1 | /*
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2 | * SaturatedFragment.hpp
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3 | *
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4 | * Created on: Mar 3, 2013
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5 | * Author: heber
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6 | */
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7 |
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8 | #ifndef SATURATEDFRAGMENT_HPP_
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9 | #define SATURATEDFRAGMENT_HPP_
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10 |
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11 | // include config.h
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12 | #ifdef HAVE_CONFIG_H
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13 | #include <config.h>
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14 | #endif
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15 |
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16 | #include <iosfwd>
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17 | #include <set>
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18 | #include <string>
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19 |
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20 | #include "Atom/atom_bondedparticleinfo.hpp"
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21 | #include "Bond/bond.hpp"
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22 | #include "Fragmentation/KeySet.hpp"
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23 | #include "Fragmentation/HydrogenSaturation_enum.hpp"
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24 | #include "Parser/FormatParserStorage.hpp"
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25 |
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26 | class atom;
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27 | class HydrogenPool;
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28 |
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29 | /** The SaturatedFragment class acts as a wrapper to a KeySet by adding a list
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30 | * of saturation hydrogens.
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31 | *
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32 | * This SaturatedFragment along with a currently leased set of hydrogens from the
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33 | * HydrogenPool is all that is required to create a fully storable molecular
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34 | * fragment from a given Keyset.
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35 | *
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36 | * The instance notes down its existence in an external container.
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37 | *
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38 | */
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39 | class SaturatedFragment
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40 | {
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41 | public:
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42 | //!> typedef to a container to mark keysets that are in use
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43 | typedef std::set<KeySet> KeySetsInUse_t;
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44 |
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45 | /** Constructor of SaturatedFragment requires \a set which we are tightly
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46 | * associated.
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47 | *
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48 | * \param _set KeySet which this instance is associated with
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49 | * \param _container container to add KeySet as in-use
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50 | * \param _hydrogens pool with hydrogens for saturation
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51 | */
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52 | SaturatedFragment(
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53 | const KeySet &_set,
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54 | KeySetsInUse_t &_container,
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55 | HydrogenPool &_hydrogens,
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56 | const enum HydrogenTreatment _treatment,
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57 | const enum HydrogenSaturation saturation);
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58 |
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59 | /** Destructor of class SaturatedFragment.
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60 | *
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61 | */
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62 | ~SaturatedFragment();
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63 |
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64 | /** Getter for the KeySet this instance is associated with.
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65 | *
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66 | * \return const ref to KeySet
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67 | */
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68 | const KeySet & getKeySet() const
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69 | {
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70 | return set;
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71 | }
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72 |
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73 | /** Getter for the FullMolecule this instance is associated with.
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74 | *
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75 | * \return const ref to FullMolecule
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76 | */
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77 | const KeySet & getFullMolecule() const
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78 | {
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79 | return FullMolecule;
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80 | }
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81 |
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82 | /** Getter for the SaturationHydrogens this instance is associated with.
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83 | *
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84 | * \return const ref to SaturationHydrogens
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85 | */
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86 | const KeySet & getSaturationHydrogens() const
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87 | {
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88 | return SaturationHydrogens;
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89 | }
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90 |
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91 | /** Prints the config of the fragment of \a _type to \a out.
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92 | *
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93 | * \param out output stream to write to
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94 | * \param _type parser type to write config
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95 | */
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96 | bool OutputConfig(
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97 | std::ostream &out,
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98 | const ParserTypes _type) const;
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99 |
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100 | private:
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101 | /** Helper function to lease and bring in place saturation hydrogens.
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102 | *
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103 | */
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104 | void saturate();
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105 |
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106 | /** Replaces all cut bonds with respect to the given atom by hydrogens.
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107 | *
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108 | * \param _atom atom whose cut bonds to saturate
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109 | * \param _cutbonds list of cut bonds for \a _atom
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110 | * \return true - bonds saturated, false - something went wrong
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111 | */
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112 | bool saturateAtom(atom * const _atom, const BondList &_cutbonds);
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113 |
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114 | /** Helper function to get a hydrogen replacement for a given \a replacement.
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115 | *
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116 | * \param replacement atom to "replace" with hydrogen in a fragment.
