1 | /*
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2 | * Project: MoleCuilder
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3 | * Description: creates and alters molecular systems
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4 | * Copyright (C) 2010-2012 University of Bonn. All rights reserved.
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5 | * Copyright (C) 2013 Frederik Heber. All rights reserved.
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6 | *
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7 | *
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8 | * This file is part of MoleCuilder.
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9 | *
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10 | * MoleCuilder is free software: you can redistribute it and/or modify
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11 | * it under the terms of the GNU General Public License as published by
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12 | * the Free Software Foundation, either version 2 of the License, or
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13 | * (at your option) any later version.
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14 | *
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15 | * MoleCuilder is distributed in the hope that it will be useful,
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16 | * but WITHOUT ANY WARRANTY; without even the implied warranty of
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17 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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18 | * GNU General Public License for more details.
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19 | *
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20 | * You should have received a copy of the GNU General Public License
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21 | * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
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22 | */
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23 |
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24 | /*
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25 | * GLMoleculeObject_molecule.cpp
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26 | *
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27 | * Created on: Mar 30, 2012
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28 | * Author: ankele
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29 | */
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30 |
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31 |
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32 | // include config.h
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33 | #ifdef HAVE_CONFIG_H
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34 | #include <config.h>
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35 | #endif
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36 |
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37 | #include "GLMoleculeObject_molecule.hpp"
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38 |
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39 | #include <Qt3D/qglscenenode.h>
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40 | #include <Qt3D/qglbuilder.h>
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41 |
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42 | #include "UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.hpp"
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43 |
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44 | #include "CodePatterns/MemDebug.hpp"
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45 |
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46 | #include <boost/assign.hpp>
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47 |
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48 | #include "CodePatterns/Assert.hpp"
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49 | #include "CodePatterns/IteratorAdaptors.hpp"
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50 | #include "CodePatterns/Log.hpp"
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51 |
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52 | #include "LinearAlgebra/Vector.hpp"
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53 | #include "LinkedCell/PointCloudAdaptor.hpp"
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54 | #include "LinkedCell/linkedcell.hpp"
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55 | #include "Tesselation/tesselation.hpp"
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56 | #include "Tesselation/BoundaryLineSet.hpp"
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57 | #include "Tesselation/BoundaryTriangleSet.hpp"
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58 | #include "Tesselation/CandidateForTesselation.hpp"
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59 | #include "UIElements/Qt4/InstanceBoard/QtObservedInstanceBoard.hpp"
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60 | #include "Atom/TesselPoint.hpp"
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61 | #include "World.hpp"
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62 |
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63 | using namespace boost::assign;
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64 |
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65 | static Observable::channels_t getAllAtomicChangesChannels()
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66 | {
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67 | Observable::channels_t channels;
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68 | channels += molecule::AtomInserted, molecule::AtomRemoved, molecule::AtomMoved;
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69 | return channels;
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70 | }
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71 |
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72 | const Observable::channels_t GLMoleculeObject_molecule::HullChannels(getAllAtomicChangesChannels());
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73 |
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74 | static QGLSceneNode *createMoleculeMesh(const QGeometryData &_geo)
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75 | {
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76 | // Build a mesh from the geometry.
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77 | QGLBuilder builder;
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78 | builder.addTriangles(_geo);
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79 | QGLSceneNode *mesh = builder.finalizedSceneNode();
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80 | return mesh;
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81 | }
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82 |
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83 | GLMoleculeObject_molecule::GLMoleculeObject_molecule(
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84 | QObject *parent,
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85 | QtObservedInstanceBoard &_board,
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86 | QtObservedMolecule::ptr _ObservedMolecule) :
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87 | GLMoleculeObject((QGLSceneNode *)NULL, parent),
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88 | owner(NULL),
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89 | molref(QtObservedMolecule::getMolecule(_ObservedMolecule->getMolIndex())),
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90 | /* We must not use boost::cref(this) as "this" has not been properly constructed and seemingly
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91 | * boost::cref tries to do some magic to grasp the inheritance hierarchy which fails because
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92 | * the class has not been fully constructed yet. "This" itself seems to be working fine.
