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1 NAME
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2 Bond
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3
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4 SYNOPSIS
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5 use Bond;
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6
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7 use Bond qw(:all);
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8
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9 DESCRIPTION
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10 Bond class provides the following methods:
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11
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12 new, Copy, DeleteBond, GetAtoms, GetBondBeginAtom, GetBondEndAtom,
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13 GetBondFromAtom, GetBondToAtom, GetBondedAtom, GetCommonAtom,
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14 GetLargestRing, GetNumOfRings, GetNumOfRingsWithEvenSize,
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15 GetNumOfRingsWithOddSize, GetNumOfRingsWithSize,
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16 GetNumOfRingsWithSizeGreaterThan, GetNumOfRingsWithSizeLessThan,
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17 GetRings, GetRingsWithEvenSize, GetRingsWithOddSize, GetRingsWithSize,
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18 GetRingsWithSizeGreaterThan, GetRingsWithSizeLessThan,
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19 GetSizeOfLargestRing, GetSizeOfSmallestRing, GetSmallestRing,
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20 IsAromatic, IsBondStereochemistrySpecified, IsBondTypeSpecified, IsCis,
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21 IsCisOrTrans, IsCoordinate, IsDative, IsDouble, IsDown, IsDownward,
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22 IsHash, IsInRing, IsInRingOfSize, IsIonic, IsNotInRing, IsOnlyInOneRing,
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23 IsQuadruple, IsQuintuple, IsSextuple, IsSingle, IsTautomeric, IsTrans,
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24 IsTriple, IsUp, IsUpOrDown, IsUpward, IsWedge, IsWedgeOrHash, SetAtoms,
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25 SetBondOrder, SetBondStereochemistry, SetBondType, StringifyBond,
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26 SwitchBondFromAndToAtoms
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27
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28 Bond class is derived from ObjectProperty base class which provides
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29 methods not explicitly defined in Atom or ObjectProperty class using
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30 Perl's AUTOLOAD functionality. These methods are generated on-the-fly
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31 for a specified object property:
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32
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33 Set<PropertyName>(<PropertyValue>);
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34 $PropertyValue = Get<PropertyName>();
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35 Delete<PropertyName>();
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36
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37 METHODS
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38 new
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39 $NewBond = new Bond([%PropertyNameAndValues]);
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40
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41 Using specified *Bond* property names and values hash, new method
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42 creates a new object and returns a reference to newly created Bond
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43 object. By default, following properties are initialized:
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44
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45 ID = SequentialObjectID
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46 @Atoms = ();
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47 BondType = ""
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48 BondOrder = ""
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49
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50 Except for *ID* property, all other default properties and other
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51 additional properties can be set during invocation of this method.
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52
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53 Examples:
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54
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55 $Bond = new Bond();
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56 $DoubleBond = new Bond('Atoms' => [$Atom2, $Atom1],
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57 'BondOrder' => 2);
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58
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59 Copy
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60 $BondCopy = $Bond->Copy();
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61
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62 Copy *Bond* and its associated data using Storable::dclone and
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63 return a new Bond object.
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64
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65 DeleteBond
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66 $Bond->DeleteBond();
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67
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68 Delete *Bond* between atoms in from a molecule.
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69
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70 GetAtoms
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71 @BondedAtoms = $Bond->GetAtoms();
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72
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73 Returns an array containing *Atoms* invoved in *Bond*.
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74
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75 GetBondedAtom
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76 $BondedAtom = $Bond->GetBondedAtom($Atom);
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77
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78 Returns BondedAtom bonded to *Atom* in *Bond*.
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79
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80 GetBondBeginAtom
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81 $BeginAtom = $Bond->GetBondBeginAtom();
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82
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83 Returns BeginAtom corresponding to bond starting atom in *Bond*.
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84
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85 GetBondEndAtom
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86 $EndAtom = $Bond->GetBondEndAtom();
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87
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88 Returns EndAtom corresponding to bond ending atom in *Bond*.
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89
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90 GetBondFromAtom
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91 $FromAtom = $Bond->GetBondFromAtom();
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92
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93 Returns FromAtom corresponding to bond starting atom in *Bond*.
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94
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95 GetBondToAtom
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96 $ToAotm = $Bond->GetBondToAtom();
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97
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98 Returns ToAtom corresponding to bond ending atom in *Bond*.
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99
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100 GetCommonAtom
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101 $CommonAtom = $Bond->GetCommonAtom($OtherBond);
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102
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103 Returns Atom common to both *Bond* and *$OtherBond*.
