source: src/Actions/UndoRedoHelpers.cpp@ 596cfa

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Last change on this file since 596cfa was 596cfa, checked in by Frederik Heber <heber@…>, 10 years ago

Extended UndoRedoHelpers by AddingMultipleMoleculesfromAtomicInfo.

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1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2012 University of Bonn. All rights reserved.
5 * Copyright (C) 2013-2014 Frederik Heber. All rights reserved.
6 *
7 *
8 * This file is part of MoleCuilder.
9 *
10 * MoleCuilder is free software: you can redistribute it and/or modify
11 * it under the terms of the GNU General Public License as published by
12 * the Free Software Foundation, either version 2 of the License, or
13 * (at your option) any later version.
14 *
15 * MoleCuilder is distributed in the hope that it will be useful,
16 * but WITHOUT ANY WARRANTY; without even the implied warranty of
17 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
18 * GNU General Public License for more details.
19 *
20 * You should have received a copy of the GNU General Public License
21 * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
22 */
23
24/*
25 * UndoRedoHelpers.cpp
26 *
27 * Created on: Apr 5, 2012
28 * Author: heber
29 */
30
31
32// include config.h
33#ifdef HAVE_CONFIG_H
34#include <config.h>
35#endif
36
37#include "CodePatterns/MemDebug.hpp"
38
39#include "UndoRedoHelpers.hpp"
40
41#include <boost/bind.hpp>
42#include <boost/foreach.hpp>
43#include <boost/function.hpp>
44
45#include "Atom/atom.hpp"
46#include "molecule.hpp"
47#include "Descriptors/AtomIdDescriptor.hpp"
48#include "Descriptors/MoleculeIdDescriptor.hpp"
49#include "CodePatterns/Assert.hpp"
50#include "CodePatterns/Log.hpp"
51#include "World.hpp"
52#include "WorldTime.hpp"
53
54bool MoleCuilder::AddAtomsFromAtomicInfo(const std::vector<AtomicInfo> &atoms)
55{
56 size_t i=0;
57 for (; i<atoms.size(); ++i) {
58 // re-create the atom
59 LOG(3, "DEBUG: Re-adding atom " << atoms[i].getId() << ".");
60 atom *Walker = World::getInstance().createAtom();
61 if (!atoms[i].setAtom(*Walker)) {
62 ELOG(1, "Failed to set id.");
63 World::getInstance().destroyAtom(Walker);
64 break;
65 }
66 }
67 if (i<atoms.size()) {
68 // remove all previous ones, too
69 for (size_t j=0;j<i;++j)
70 World::getInstance().destroyAtom(atoms[j].getId());
71 // and announce the failure
72 return false;
73 }
74 return true;
75}
76
77bool MoleCuilder::AddMoleculesFromAtomicInfo(std::map< moleculeId_t, std::vector<AtomicInfo> > &mol_atoms)
78{
79 bool status = true;
80 for (std::map< moleculeId_t, std::vector<AtomicInfo> >::const_iterator iter = mol_atoms.begin();
81 iter != mol_atoms.end(); ++iter) {
82 // re-create the atom
83 LOG(3, "DEBUG: Re-adding molecule " << iter->first << ".");
84 molecule *mol_Walker = World::getInstance().createMolecule();
85
86 // reset the mol id
87 bool status = true;
88 if (mol_Walker->getId() != iter->first)
89 status &= mol_Walker->changeId(iter->first);
90
91 // add all its atoms
92 status &= AddAtomsFromAtomicInfo(iter->second);
93 }
94 if (!status) {
95 // remove all molecules again
96 for (std::map< moleculeId_t, std::vector<AtomicInfo> >::const_iterator iter = mol_atoms.begin();
97 iter != mol_atoms.end(); ++iter) {
98 molecule * mol = World::getInstance().getMolecule(MoleculeById(iter->first));
99 if (mol != NULL)
100 removeAtomsinMolecule(mol);
101 }
102 // and announce the failure
103 return false;
104 }
105 return true;
106}
107
108void MoleCuilder::RemoveAtomsFromAtomicInfo(std::vector<AtomicInfo> &atoms)
109{
110 BOOST_FOREACH(const AtomicInfo &_atom, atoms) {
111 World::getInstance().destroyAtom(_atom.getId());
112 }
113}
114
115void MoleCuilder::StoreBondInformationFromAtoms(
116 const std::vector<const atom*> &atoms,
117 std::vector< BondInfo > &bonds)
118{
119 ASSERT( bonds.empty(),
120 "StoreBondInformationFromAtoms() - give bonds vector is not empty.");
121 bonds.reserve(atoms.size()*4);
122 for (std::vector<const atom*>::const_iterator atomiter = atoms.begin();
123 atomiter != atoms.end(); ++atomiter) {
124 const BondList & _atom_bonds = (*atomiter)->getListOfBonds();
125 for(BondList::const_iterator iter = _atom_bonds.begin(); iter != _atom_bonds.end(); ++iter)
126 bonds.push_back( BondInfo(*iter) );
127 }
128}
129