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93 | */
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94 | TesselationHullUpdater(
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95 | boost::bind(&GLMoleculeObject_molecule::updateTesselationHull, this)
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96 | ),
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97 | TesselationHull(
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98 | molref,
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99 | TesselationHullUpdater,
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100 | "MoleculeTesselationHull_"+toString(_ObservedMolecule->getMolIndex()),
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101 | HullChannels),
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102 | hoverAtomId(-1),
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103 | board(_board),
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104 | ObservedMolecule(_ObservedMolecule)
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105 | {
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106 | init(ObservedMolecule->getMolIndex());
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107 | }
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108 |
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109 | GLMoleculeObject_molecule::GLMoleculeObject_molecule(
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110 | QGLSceneNode *mesh[],
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111 | QObject *parent,
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112 | QtObservedInstanceBoard &_board,
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113 | QtObservedMolecule::ptr _ObservedMolecule) :
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114 | GLMoleculeObject(mesh, parent),
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115 | owner(NULL),
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116 | molref(QtObservedMolecule::getMolecule(_ObservedMolecule->getMolIndex())),
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117 | /* We must not use boost::cref(this) as "this" has not been properly constructed and seemingly
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118 | * boost::cref tries to do some magic to grasp the inheritance hierarchy which fails because
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119 | * the class has not been fully constructed yet. "This" itself seems to be working fine.
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120 | */
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121 | TesselationHullUpdater(
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122 | boost::bind(&GLMoleculeObject_molecule::updateTesselationHull, this)
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123 | ),
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124 | TesselationHull(
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125 | molref,
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126 | TesselationHullUpdater,
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127 | "MoleculeTesselationHull_"+toString(_ObservedMolecule->getMolIndex()),
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128 | HullChannels),
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129 | hoverAtomId(-1),
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130 | board(_board),
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131 | ObservedMolecule(_ObservedMolecule)
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132 | {
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133 | init(ObservedMolecule->getMolIndex());
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134 | }
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135 |
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136 | void GLMoleculeObject_molecule::init(const moleculeId_t _molid)
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137 | {
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138 | setObjectId(_molid);
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139 | setMaterial(getMaterial(1));
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140 |
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141 | m_selected = const_cast<const World &>(World::getInstance()).isMoleculeSelected(_molid);
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142 |
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143 | // initially, atoms and bonds should be visible
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144 | m_visible = false;
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145 |
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146 | connect (this, SIGNAL(hoverChanged(GLMoleculeObject *)), this, SLOT(hoverChangedSignalled(GLMoleculeObject *)));
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147 | connect (this, SIGNAL(hoverChanged(GLMoleculeObject *)), this, SIGNAL(changed()));
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148 | connect (ObservedMolecule.get(), SIGNAL(tesselationhullChanged()), this, SLOT(resetTesselationHull()));
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149 | connect (ObservedMolecule.get(), SIGNAL(boundingboxChanged()), this, SLOT(resetBoundingBox()));
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150 | connect (ObservedMolecule.get(), SIGNAL(indexChanged()), this, SLOT(resetIndex()));
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151 | connect (ObservedMolecule.get(), SIGNAL(atomInserted(const atomId_t)), this, SLOT(atomInserted(const atomId_t)));
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152 | connect (ObservedMolecule.get(), SIGNAL(atomRemoved(const atomId_t)), this, SLOT(atomRemoved(const atomId_t)));
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153 |
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154 | connect( this, SIGNAL(clicked()), this, SLOT(wasClicked()));
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155 | }
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156 |
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157 | GLMoleculeObject_molecule::~GLMoleculeObject_molecule()
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158 | {}
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159 |
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160 | void GLMoleculeObject_molecule::addAtomBonds(
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161 | const bond::ptr &_bond,
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162 | const GLMoleculeObject_bond::SideOfBond _side
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163 | )
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164 | {
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165 | bool bond_present = false;
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166 | const BondIds ids = getBondIds(_bond, _side);
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167 | // check whether bond is not present already
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168 | bond_present = BondsinSceneMap.count(ids);