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104
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105 GetLargestRing
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106 @RingAtoms = $Bond->GetLargestRing();
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107
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108 Returns an array of ring *Atoms* corresponding to the largest ring
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109 containing *Bond*. in a molecule
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110
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111 GetNumOfRings
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112 $NumOfRings = $Bond->GetNumOfRings();
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113
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114 Returns number of rings containing *Bond* in a molecule.
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115
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116 GetNumOfRingsWithEvenSize
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117 $NumOfRings = $Bond->GetNumOfRingsWithEvenSize();
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118
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119 Returns number of rings with even size containing *Bond* in a
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120 molecule.
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121
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122 GetNumOfRingsWithOddSize
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123 $NumOfRings = $Bond->GetNumOfRingsWithOddSize();
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124
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125 Returns number of rings with odd size containing *Bond* in a
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126 molecule.
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127
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128 GetNumOfRingsWithSize
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129 $NumOfRings = $Bond->GetNumOfRingsWithSize($RingSize);
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130
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131 Returns number of rings with specific *RingSize* containing *Bond*
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132 in a molecule.
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133
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134 GetNumOfRingsWithSizeGreaterThan
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135 $NumOfRings = $Bond->GetNumOfRingsWithSizeGreaterThan($RingSize);
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136
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137 Returns number of rings with size greater than specific *RingSize*
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138 containing *Bond* in a molecule.
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139
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140 GetNumOfRingsWithSizeLessThan
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141 $NumOfRings = $Bond->GetNumOfRingsWithSizeLessThan($RingSize);
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142
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143 Returns number of rings with size less than specific *RingSize*
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144 containing *Bond* in a molecule.
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145
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146 GetRings
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147 @Rings = $Bond->GetRings();
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148
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149 Returns an array of references to arrays containing ring atoms
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150 corressponding to all rings containing *Bond* in a molecule.
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151
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152 GetRingsWithEvenSize
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153 @Rings = $Bond->GetRingsWithEvenSize();
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154
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155 Returns an array of references to arrays containing ring atoms
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156 corressponding to all rings with even size containing *Bond* in a
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157 molecule.
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158
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159 GetRingsWithOddSize
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160 @Rings = $Bond->GetRingsWithOddSize();
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161
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162 Returns an array of references to arrays containing ring atoms
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163 corressponding to all rings with odd size containing *Bond* in a
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164 molecule.
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165
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166 GetRingsWithSize
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167 @Rings = $Bond->GetRingsWithSize($RingSize);
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168
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169 Returns an array of references to arrays containing ring atoms
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170 corressponding to all rings with specific *RingSize *containing
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171 *Bond* in a molecule.
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172
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173 GetRingsWithSizeGreaterThan
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174 @Rings = $Bond->GetRingsWithSizeGreaterThan($RingSize);
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175
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176 Returns an array of references to arrays containing ring atoms
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177 corressponding to all rings with size greater than specific
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178 *RingSize *containing *Bond* in a molecule.
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179
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180 GetRingsWithSizeLessThan
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181 @Rings = $Bond->GetRingsWithSizeLessThan($RingSize);
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182
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183 Returns an array of references to arrays containing ring atoms
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184 corressponding to all rings with size less than specific *RingSize
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185 *containing *Bond* in a molecule.
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186
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187 GetSizeOfLargestRing
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188 $Size = $Bond->GetSizeOfLargestRing();
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189
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190 Returns size of the largest ring containing *Bond* in a molecule.
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191
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192 GetSizeOfSmallestRing
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193 $Size = $Bond->GetSizeOfSmallestRing();
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194
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195 Returns size of the smallest ring containing *Bond* in a molecule.
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196
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197 GetSmallestRing
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198 @RingAtoms = $Bond->GetSmallestRing();
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199
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200 Returns an array of ring *Atoms* corresponding to the largest ring
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201 containing *Bond* in a molecule.
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202
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203 IsAromatic
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204 $Status = $Bond->IsAromatic();
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205
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206 Returns 1 or 0 based on whether it's an aromatic *Bond*.
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207
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208 IsBondStereochemistrySpecified
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209 $Status = $Bond->IsBondStereochemistrySpecified();
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210
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211 Returns 1 or 0 based on whether *Bond*'s sterochemistry is
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212 specified.
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213
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214 IsBondTypeSpecified
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215 $Status = $Bond->IsBondTypeSpecified();
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216
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217 Returns 1 or 0 based on whether *Bond*'s type is specified.
