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) 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 | * Fragment.cpp
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26 | *
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27 | * Created on: Aug 8, 2012
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28 | * Author: heber
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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 headers that implement a archive in simple text format
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38 | // otherwise BOOST_CLASS_EXPORT_IMPLEMENT has no effect
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39 | #include <boost/archive/text_oarchive.hpp>
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40 | #include <boost/archive/text_iarchive.hpp>
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41 |
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42 | //#include "CodePatterns/MemDebug.hpp"
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43 |
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44 | #include "Fragment.hpp"
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45 |
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46 | #include <algorithm>
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47 | #include <cmath>
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48 | #include <iostream>
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49 | #include <limits>
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50 |
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51 | #include "CodePatterns/Assert.hpp"
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52 |
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53 | Fragment::Fragment()
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54 | {}
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55 |
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56 | Fragment::Fragment(
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57 | const positions_t &_positions,
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58 | const atomicnumbers_t &_atomicnumbers,
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59 | const charges_t &_charges)
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60 | {
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61 | ASSERT( _positions.size() == _charges.size(),
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62 | "Fragment::Fragment() - given charges and positions don't match in size.");
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63 | positions_t::const_iterator piter = _positions.begin();
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64 | atomicnumbers_t::const_iterator aiter = _atomicnumbers.begin();
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65 | charges_t::const_iterator citer = _charges.begin();
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66 | for (;piter != _positions.end(); ++piter, ++aiter, ++citer)
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67 | nuclei.push_back( createNucleus(*piter, *aiter, *citer) );
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68 | }
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69 |
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70 |
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71 | Fragment& Fragment::operator+=(const Fragment &other)
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72 | {
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73 | for (nuclei_t::const_iterator iter = other.nuclei.begin();
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74 | iter != other.nuclei.end(); ++iter) {
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75 | if (!containsNuclei(*iter)) {
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76 | nuclei.push_back(*iter);
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77 | }
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78 | }
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79 | return *this;
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80 | }
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81 |
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82 | Fragment& Fragment::operator=(const Fragment &other)
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83 | {
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84 | if (this != &other) {
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85 | nuclei.clear();
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86 | nuclei = other.nuclei;
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87 | }
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88 | return *this;
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89 | }
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90 |
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91 | Fragment& Fragment::operator-=(const Fragment &other)
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92 | {
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93 | for (nuclei_t::const_iterator iter = other.nuclei.begin();
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94 | iter != other.nuclei.end(); ++iter)
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95 | removeNuclei(*iter);
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96 | return *this;
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97 | }
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98 |
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99 | bool Fragment::containsNuclei(const nucleus_t &n) const
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100 | {
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101 | for (nuclei_t::const_iterator iter = nuclei.begin();
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102 | iter != nuclei.end(); ++iter)
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103 | if (Fragment::isPositionEqual(iter->first, n.first))
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104 | return true;
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105 | return false;
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106 | }
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107 |
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108 | void Fragment::removeNuclei(const nucleus_t &n)
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109 | {
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110 | for (nuclei_t::iterator iter = nuclei.begin();
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111 | iter != nuclei.end(); ++iter)
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112 | if (Fragment::isPositionEqual(iter->first, n.first)) {
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113 | nuclei.erase(iter);
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114 | break;
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115 | }
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116 | }
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117 |
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118 | Fragment::positions_t Fragment::getPositions() const
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119 | {
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120 | positions_t positions;
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121 | for (nuclei_t::const_iterator iter = nuclei.begin();
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122 | iter != nuclei.end(); ++iter)
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123 | positions.push_back(iter->first);
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124 | return positions;
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125 | }
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126 |
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127 | Fragment::atomicnumbers_t Fragment::getAtomicNumbers() const
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128 | {
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129 | atomicnumbers_t positions;
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130 | for (nuclei_t::const_iterator iter = nuclei.begin();
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131 | iter != nuclei.end(); ++iter)
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132 | positions.push_back(iter->second.first);
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133 | return positions;
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134 | }
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135 |
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136 | Fragment::charges_t Fragment::getCharges() const
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137 | {
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138 | charges_t charges;
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139 | for (nuclei_t::const_iterator iter = nuclei.begin();
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140 | iter != nuclei.end(); ++iter)
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141 | charges.push_back(iter->second.second);
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142 | return charges;
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143 | }
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144 |
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145 | Fragment::nucleus_t Fragment::createNucleus(
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146 | const position_t &position,
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147 | const atomicNumber_t &atomicnumber,
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148 | const double charge)
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149 | {
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150 | return nucleus_t( make_pair( position, std::make_pair(atomicnumber, charge) ) );
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151 | }
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152 |
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153 | bool Fragment::isPositionEqual(const position_t &a, const position_t &b)
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154 | {
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155 | bool status = true;
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156 | for (size_t i=0;i<3;++i)
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157 | status &= fabs(a[i] - b[i]) < std::numeric_limits<double>::epsilon();
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158 | return status;
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159 | }
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160 |
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161 | bool Fragment::operator==(const Fragment& other) const
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162 | {
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163 | bool status = true;
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164 | // compare sizes
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165 | if (nuclei.size() != other.nuclei.size()) {
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166 | return false;
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167 | } else {
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168 | // if equal, sort, and compare each nuclei
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169 | Fragment::nuclei_t thisnuclei(nuclei);
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170 | Fragment::nuclei_t othernuclei(other.nuclei);
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171 | std::sort(thisnuclei.begin(), thisnuclei.end());
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172 | std::sort(othernuclei.begin(), othernuclei.end());
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173 | Fragment::nuclei_t::const_iterator iter = thisnuclei.begin();
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174 | Fragment::nuclei_t::const_iterator oiter = othernuclei.begin();
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175 | for (; iter != thisnuclei.end(); ++iter,++oiter)
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176 | status &= (*iter == *oiter);
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177 | }
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178 | return status;
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179 | }
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180 |
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181 | std::ostream & operator<<(std::ostream &ost, const Fragment &f)
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182 | {
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183 | size_t NucleiCounter = 1;
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184 | for (Fragment::nuclei_t::const_iterator iter = f.nuclei.begin();
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185 | iter != f.nuclei.end(); ++iter)
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186 | ost << "[" << NucleiCounter++ << "]:" << *iter << ", ";
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187 | return ost;
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188 | }
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189 |
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190 | std::ostream & operator<<(std::ostream &ost, const Fragment::nucleus_t &n)
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191 | {
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192 | ost << n.first << " with Z of " << n.second.first << " charge " << n.second.second;
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193 | return ost;
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194 | }
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195 |
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196 | bool operator==(const Fragment::nucleus_t &a, const Fragment::nucleus_t &b)
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197 | {
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198 | bool status = true;
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199 | // check positions
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200 | status &= Fragment::isPositionEqual(a.first, b.first);
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201 | status &= (a.second.first == b.second.first);
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202 | status &= fabs(a.second.second - b.second.second) < std::numeric_limits<double>::epsilon();
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203 | return status;
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204 | }
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205 |
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206 | template<> Fragment ZeroInstance<Fragment>()
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207 | {
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208 | Fragment::positions_t positions;
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209 | Fragment::atomicnumbers_t atomicnumbers;
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210 | Fragment::charges_t charges;
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211 | Fragment returnvalue(positions, atomicnumbers, charges);
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212 | return returnvalue;
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213 | }
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214 |
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215 | // below is not needed as we have above static ZeroInstace instantiating the code
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216 |
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217 | //// we need to explicitly instantiate the serialization functions
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218 | //BOOST_CLASS_EXPORT_IMPLEMENT(Fragment)
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