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169 | if (!bond_present)
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170 | bondInserted(ids.first, ids.second, _side);
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171 | else {
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172 | BondsinSceneMap[ids]->resetPosition();
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173 | BondsinSceneMap[ids]->resetWidth();
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174 | }
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175 | }
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176 |
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177 | QGeometryData GLMoleculeObject_molecule::updateTesselationHull() const
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178 | {
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179 | QGeometryData geo;
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180 |
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181 | const molecule * const molref =
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182 | QtObservedMolecule::getMolecule(ObservedMolecule->getMolIndex());
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183 | if (molref == NULL) {
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184 | ELOG(1, "Could not createMoleculeMesh, molecule with id "
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185 | << ObservedMolecule->getMolIndex() << " already gone.");
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186 | return geo;
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187 | }
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188 | double minradius = 2.; // TODO: set to maximum bond length value
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189 | LOG(3, "DEBUG: Molecule fits into sphere of radius " << minradius);
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190 | // check minimum bond radius in molecule
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191 | double minlength = std::numeric_limits<double>::max();
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192 | for (molecule::const_iterator iter = molref->begin();
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193 | iter != molref->end(); ++iter) {
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194 | const BondList &ListOfBonds = (*iter)->getListOfBonds();
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195 | for (BondList::const_iterator bonditer = ListOfBonds.begin();
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196 | bonditer != ListOfBonds.end(); ++bonditer) {
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197 | const double bond_distance = (*bonditer)->GetDistance();
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198 | minlength = std::min(bond_distance, minlength);
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199 | }
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200 | }
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201 | minradius = std::max( std::max(minradius, minlength), 1.);
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202 |
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203 | // we need at least three points for tesselation
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204 | if (getPresentAtoms().size() >= 3) {
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205 | // Tesselate the points.
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206 | Tesselation T;
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207 | PointCloudAdaptor<molecule> cloud(
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208 | const_cast<molecule *>(molref),
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209 | ObservedMolecule->getMolName());
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210 | T(cloud, minradius);
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211 |
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212 | // Fill the points into a Qt geometry.
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213 | LinkedCell_deprecated LinkedList(cloud, minradius);
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214 | std::map<int, int> indices;
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215 | std::map<int, Vector> normals;
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216 | int index = 0;
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217 | for (PointMap::const_iterator piter = T.PointsOnBoundary.begin();
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218 | piter != T.PointsOnBoundary.end(); ++piter) {
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219 | const Vector &point = piter->second->getPosition();
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220 | // add data to the primitive
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221 | geo.appendVertex(QVector3D(point[0], point[1], point[2]));
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222 | Vector normalvector;
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223 | for (LineMap::const_iterator lineiter = piter->second->lines.begin();
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224 | lineiter != piter->second->lines.end(); ++lineiter)
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225 | for (TriangleMap::const_iterator triangleiter = lineiter->second->triangles.begin();
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226 | triangleiter != lineiter->second->triangles.end(); ++triangleiter)
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227 | normalvector +=
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228 | triangleiter->second->NormalVector;
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229 | normalvector.Normalize();
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230 | geo.appendNormal(QVector3D(normalvector[0], normalvector[1], normalvector[2]));
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231 | geo.appendColor(QColor(1, 1, 1, 1));
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232 | geo.appendTexCoord(QVector2D(0, 0));
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233 | indices.insert( std::make_pair( piter->second->getNr(), index++));
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234 | }
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235 |
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236 | // Fill the tesselated triangles into the geometry.
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237 | for (TriangleMap::const_iterator runner = T.TrianglesOnBoundary.begin();
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238 | runner != T.TrianglesOnBoundary.end(); runner++) {
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239 | int v[3];
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240 | for (size_t i=0; i<3; ++i)
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241 | v[i] = runner->second->endpoints[i]->getNr();
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242 |
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243 | // Sort the vertices so the triangle is clockwise (relative to the normal vector).
