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3 <title>MayaChemTools:Documentation:Bond.pm</title>
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14 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./BitVector.html" title="BitVector.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./Constants.html" title="Constants.html">Next</a></td><td width="34%" align="middle"><strong>Bond.pm</strong></td><td width="33%" align="right"><a href="././code/Bond.html" title="View source code">Code</a> | <a href="./../pdf/Bond.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/Bond.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/Bond.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/Bond.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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16 </table>
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17 </div>
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18 <p>
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19 </p>
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20 <h2>NAME</h2>
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21 <p>Bond</p>
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22 <p>
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23 </p>
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24 <h2>SYNOPSIS</h2>
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25 <p>use Bond;</p>
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26 <p>use Bond qw(:all);</p>
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27 <p>
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28 </p>
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29 <h2>DESCRIPTION</h2>
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30 <p><strong>Bond</strong> class provides the following methods:</p>
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31 <p> <a href="#new">new</a>, <a href="#copy">Copy</a>, <a href="#deletebond">DeleteBond</a>, <a href="#getatoms">GetAtoms</a>, <a href="#getbondbeginatom">GetBondBeginAtom</a>, <a href="#getbondendatom">GetBondEndAtom</a>
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32 , <a href="#getbondfromatom">GetBondFromAtom</a>, <a href="#getbondtoatom">GetBondToAtom</a>, <a href="#getbondedatom">GetBondedAtom</a>, <a href="#getcommonatom">GetCommonAtom</a>, <a href="#getlargestring">GetLargestRing</a>
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33 , <a href="#getnumofrings">GetNumOfRings</a>, <a href="#getnumofringswithevensize">GetNumOfRingsWithEvenSize</a>, <a href="#getnumofringswithoddsize">GetNumOfRingsWithOddSize</a>
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34 , <a href="#getnumofringswithsize">GetNumOfRingsWithSize</a>, <a href="#getnumofringswithsizegreaterthan">GetNumOfRingsWithSizeGreaterThan</a>
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35 , <a href="#getnumofringswithsizelessthan">GetNumOfRingsWithSizeLessThan</a>, <a href="#getrings">GetRings</a>, <a href="#getringswithevensize">GetRingsWithEvenSize</a>
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36 , <a href="#getringswithoddsize">GetRingsWithOddSize</a>, <a href="#getringswithsize">GetRingsWithSize</a>, <a href="#getringswithsizegreaterthan">GetRingsWithSizeGreaterThan</a>
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37 , <a href="#getringswithsizelessthan">GetRingsWithSizeLessThan</a>, <a href="#getsizeoflargestring">GetSizeOfLargestRing</a>, <a href="#getsizeofsmallestring">GetSizeOfSmallestRing</a>
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38 , <a href="#getsmallestring">GetSmallestRing</a>, <a href="#isaromatic">IsAromatic</a>, <a href="#isbondstereochemistryspecified">IsBondStereochemistrySpecified</a>, <a href="#isbondtypespecified">IsBondTypeSpecified</a>
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39 , <a href="#iscis">IsCis</a>, <a href="#iscisortrans">IsCisOrTrans</a>, <a href="#iscoordinate">IsCoordinate</a>, <a href="#isdative">IsDative</a>, <a href="#isdouble">IsDouble</a>, <a href="#isdown">IsDown</a>, <a href="#isdownward">IsDownward</a>, <a href="#ishash">IsHash</a>
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40 , <a href="#isinring">IsInRing</a>, <a href="#isinringofsize">IsInRingOfSize</a>, <a href="#isionic">IsIonic</a>, <a href="#isnotinring">IsNotInRing</a>, <a href="#isonlyinonering">IsOnlyInOneRing</a>, <a href="#isquadruple">IsQuadruple</a>
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41 , <a href="#isquintuple">IsQuintuple</a>, <a href="#issextuple">IsSextuple</a>, <a href="#issingle">IsSingle</a>, <a href="#istautomeric">IsTautomeric</a>, <a href="#istrans">IsTrans</a>, <a href="#istriple">IsTriple</a>, <a href="#isup">IsUp</a>
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42 , <a href="#isupordown">IsUpOrDown</a>, <a href="#isupward">IsUpward</a>, <a href="#iswedge">IsWedge</a>, <a href="#iswedgeorhash">IsWedgeOrHash</a>, <a href="#setatoms">SetAtoms</a>, <a href="#setbondorder">SetBondOrder</a>
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43 , <a href="#setbondstereochemistry">SetBondStereochemistry</a>, <a href="#setbondtype">SetBondType</a>, <a href="#stringifybond">StringifyBond</a>, <a href="#switchbondfromandtoatoms">SwitchBondFromAndToAtoms</a>
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44 </p><p><strong>Bond</strong> class is derived from <strong>ObjectProperty</strong> base class which provides methods not explicitly
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45 defined in <strong>Atom</strong> or <strong>ObjectProperty</strong> class using Perl's AUTOLOAD functionality. These methods
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46 are generated on-the-fly for a specified object property:</p>
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47 <div class="OptionsBox">
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48 Set<PropertyName>(<PropertyValue>);
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49 <br/> $PropertyValue = Get<PropertyName>();
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50 <br/> Delete<PropertyName>();</div>
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51 <p>
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52 </p>