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218
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219 IsCis
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220 $Status = $Bond->IsCis();
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221
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222 Returns 1 or 0 based on whether it's a cis *Bond*.
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223
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224 IsCisOrTrans
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225 $Status = $Bond->IsCisOrTrans();
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226
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227 Returns 1 or 0 based on whether it's a cis or trans *Bond*.
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228
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229 IsCoordinate
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230 $Status = $Bond->IsCoordinate();
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231
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232 Returns 1 or 0 based on whether it's a coordinate or dative *Bond*.
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233
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234 IsDative
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235 $Status = $Bond->IsDative();
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236
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237 Returns 1 or 0 based on whether it's a coordinate or dative *Bond*.
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238
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239 IsDouble
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240 $Status =$Bond->IsDouble();
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241
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242 Returns 1 or 0 based on whether it's a double *Bond*.
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243
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244 IsDown
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245 $Status = $Bond->IsDown();
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246
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247 Returns 1 or 0 based on whether it's a hash or down single *Bond*.
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248
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249 IsDownward
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250 $Return = $Bond->IsDownward();
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251
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252 Returns 1 or 0 based on whether it's a downward *Bond*.
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253
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254 IsHash
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255 $Status = $Bond->IsHash();
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256
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257 Returns 1 or 0 based on whether it's a hash or down single *Bond*.
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258
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259 IsInRing
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260 $Status = $Bond->IsInRing();
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261
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262 Returns 1 or 0 based on whether *Bond* is present in a ring.
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263
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264 IsInRingOfSize
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265 $Status = $Bond->IsInRingOfSize($Size);
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266
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267 Returns 1 or 0 based on whether *Bond* is present in a ring of
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268 specific *Size*.
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269
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270 IsIonic
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271 $Status = $Bond->IsIonic();
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272
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273 Returns 1 or 0 based on whether it's an ionic *Bond*.
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274
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275 IsNotInRing
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276 $Status = $Bond->IsNotInRing();
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277
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278 Returns 1 or 0 based on whether *Bond* is not present in a ring.
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279
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280 IsOnlyInOneRing
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281 $Status = $Bond->IsOnlyInOneRing();
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282
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283 Returns 1 or 0 based on whether *Bond* is only present in one ring.
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284
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285 IsQuadruple
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286 $Status = $Bond->IsQuadruple();
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287
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288 Returns 1 or 0 based on whether it's a quadruple *Bond*.
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289
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290 IsQuintuple
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291 $Status = $Bond->IsQuintuple();
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292
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293 Returns 1 or 0 based on whether it's a quintuple *Bond*.
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294
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295 IsSextuple
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296 $Status = $Bond->IsSextuple();
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297
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298 Returns 1 or 0 based on whether it's a sextuple *Bond*.
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299
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300 IsSingle
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301 $Status =$Bond->IsSingle();
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302
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303 Returns 1 or 0 based on whether it's a single *Bond*.
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304
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305 IsTriple
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306 $Status =$Bond->IsTriple();
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307
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308 Returns 1 or 0 based on whether it's a triple *Bond*.
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309
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310 IsTautomeric
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311 $Status = $Bond->IsTautomeric();
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312
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313 Returns 1 or 0 based on whether it's a *Bond*.
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314
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315 IsTrans
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316 $Status = $Bond->IsTrans();
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317
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318 Returns 1 or 0 based on whether it's a trans *Bond*.
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319
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320 IsUp
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321 $Status = $Bond->IsUp();
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322
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323 Returns 1 or 0 based on whether it's a up *Bond*.
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324
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325 IsUpOrDown
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326 $Status = $Bond->IsUpOrDown();
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327
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328 Returns 1 or 0 based on whether it's an up or down *Bond*.
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329
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330 IsUpward
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331 $Status = $Bond->IsUpward();
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332
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333 Returns 1 or 0 based on whether it's an upward *Bond*.
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334
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335 IsWedge
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336 $Status = $Bond->IsWedge();
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337
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338 Returns 1 or 0 based on whether it's a wedge *Bond*.
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339
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340 IsWedgeOrHash
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341 $Status = $Bond->IsWedgeOrHash();
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342
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343 Returns 1 or 0 based on whether it's a wedge or hash *Bond*.
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344
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345 SetAtoms
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346 $Bond->SetAtoms($AtomsRef);
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347 $Bond->SetAtoms(@Atoms);
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348
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349 Set atoms of *Bond* to atoms in *Atoms* array or in a reference to
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350 an array of atoms and return *Bond*.