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244 | Vector cross = T.PointsOnBoundary[v[1]]->getPosition() - T.PointsOnBoundary[v[0]]->getPosition();
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245 | cross.VectorProduct(T.PointsOnBoundary[v[2]]->getPosition() - T.PointsOnBoundary[v[0]]->getPosition());
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246 | if (cross.ScalarProduct(runner->second->NormalVector) > 0)
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247 | geo.appendIndices(indices[v[0]], indices[v[1]], indices[v[2]]);
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248 | else
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249 | geo.appendIndices(indices[v[0]], indices[v[2]], indices[v[1]]);
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250 | }
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251 | }
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252 |
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253 | return geo;
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254 | }
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255 |
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256 | void GLMoleculeObject_molecule::resetTesselationHull()
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257 | {
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258 | // only when Observable still lives so far, we may check on Cacheable::isValid
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259 | if ((owner != NULL) && (!TesselationHull.isValid()))
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260 | updateMesh(createMoleculeMesh(*TesselationHull));
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261 | }
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262 |
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263 | void GLMoleculeObject_molecule::resetBoundingBox()
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264 | {
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265 | molecule::BoundingBoxInfo info = ObservedMolecule->getBoundingBox();
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266 | setPosition(QVector3D(info.position[0], info.position[1], info.position[2]));
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267 | setScale(info.radius + 0.3); // getBoundingSphere() only sees atoms as points, so make the box a bit bigger
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268 | }
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269 |
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270 | void GLMoleculeObject_molecule::resetIndex()
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271 | {
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272 | const atomId_t newId = ObservedMolecule->getMolIndex();
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273 | const size_t oldId = objectId();
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274 | ASSERT( newId != oldId,
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275 | "GLMoleculeObject_molecule::resetIndex() - index "+toString(newId)+" did not change.");
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276 | LOG(4, "INFO: GLMoleculeObject_molecule: new index is "+toString(newId)+".");
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277 | setObjectId(newId);
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278 |
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279 | emit indexChanged(this, oldId, newId);
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280 | }
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281 |
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282 | void GLMoleculeObject_molecule::AtomSelected(const atomId_t _id)
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283 | {
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284 | AtomNodeMap::iterator iter = AtomsinSceneMap.find(_id);
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285 | if (iter != AtomsinSceneMap.end())
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286 | QMetaObject::invokeMethod(iter->second, // pointer to a QObject
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287 | "Selected", // member name (no parameters here)
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288 | Qt::QueuedConnection); // connection type
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289 | else
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290 | ELOG(2, "GLMoleculeObject_molecule::AtomSelected() - atom "
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291 | << _id << " unknown to GLMoleculeObject_molecule.");
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292 | }
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293 |
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294 | void GLMoleculeObject_molecule::AtomUnselected(const atomId_t _id)
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295 | {
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296 | AtomNodeMap::iterator iter = AtomsinSceneMap.find(_id);
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297 | if (iter != AtomsinSceneMap.end())
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298 | QMetaObject::invokeMethod(iter->second, // pointer to a QObject
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299 | "Unselected", // member name (no parameters here)
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300 | Qt::QueuedConnection); // connection type
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301 | else ELOG(2, "GLMoleculeObject_molecule::AtomUnselected() - atom "
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302 | << _id << " unknown to GLMoleculeObject_molecule.");
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303 | }
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304 |
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305 | void GLMoleculeObject_molecule::Selected()
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306 | {
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307 | ASSERT( !m_selected,
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308 | "GLMoleculeObject_molecule::Selected() - 3D rep of molecule is already selected.");
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309 | m_selected = true;
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310 |
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311 | emit changed();
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312 | }
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313 |
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314 | void GLMoleculeObject_molecule::Unselected()
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315 | {
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316 | ASSERT( m_selected,
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317 | "GLMoleculeObject_molecule::Unselected() - 3D rep of molecule is already unselected.");
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318 | m_selected = false;
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319 |
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320 | emit changed();
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321 | }
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322 |
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323 |
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324 | void GLMoleculeObject_molecule::initialize(QGLView *view, QGLPainter *painter)
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325 | {
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326 | // Initialize all of the mesh objects that we have as children.
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327 | if (m_visible) {
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328 | GLMoleculeObject::initialize(view, painter);
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329 | } else {
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330 | foreach (QObject *obj, children()) {
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331 | GLMoleculeObject *meshobj = qobject_cast<GLMoleculeObject *>(obj);
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332 | if (meshobj)
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333 | meshobj->initialize(view, painter);
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334 | }
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335 | }
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336 | }
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337 |
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338 | void GLMoleculeObject_molecule::draw(QGLPainter *painter, const QVector4D &cameraPlane)
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339 | {
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340 | // draw either molecule's mesh or all atoms and bonds
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341 | if (m_visible) {
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342 | resetTesselationHull();
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343 |
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344 | painter->modelViewMatrix().push();
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345 |
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346 | // Apply the material and effect to the painter.