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117 | * \return ref to leased hydrogen atom
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118 | */
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119 | atom * const getHydrogenReplacement(atom * const replacement);
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120 |
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121 | /** Leases and adds a Hydrogen atom in replacement for the given atom \a *partner in bond with a *origin.
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122 | * Here, we have to distinguish between single, double or triple bonds as stated by \a BondDegree, that each demand
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123 | * a different scheme when adding \a *replacement atom for the given one.
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124 | * -# Single Bond: Simply add new atom with bond distance rescaled to typical hydrogen one
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125 | * -# Double Bond: Here, we need the **BondList of the \a *origin atom, by scanning for the other bonds instead of
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126 | * *Bond, we use the through these connected atoms to determine the plane they lie in, vector::MakeNormalvector().
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127 | * The orthonormal vector to this plane along with the vector in *Bond direction determines the plane the two
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128 | * replacing hydrogens shall lie in. Now, all remains to do is take the usual hydrogen double bond angle for the
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129 | * element of *origin and form the sin/cos admixture of both plane vectors for the new coordinates of the two
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130 | * hydrogens forming this angle with *origin.
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131 | * -# Triple Bond: The idea is to set up a tetraoid (C1-H1-H2-H3) (however the lengths \f$b\f$ of the sides of the base
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132 | * triangle formed by the to be added hydrogens are not equal to the typical bond distance \f$l\f$ but have to be
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133 | * determined from the typical angle \f$\alpha\f$ for a hydrogen triple connected to the element of *origin):
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134 | * We have the height \f$d\f$ as the vector in *Bond direction (from triangle C1-H1-H2).
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135 | * \f[ h = l \cdot \cos{\left (\frac{\alpha}{2} \right )} \qquad b = 2l \cdot \sin{\left (\frac{\alpha}{2} \right)} \quad \rightarrow \quad d = l \cdot \sqrt{\cos^2{\left (\frac{\alpha}{2} \right)}-\frac{1}{3}\cdot\sin^2{\left (\frac{\alpha}{2}\right )}}
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136 | * \f]
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137 | * vector::GetNormalvector() creates one orthonormal vector from this *Bond vector and vector::MakeNormalvector creates
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138 | * the third one from the former two vectors. The latter ones form the plane of the base triangle mentioned above.
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139 | * The lengths for these are \f$f\f$ and \f$g\f$ (from triangle H1-H2-(center of H1-H2-H3)) with knowledge that
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140 | * the median lines in an isosceles triangle meet in the center point with a ratio 2:1.
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141 | * \f[ f = \frac{b}{\sqrt{3}} \qquad g = \frac{b}{2}
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142 | * \f]
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143 | * as the coordination of all three atoms in the coordinate system of these three vectors:
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144 | * \f$\pmatrix{d & f & 0}\f$, \f$\pmatrix{d & -0.5 \cdot f & g}\f$ and \f$\pmatrix{d & -0.5 \cdot f & -g}\f$.
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145 | *
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146 | * \param TopBond pointer to bond between \a *origin and \a *replacement
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147 | * \param Origin atom that is actually contained in the fragment
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148 | * \param Replacement pointer to the atom which shall be copied as a hydrogen atom in this molecule
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149 | * \param isAngstroem whether the coordination of the given atoms is in AtomicLength (false) or Angstrom(true)
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150 | * \return number of atoms added, if < bond::BondDegree then something went wrong
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151 | */
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152 | bool AddHydrogenReplacementAtom(
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153 | bond::ptr TopBond,
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154 | atom *Origin,
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155 | atom *Replacement,
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156 | bool IsAngstroem);
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157 |
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158 | private:
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159 | //!> container to mark ourselves RAII-style
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160 | KeySetsInUse_t &container;
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161 | //!> key set this fragment is associated with.
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162 | const KeySet &set;
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163 | //!> pool with saturation hydrogens
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164 | HydrogenPool &hydrogens;
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165 | //!> key set containing all atoms used for e.g. storing this to file
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166 | KeySet FullMolecule;
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167 | //!> key set containing the ids of all hydrogens added for saturation
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168 | KeySet SaturationHydrogens;
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169 | //!> whether hydrogens are generally contained in set or not
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170 | const enum HydrogenTreatment treatment;
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171 | //!> whether to actually saturate or not
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172 | const enum HydrogenSaturation saturation;
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173 | };
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174 |
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175 | #endif /* SATURATEDFRAGMENT_HPP_ */
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