130bool MoleCuilder::AddBondsFromBondInfo(const std::vector< BondInfo > &bonds)
131{
132 bool status = true;
133 for(std::vector< BondInfo >::const_iterator iter = bonds.begin();
134 iter != bonds.end(); ++iter)
135 if (!(*iter).RecreateBond())
136 status = false;
137 return status;
138}
139
140void MoleCuilder::SetAtomsFromAtomicInfo(const std::vector<AtomicInfo> &_movedatoms)
141{
142 BOOST_FOREACH( const AtomicInfo &_atominfo, _movedatoms) {
143 const atomId_t id = _atominfo.getId();
144 atom * const _atom = World::getInstance().getAtom(AtomById(id));
145 ASSERT( _atom != NULL,
146 "MoleCuilder::SetAtomsFromAtomicInfo() - cannot find atom with id "
147 +toString(id)+" in the world.");
148 _atominfo.setAtom( *_atom );
149 }
150}
151
152void MoleCuilder::SelectAtomsFromAtomicInfo(const std::vector<AtomicInfo> &_movedatoms)
153{
154 BOOST_FOREACH( const AtomicInfo &_atominfo, _movedatoms) {
155 const atomId_t id = _atominfo.getId();
156 World::getInstance().selectAtom(id);
157 }
158}
159
160void MoleCuilder::ResetAtomPosition(const std::vector<AtomicInfo> &movedatoms, const std::vector<Vector> &MovedToVector)
161{
162 boost::function<void(atom *, const Vector&)> setter =
163 boost::bind(&atom::setPosition, _1, _2);
164 ResetByFunction(movedatoms, MovedToVector, setter);
165}
166
167void MoleCuilder::ResetAtomVelocity(const std::vector<AtomicInfo> &movedatoms, const std::vector<Vector> &VelocityVector)
168{
169 boost::function<void(atom *, const Vector&)> setter =
170 boost::bind(&atom::setAtomicVelocity, _1, _2);
171 ResetByFunction(movedatoms, VelocityVector, setter);
172}
173
174void MoleCuilder::ResetAtomForce(const std::vector<AtomicInfo> &movedatoms, const std::vector<Vector> &ForceVector)
175{
176 boost::function<void(atom *, const Vector&)> setter =
177 boost::bind(&atom::setAtomicForce, _1, _2);
178 ResetByFunction(movedatoms, ForceVector, setter);
179}
180
181void MoleCuilder::ResetByFunction(
182 const std::vector<AtomicInfo> &movedatoms,
183 const std::vector<Vector> &MovedToVector,
184 boost::function<void(atom *, const Vector&)> &setter)
185{
186 std::vector<Vector>::const_iterator positer = MovedToVector.begin();
187 ASSERT(movedatoms.size() == MovedToVector.size(),
188 "MoleCuilder::ResetAtomPosition() - the number of atoms "
189 +toString(movedatoms.size())+" and the number of positions "
190 +toString(MovedToVector.size())+" is not the same.");
191 BOOST_FOREACH( const AtomicInfo &_atominfo, movedatoms) {
192 const atomId_t id = _atominfo.getId();
193 atom * const _atom = World::getInstance().getAtom(AtomById(id));
194 ASSERT( _atom != NULL,
195 "FillSphericalSurfaceAction::performRedo() - cannot find atom with id "
196 +toString(id)+" in the world.");
197 setter(_atom, *positer );
198 ++positer;
199 }
200}
201
202void MoleCuilder::RemoveMoleculesWithAtomsByIds(const std::vector<moleculeId_t> &ids)
203{
204 for (std::vector<moleculeId_t>::const_iterator iter = ids.begin();
205 iter != ids.end(); ++iter) {
206 molecule * mol = World::getInstance().getMolecule(MoleculeById(*iter));
207 if (mol != NULL) {
208 removeAtomsinMolecule(mol);
209 // molecules are automatically removed when empty
210 }
211 }
212}
213
214void MoleCuilder::removeLastStep(const std::vector<atomId_t> &_atoms, const unsigned int _step)
215{
216 for (size_t i=0; i<_atoms.size(); ++i) {
217 atom * const _atom = World::getInstance().getAtom(AtomById(_atoms[i]));
218 _atom->removeStep(_step);
219 }
220}
221
222void MoleCuilder::addNewStep(const std::vector<AtomicInfo> &_movedatoms, const unsigned int _step)
223{
224 for(size_t i=0; i< _movedatoms.size(); ++i) {
225 atom * const _atom = World::getInstance().getAtom(AtomById(_movedatoms[i].getId()));
226 _atom->UpdateStep(_step);
227 }
228}
229
230void MoleCuilder::addNewStep(const std::vector<atomId_t> &_ids, const unsigned int _step)
231{
232 for(size_t i=0; i< _ids.size(); ++i) {
233 atom * const _atom = World::getInstance().getAtom(AtomById(_ids[i]));
234 _atom->UpdateStep(_step);
235 }
236}
237
238std::vector<atomId_t> MoleCuilder::getIdsFromAtomicInfo(const std::vector<AtomicInfo> &movedatoms)
239{
240 std::vector<atomId_t> ids(movedatoms.size(), (size_t)-1);
241 std::transform(
242 movedatoms.begin(), movedatoms.end(),
243 ids.begin(),
244 boost::bind(&AtomicInfo::getId, _1));
245 return ids;
246}
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