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347 | QGLMaterial *material;
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348 | if (m_hovering)
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349 | material = m_hoverMaterial;
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350 | else if (m_selected)
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351 | material = m_selectionMaterial;
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352 | else
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353 | material = m_material;
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354 |
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355 | ASSERT(material, "GLMoleculeObject::draw: chosen material is NULL");
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356 |
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357 | painter->setColor(material->diffuseColor());
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358 | painter->setFaceMaterial(QGL::AllFaces, material);
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359 | if (m_effect)
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360 | painter->setUserEffect(m_effect);
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361 | else
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362 | painter->setStandardEffect(QGL::LitMaterial);
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363 |
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364 | // Mark the object for object picking purposes.
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365 | int prevObjectId = painter->objectPickId();
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366 | if (m_objectId != -1)
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367 | painter->setObjectPickId(m_objectId);
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368 |
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369 | m_mesh[0]->draw(painter);
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370 |
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371 | // Turn off the user effect, if present.
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372 | if (m_effect)
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373 | painter->setStandardEffect(QGL::LitMaterial);
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374 |
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375 | // Revert to the previous object identifier.
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376 | painter->setObjectPickId(prevObjectId);
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377 |
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378 | // Restore the modelview matrix.
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379 | painter->modelViewMatrix().pop();
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380 |
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381 | // GLMoleculeObject::draw(painter, cameraPlane);
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382 | } else {
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383 | // Draw all of the mesh objects that we have as children.
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384 | foreach (QObject *obj, children()) {
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385 | GLMoleculeObject *meshobj = qobject_cast<GLMoleculeObject *>(obj);
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386 | if (meshobj)
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387 | meshobj->draw(painter, cameraPlane);
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388 | }
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389 |
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390 | // update bounding box prior to selection
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391 | resetBoundingBox();
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392 |
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393 | painter->modelViewMatrix().push();
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394 | painter->modelViewMatrix().translate(m_position);
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395 | if (m_rotationAngle != 0.0f)
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396 | painter->modelViewMatrix().rotate(m_rotationAngle, m_rotationVector);
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397 | if ((m_scaleX != 1.0f) || (m_scaleY != 1.0f) || (m_scaleZ != 1.0f))
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398 | painter->modelViewMatrix().scale(m_scaleX, m_scaleY, m_scaleZ);
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399 |
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400 | // Draw a box around the mesh, if selected.
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401 | if (m_selected)
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402 | drawSelectionBox(painter);
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403 |
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404 | // Restore the modelview matrix.
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405 | painter->modelViewMatrix().pop();
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406 | }
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407 | }
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408 |