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351
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352 SetBondOrder
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353 $Bond->SetBondOrder($BondOrder);
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354
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355 Sets bond order of *Bond* to specified *BondOrder* and returns
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356 *Bond*. Possible bond order values: 1 = Single, 1.5 = Aromatic, 2 =
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357 Double, 3 = Triple, 4 = Quadruple, 5 = Quintuple, 6 = Sextuple, 7 =
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358 Septuple
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359
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360 Notes:
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361
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362 . BondType property is automatically assigned using default BondType
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363 values for specified BondOrder.
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364 . BondType values can also be explicit set.
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365 . To make bonds aromatic in a ring, explicitly set "Aromatic"
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366 property for bond/atoms and make sure appropriate BondOrder
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367 values are assigned.
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368 . Dative or coordinate bond types are treated as single bond types with
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369 explicit formal charge of + and - on first and second bond atoms.
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370
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371 SetBondType
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372 $Bond->SetBondType($BondType);
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373
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374 Sets bond type for *Bond* to specified *BondType* and returns
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375 *Bond*. Possible bond type values for different bond orders are:
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376
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377 0: None, Ionic, Unspecified
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378 1 : Single, Dative, Coordinate, SingleOrDouble, SingleOrAromatic, Tautomeric
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379 2 : Double, SingleOrDouble, DoubleOrAromatic, Tautomeric
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380 3 : Triple
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381 4 : Quadruple
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382 5 : Quintuple
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383 6 : Sextuple
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384 7 : Septuple
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385 1.5 : Aromatic, Resonance, SingleOrAromatic, DoubleOrAromatic
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386
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387 Notes:
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388
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389 o BondType Any is valid for all BondOrders.
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390 o BondOrder property is automatically assigned using default BondOrder
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391 values for specified BondType.
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392
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393 Possible bond stereochemistry values for different bond orders are:
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394
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395 0 : None, Unspecified
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396 1 : Wedge, Up, Hash, Down, Wavy, WedgeOrHash, UpOrDown, Upward, Downward,
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397 None, Unspecified
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398 2 : Cis, Trans, Z, E, DoubleCross, CisOrTrans, None, Unspecified
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399
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400 SetBondStereochemistry
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401 $Bond = $Bond->SetBondStereochemistry($BondStereochemistry);
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402
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403 Sets bond stereochemistry of *Bond* to specified
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404 *BondStereochemistry* and returns *Bond*. Possible
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405 *BondStereoChemistry* values for different bond orders are:
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406
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407 BondOrder: 1
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408
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409 None, Unspecified: Not a stereo bond or unspecified
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410
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411 Wedge, Up : Wedge end pointing up
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412 Hash, Down: Wedge end pointing down
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413 Wavy, WedgeOrHash, UpOrDown: Wedge end up or down
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414
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415 Upward: Single bond around cis/trans double bonds pointing upward
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416 Downward: Single bond around cis/trans double bonds pointing upward
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417
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418 Notes:
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419
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420 o Wedge starts at begin atom of a bond making wedge pointed end always
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421 at this atom.
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422 o Upward/downward bonds start at atoms involved in cis/trans double bonds.
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423
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424 BondOrder: 2
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425
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426 None, Unspecified: Not a stereo bond or unspecified
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427
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428 Z, cis: Similar groups on same side of double bond
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429 E, trans: Similar groups on different side of double bond
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430
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431 CisOrTrans, DoubleCross: cis or trans
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432
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433 StringifyBond
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434 $BondString = $Bond->StringifyBond();
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435
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436 Returns a string containing information about *bond* object.
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437
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438 SwitchBondFromAndToAtoms
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439 $Bond = $Bond->SwitchBondFromAndToAtoms();
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440
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441 Swaps bond from and to atoms in *Bond* and returns *Bond*.
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442
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443 AUTHOR
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444 Manish Sud <msud@san.rr.com>
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445
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446 SEE ALSO
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447 Atom.pm, Molecule.pm
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448
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449 COPYRIGHT
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450 Copyright (C) 2015 Manish Sud. All rights reserved.
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451
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452 This file is part of MayaChemTools.
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453
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454 MayaChemTools is free software; you can redistribute it and/or modify it
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455 under the terms of the GNU Lesser General Public License as published by
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456 the Free Software Foundation; either version 3 of the License, or (at
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457 your option) any later version.
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458
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