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53 <h2>METHODS</h2>
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54 <dl>
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55 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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56 <dd>
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57 <div class="OptionsBox">
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58 $NewBond = new Bond([%PropertyNameAndValues]);</div>
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59 <p>Using specified <em>Bond</em> property names and values hash, <strong>new</strong> method creates a new object
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60 and returns a reference to newly created <strong>Bond</strong> object. By default, following properties are
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61 initialized:</p>
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62 <div class="OptionsBox">
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63 ID = SequentialObjectID
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64 <br/> @Atoms = ();
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65 <br/> BondType = ""
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66 <br/> BondOrder = ""</div>
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67 <p>Except for <em>ID</em> property, all other default properties and other additional properties can
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68 be set during invocation of this method.</p>
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69 <p>Examples:</p>
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70 <div class="OptionsBox">
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71 $Bond = new Bond();
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72 <br/> $DoubleBond = new Bond('Atoms' => [$Atom2, $Atom1],
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73 'BondOrder' => 2);</div>
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74 </dd>
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75 <dt><strong><a name="copy" class="item"><strong>Copy</strong></a></strong></dt>
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76 <dd>
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77 <div class="OptionsBox">
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78 $BondCopy = $Bond->Copy();</div>
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79 <p>Copy <em>Bond</em> and its associated data using <strong>Storable::dclone</strong> and return a new
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80 <strong>Bond</strong> object.</p>
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81 </dd>
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82 <dt><strong><a name="deletebond" class="item"><strong>DeleteBond</strong></a></strong></dt>
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83 <dd>
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84 <div class="OptionsBox">
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85 $Bond->DeleteBond();</div>
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86 <p>Delete <em>Bond</em> between atoms in from a molecule.</p>
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87 </dd>
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88 <dt><strong><a name="getatoms" class="item"><strong>GetAtoms</strong></a></strong></dt>
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89 <dd>
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90 <div class="OptionsBox">
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91 @BondedAtoms = $Bond->GetAtoms();</div>
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92 <p>Returns an array containing <em>Atoms</em> invoved in <em>Bond</em>.</p>
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93 </dd>
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94 <dt><strong><a name="getbondedatom" class="item"><strong>GetBondedAtom</strong></a></strong></dt>
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95 <dd>
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96 <div class="OptionsBox">
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97 $BondedAtom = $Bond->GetBondedAtom($Atom);</div>
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98 <p>Returns <strong>BondedAtom</strong> bonded to <em>Atom</em> in <em>Bond</em>.</p>
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99 </dd>
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100 <dt><strong><a name="getbondbeginatom" class="item"><strong>GetBondBeginAtom</strong></a></strong></dt>
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101 <dd>
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102 <div class="OptionsBox">
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103 $BeginAtom = $Bond->GetBondBeginAtom();</div>
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104 <p>Returns <strong>BeginAtom</strong> corresponding to bond starting atom in <em>Bond</em>.</p>
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105 </dd>
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106 <dt><strong><a name="getbondendatom" class="item"><strong>GetBondEndAtom</strong></a></strong></dt>
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107 <dd>
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108 <div class="OptionsBox">
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109 $EndAtom = $Bond->GetBondEndAtom();</div>
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110 <p>Returns <strong>EndAtom</strong> corresponding to bond ending atom in <em>Bond</em>.</p>
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111 </dd>
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112 <dt><strong><a name="getbondfromatom" class="item"><strong>GetBondFromAtom</strong></a></strong></dt>
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113 <dd>
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114 <div class="OptionsBox">
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115 $FromAtom = $Bond->GetBondFromAtom();</div>
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116 <p>Returns <strong>FromAtom</strong> corresponding to bond starting atom in <em>Bond</em>.</p>
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117 </dd>