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409 | /** Adds an atom of this molecule to the scene.
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410 | *
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411 | * @param _atom atom to add
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412 | */
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413 | void GLMoleculeObject_molecule::atomInserted(const atomId_t _id)
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414 | {
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415 | LOG(3, "INFO: GLMoleculeObject_molecule: Received signal atomInserted for atom "+toString(_id)+".");
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416 |
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417 | GLMoleculeObject_atom *atomObject =
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418 | new GLMoleculeObject_atom(
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419 | GLMoleculeObject::meshSphere,
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420 | this,
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421 | board.getObservedAtom(_id));
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422 | ASSERT( atomObject != NULL,
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423 | "GLMoleculeObject_molecule::atomInserted - could not create atom object for "+toString(_id));
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424 | AtomNodeMap::iterator iter = AtomsinSceneMap.find(_id);
|
---|
425 | ASSERT(iter == AtomsinSceneMap.end(),
|
---|
426 | "GLMoleculeObject_molecule::atomInserted - same atom with id "+toString(_id)+" added again.");
|
---|
427 | AtomsinSceneMap.insert( make_pair(_id, atomObject) );
|
---|
428 |
|
---|
429 | qRegisterMetaType<atomId_t>("atomId_t");
|
---|
430 | qRegisterMetaType<GLMoleculeObject_bond::SideOfBond>("GLMoleculeObject_bond::SideOfBond");
|
---|
431 | connect (atomObject, SIGNAL(clicked(atomId_t)), this, SIGNAL(atomClicked(atomId_t)));
|
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432 | connect (atomObject, SIGNAL(changed()), this, SIGNAL(changed()));
|
---|
433 | connect (atomObject, SIGNAL(hoverChanged(GLMoleculeObject *)), this, SIGNAL(changed()));
|
---|
434 | connect (atomObject, SIGNAL(hoverChanged(GLMoleculeObject *)), this, SLOT(hoverChangedSignalled(GLMoleculeObject *)));
|
---|
435 | // connect (atomObject, SIGNAL(bondsChanged()), this, SLOT(bondInserted(const atomId_t, const atomId_t, const GLMoleculeObject_bond::SideOfBond)));
|
---|
436 | connect (atomObject, SIGNAL(BondsAdded(const atomId_t, const atomId_t, const GLMoleculeObject_bond::SideOfBond)), this, SLOT(bondInserted(const atomId_t, const atomId_t, const GLMoleculeObject_bond::SideOfBond)));
|
---|
437 | connect (atomObject, SIGNAL(BondsRemoved(const atomId_t, const atomId_t)), this, SLOT(bondRemoved(const atomId_t, const atomId_t)));
|
---|
438 | connect (atomObject, SIGNAL(indexChanged(GLMoleculeObject_atom*, const atomId_t, const atomId_t)), this, SLOT(changeAtomId(GLMoleculeObject_atom*, const atomId_t, const atomId_t)));
|
---|
439 |
|
---|
440 | if (m_objectId == -1)
|
---|
441 | setObjectId(_id);
|
---|
442 |
|
---|
443 | emit changed();
|
---|
444 | emit changeOccured();
|
---|
445 | }
|
---|
446 |
|
---|
447 | /** Removes an atom of this molecule from the scene.
|
---|
448 | *
|
---|
449 | * We just the id as the atom might have already been destroyed.
|
---|
450 | *
|
---|
451 | * @param _id id of atom to remove
|
---|
452 | */
|
---|
453 | void GLMoleculeObject_molecule::atomRemoved(const atomId_t _id)
|
---|
454 | {
|
---|
455 | LOG(3, "INFO: GLMoleculeObject_molecule: Received signal atomRemoved for atom "+toString(_id)+".");
|
---|
456 | // bonds are removed by signal coming from ~bond
|
---|
457 |
|
---|
458 | if ((unsigned int)m_objectId == _id)
|
---|
459 | setObjectId(-1);
|
---|
460 |
|
---|
461 | // remove atoms
|
---|
462 | AtomNodeMap::iterator iter = AtomsinSceneMap.find(_id);
|
---|
463 | ASSERT(iter != AtomsinSceneMap.end(),
|
---|
464 | "GLMoleculeObject_molecule::atomRemoved() - atom "+toString(_id)+" not on display.");
|
---|
465 | GLMoleculeObject_atom *atomObject = iter->second;
|
---|
466 | AtomsinSceneMap.erase(iter);
|
---|
467 | atomObject->disconnect();
|
---|
468 | delete atomObject;
|
---|
469 |
|
---|
470 | emit changed();
|
---|
471 | emit changeOccured();
|
---|
472 | }
|
---|
473 |
|
---|
474 | void GLMoleculeObject_molecule::hoverChangedSignalled(GLMoleculeObject *ob)
|
---|
475 | {
|
---|
476 | // Find the atom, ob corresponds to.
|
---|
477 | hoverAtomId = -1;
|
---|
478 | GLMoleculeObject_atom *atomObject = dynamic_cast<GLMoleculeObject_atom *>(ob);
|
---|
479 | if (atomObject){
|
---|
480 | for (AtomNodeMap::iterator iter = AtomsinSceneMap.begin();iter != AtomsinSceneMap.end(); ++ iter){
|
---|
481 | if (iter->second == atomObject)
|
---|
482 | hoverAtomId = iter->first;
|
---|
483 | }
|
---|
484 |
|
---|
485 | // Propagate signal.
|
---|
486 | emit hoverChanged(hoverAtomId);
|
---|
487 | } else {
|
---|
488 | // Find the atom, ob corresponds to.
|
---|
489 | GLMoleculeObject_molecule *moleculeObject = dynamic_cast<GLMoleculeObject_molecule *>(ob);
|
---|
490 | if (moleculeObject == this){
|
---|
491 | // Propagate signal.
