iter, ++PosIter)
217 (*iter)->setPosition(*PosIter);
218
219 return Action::state_ptr(_state);
220}
221
222Action::state_ptr MoleculeCreateMicelleAction::performRedo(Action::state_ptr _state)
223{
224 LOG(0, "STATUS: CreateMicelleAction::performRedo() is nit implemented yet.");
225 return Action::failure;
226}
227
228
229bool MoleculeCreateMicelleAction::canUndo()
230{
231 return true;
232}
233
234bool MoleculeCreateMicelleAction::shouldUndo()
235{
236 return true;
237}
238
239/** =========== end of function ====================== */
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