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118 <dt><strong><a name="getbondtoatom" class="item"><strong>GetBondToAtom</strong></a></strong></dt>
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119 <dd>
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120 <div class="OptionsBox">
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121 $ToAotm = $Bond->GetBondToAtom();</div>
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122 <p>Returns <strong>ToAtom</strong> corresponding to bond ending atom in <em>Bond</em>.</p>
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123 </dd>
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124 <dt><strong><a name="getcommonatom" class="item"><strong>GetCommonAtom</strong></a></strong></dt>
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125 <dd>
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126 <div class="OptionsBox">
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127 $CommonAtom = $Bond->GetCommonAtom($OtherBond);</div>
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128 <p>Returns <strong>Atom</strong> common to both <em>Bond</em> and <em>$OtherBond</em>.</p>
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129 </dd>
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130 <dt><strong><a name="getlargestring" class="item"><strong>GetLargestRing</strong></a></strong></dt>
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131 <dd>
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132 <div class="OptionsBox">
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133 @RingAtoms = $Bond->GetLargestRing();</div>
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134 <p>Returns an array of ring <em>Atoms</em> corresponding to the largest ring containing <em>Bond</em>.
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135 in a molecule</p>
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136 </dd>
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137 <dt><strong><a name="getnumofrings" class="item"><strong>GetNumOfRings</strong></a></strong></dt>
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138 <dd>
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139 <div class="OptionsBox">
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140 $NumOfRings = $Bond->GetNumOfRings();</div>
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141 <p>Returns number of rings containing <em>Bond</em> in a molecule.</p>
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142 </dd>
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143 <dt><strong><a name="getnumofringswithevensize" class="item"><strong>GetNumOfRingsWithEvenSize</strong></a></strong></dt>
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144 <dd>
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145 <div class="OptionsBox">
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146 $NumOfRings = $Bond->GetNumOfRingsWithEvenSize();</div>
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147 <p>Returns number of rings with even size containing <em>Bond</em> in a molecule.</p>
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148 </dd>
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149 <dt><strong><a name="getnumofringswithoddsize" class="item"><strong>GetNumOfRingsWithOddSize</strong></a></strong></dt>
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150 <dd>
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151 <div class="OptionsBox">
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152 $NumOfRings = $Bond->GetNumOfRingsWithOddSize();</div>
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153 <p>Returns number of rings with odd size containing <em>Bond</em> in a molecule.</p>
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154 </dd>
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155 <dt><strong><a name="getnumofringswithsize" class="item"><strong>GetNumOfRingsWithSize</strong></a></strong></dt>
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156 <dd>
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157 <div class="OptionsBox">
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158 $NumOfRings = $Bond->GetNumOfRingsWithSize($RingSize);</div>
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159 <p>Returns number of rings with specific <em>RingSize</em> containing <em>Bond</em> in a molecule.</p>
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160 </dd>
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161 <dt><strong><a name="getnumofringswithsizegreaterthan" class="item"><strong>GetNumOfRingsWithSizeGreaterThan</strong></a></strong></dt>
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162 <dd>
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163 <div class="OptionsBox">
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164 $NumOfRings = $Bond->GetNumOfRingsWithSizeGreaterThan($RingSize);</div>
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165 <p>Returns number of rings with size greater than specific <em>RingSize</em> containing
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166 <em>Bond</em> in a molecule.</p>
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167 </dd>
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168 <dt><strong><a name="getnumofringswithsizelessthan" class="item"><strong>GetNumOfRingsWithSizeLessThan</strong></a></strong></dt>
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169 <dd>
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170 <div class="OptionsBox">
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171 $NumOfRings = $Bond->GetNumOfRingsWithSizeLessThan($RingSize);</div>
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172 <p>Returns number of rings with size less than specific <em>RingSize</em> containing <em>Bond</em>
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173 in a molecule.</p>
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174 </dd>
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175 <dt><strong><a name="getrings" class="item"><strong>GetRings</strong></a></strong></dt>
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176 <dd>
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177 <div class="OptionsBox">