|
---|
492 | emit hoverChanged(ObservedMolecule->getMolIndex(), 0);
|
---|
493 | }
|
---|
494 | }
|
---|
495 | }
|
---|
496 |
|
---|
497 |
|
---|
498 | /** Helper function to get bond ids in the correct order for BondNodeMap.
|
---|
499 | *
|
---|
500 | * \return pair of ids in correct order.
|
---|
501 | */
|
---|
502 | GLMoleculeObject_molecule::BondIds GLMoleculeObject_molecule::getBondIds(
|
---|
503 | const bond::ptr _bond,
|
---|
504 | const enum GLMoleculeObject_bond::SideOfBond _side)
|
---|
505 | {
|
---|
506 | BondIds ids;
|
---|
507 | switch (_side) {
|
---|
508 | case GLMoleculeObject_bond::left:
|
---|
509 | ids = std::make_pair(_bond->leftatom->getId(), _bond->rightatom->getId());
|
---|
510 | break;
|
---|
511 | case GLMoleculeObject_bond::right:
|
---|
512 | ids = std::make_pair(_bond->rightatom->getId(), _bond->leftatom->getId());
|
---|
513 | break;
|
---|
514 | }
|
---|
515 | return ids;
|
---|
516 | }
|
---|
517 |
|
---|
518 | /** Adds a bond to the scene.
|
---|
519 | *
|
---|
520 | * @param _bond bond to add
|
---|
521 | * @param side which side of the bond (left or right)
|
---|
522 | */
|
---|
523 | void GLMoleculeObject_molecule::bondInserted(
|
---|
524 | const atomId_t _left, const atomId_t _right,
|
---|
525 | const enum GLMoleculeObject_bond::SideOfBond _side)
|
---|
526 | {
|
---|
527 | LOG(3, "INFO: GLWorldScene::bondInserted() - Adding bond "+toString(_left)
|
---|
528 | +toString(_right)+".");
|
---|
529 | //LOG(4, "INFO: Currently present bonds " << BondsinSceneMap << ".");
|
---|
530 |
|
---|
531 | const BondIds ids( std::make_pair(_left, _right) );
|
---|
532 | BondNodeMap::iterator iter = BondsinSceneMap.find(ids);
|
---|
533 | if (iter == BondsinSceneMap.end()) {
|
---|
534 | GLMoleculeObject_bond * bondObject =
|
---|
535 | new GLMoleculeObject_bond(GLMoleculeObject::meshCylinder, this, ids, _side);
|
---|
536 | connect (
|
---|
537 | bondObject, SIGNAL(BondRemoved(const atomId_t, const atomId_t)),
|
---|
538 | this, SLOT(bondRemoved(const atomId_t, const atomId_t)));
|
---|
539 | connect (bondObject, SIGNAL(changed()), this, SIGNAL(changed()));
|
---|
540 | BondsinSceneMap.insert( make_pair(ids, bondObject) );
|
---|
541 | // BondIdsinSceneMap.insert( Leftids );
|
---|
542 | } else {
|
---|
543 | iter->second->resetPosition();
|
---|
544 | iter->second->resetWidth();
|
---|
545 | }
|
---|
546 | emit changed();
|
---|
547 | emit changeOccured();
|
---|
548 | }
|
---|
549 |
|
---|
550 | /** Removes a bond from the scene.
|
---|
551 | *
|
---|
552 | * @param _bond bond to remove
|
---|
553 | */
|
---|
554 | void GLMoleculeObject_molecule::bondRemoved(const atomId_t leftnr, const atomId_t rightnr)
|
---|
555 | {
|
---|
556 | LOG(3, "INFO: GLWorldScene::bondRemoved() - Removing bond between "+toString(leftnr)+" and "+toString(rightnr)+".");
|
---|
557 | {
|
---|
558 | // left bond
|
---|
559 | const BondIds Leftids( make_pair(leftnr, rightnr) );
|
---|
560 | BondNodeMap::iterator leftiter = BondsinSceneMap.find( Leftids );
|
---|
561 | ASSERT(leftiter != BondsinSceneMap.end(),
|
---|
562 | "GLWorldScene::bondRemoved() - bond "+toString(leftnr)+"-"
|
---|
563 | +toString(rightnr)+" not on display.");
|
---|
564 | GLMoleculeObject_bond *bondObject = leftiter->second;
|
---|
565 | bondObject->disconnect();
|
---|
566 | BondsinSceneMap.erase(leftiter);
|
---|
567 | delete bondObject; // is done by signal from bond itself
|
---|
568 | //LOG(4, "INFO: Still present bonds " << BondsinSceneMap << ".");
|
---|
569 | }
|
---|
570 |
|
---|
571 | emit changed();
|
---|
572 | emit changeOccured();
|
---|
573 | }
|
---|
574 |
|
---|
575 | void GLMoleculeObject_molecule::setVisible(bool value)
|
---|
576 | {
|
---|
577 | // first update the mesh if we are going to be visible now
|
---|
578 | if (value)
|
---|
579 | updateTesselationHull();
|
---|
580 | // then emit onward
|
---|
581 | GLMoleculeObject::setVisible(value);
|
---|
582 |
|
---|
583 | emit changed();
|
---|
584 | emit changeOccured();
|
---|
585 | }
|
---|
586 |
|
---|
587 | std::ostream &operator<<(std::ostream &ost, const GLMoleculeObject_molecule::BondIds &t)
|
---|
588 | {
|
---|
589 | ost << t.first << "," << t.second;
|
---|
590 | return ost;
|
---|
591 | }
|
---|
592 |
|
---|
593 | void GLMoleculeObject_molecule::wasClicked()
|
---|
594 | {
|
---|
595 | LOG(4, "INFO: GLMoleculeObject_molecule: atom "
|
---|
596 | << ObservedMolecule->getMolIndex() << " has been clicked");
|
---|
597 | emit moleculeClicked(ObservedMolecule->getMolIndex());
|
---|
598 | }
|
---|
599 |
|
---|
600 | void GLMoleculeObject_molecule::changeAtomId(
|
---|
601 | GLMoleculeObject_atom *ob,
|
---|
602 | const atomId_t oldId,
|
---|
603 | const atomId_t newId)
|
---|
604 | {
|
---|
605 | LOG(3, "INFO: GLMoleculeObject_molecule - change atom id " << oldId << " to " << newId << ".");
|
---|
606 |
|
---|
607 | // Remove from map.
|
---|
608 | AtomNodeMap::iterator iter = AtomsinSceneMap.find(oldId);
|
---|
609 | ASSERT(iter != AtomsinSceneMap.end(),
|
---|
610 | "GLMoleculeObject_molecule::changeAtomId() - atom with old id "+toString(oldId)+" not on display.");
|
---|
611 | ASSERT(iter->second == ob,
|
---|
612 | "GLMoleculeObject_molecule::changeAtomId() - atom with id "
|
---|
613 | +toString(oldId)+" does not match with object in AtomsinSceneMap.");
|
---|
614 | AtomsinSceneMap.erase(iter);
|
---|
615 |
|
---|
616 | // Reinsert with new id.
|
---|
617 | {
|
---|
618 | AtomNodeMap::iterator iter = AtomsinSceneMap.find(newId);
|
---|
619 | ASSERT(iter == AtomsinSceneMap.end(),
|
---|
620 | "GLMoleculeObject_molecule::changeAtomId() - atom with new id "+toString(newId)+" already known.");
|
---|
621 | }
|
---|
622 | AtomsinSceneMap.insert( make_pair(newId, ob) );
|
---|
623 | }
|
---|
624 |
|
---|
625 |
|
---|
626 | GLMoleculeObject_molecule::atoms_t GLMoleculeObject_molecule::getPresentAtoms() const
|
---|
627 | {
|
---|
628 | atoms_t returnAtomIds;
|
---|
629 | returnAtomIds.insert(
|
---|
630 | MapKeyConstIterator<AtomNodeMap::const_iterator>(const_cast<const AtomNodeMap &>(AtomsinSceneMap).begin()),
|
---|
631 | MapKeyConstIterator<AtomNodeMap::const_iterator>(const_cast<const AtomNodeMap &>(AtomsinSceneMap).end()));
|
---|
632 | return returnAtomIds;
|
---|
633 | }
|
---|