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178 @Rings = $Bond->GetRings();</div>
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179 <p>Returns an array of references to arrays containing ring atoms corressponding
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180 to all rings containing <em>Bond</em> in a molecule.</p>
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181 </dd>
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182 <dt><strong><a name="getringswithevensize" class="item"><strong>GetRingsWithEvenSize</strong></a></strong></dt>
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183 <dd>
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184 <div class="OptionsBox">
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185 @Rings = $Bond->GetRingsWithEvenSize();</div>
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186 <p>Returns an array of references to arrays containing ring atoms corressponding to all rings with even size
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187 containing <em>Bond</em> in a molecule.</p>
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188 </dd>
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189 <dt><strong><a name="getringswithoddsize" class="item"><strong>GetRingsWithOddSize</strong></a></strong></dt>
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190 <dd>
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191 <div class="OptionsBox">
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192 @Rings = $Bond->GetRingsWithOddSize();</div>
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193 <p>Returns an array of references to arrays containing ring atoms corressponding to all rings with odd size
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194 containing <em>Bond</em> in a molecule.</p>
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195 </dd>
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196 <dt><strong><a name="getringswithsize" class="item"><strong>GetRingsWithSize</strong></a></strong></dt>
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197 <dd>
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198 <div class="OptionsBox">
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199 @Rings = $Bond->GetRingsWithSize($RingSize);</div>
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200 <p>Returns an array of references to arrays containing ring atoms corressponding to all rings with specific
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201 <em>RingSize </em>containing <em>Bond</em> in a molecule.</p>
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202 </dd>
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203 <dt><strong><a name="getringswithsizegreaterthan" class="item"><strong>GetRingsWithSizeGreaterThan</strong></a></strong></dt>
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204 <dd>
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205 <div class="OptionsBox">
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206 @Rings = $Bond->GetRingsWithSizeGreaterThan($RingSize);</div>
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207 <p>Returns an array of references to arrays containing ring atoms corressponding to all rings with size
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208 greater than specific <em>RingSize </em>containing <em>Bond</em> in a molecule.</p>
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209 </dd>
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210 <dt><strong><a name="getringswithsizelessthan" class="item"><strong>GetRingsWithSizeLessThan</strong></a></strong></dt>
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211 <dd>
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212 <div class="OptionsBox">
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213 @Rings = $Bond->GetRingsWithSizeLessThan($RingSize);</div>
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214 <p>Returns an array of references to arrays containing ring atoms corressponding to all rings with size
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215 less than specific <em>RingSize </em>containing <em>Bond</em> in a molecule.</p>
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216 </dd>
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217 <dt><strong><a name="getsizeoflargestring" class="item"><strong>GetSizeOfLargestRing</strong></a></strong></dt>
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218 <dd>
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219 <div class="OptionsBox">
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220 $Size = $Bond->GetSizeOfLargestRing();</div>
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221 <p>Returns size of the largest ring containing <em>Bond</em> in a molecule.</p>
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222 </dd>
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223 <dt><strong><a name="getsizeofsmallestring" class="item"><strong>GetSizeOfSmallestRing</strong></a></strong></dt>
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224 <dd>
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225 <div class="OptionsBox">
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226 $Size = $Bond->GetSizeOfSmallestRing();</div>
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227 <p>Returns size of the smallest ring containing <em>Bond</em> in a molecule.</p>
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228 </dd>
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229 <dt><strong><a name="getsmallestring" class="item"><strong>GetSmallestRing</strong></a></strong></dt>
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230 <dd>
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231 <div class="OptionsBox">
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232 @RingAtoms = $Bond->GetSmallestRing();</div>
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233 <p>Returns an array of ring <em>Atoms</em> corresponding to the largest ring containing <em>Bond</em>
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234 in a molecule.</p>
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235 </dd>
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236 <dt><strong><a name="isaromatic" class="item"><strong>IsAromatic</strong></a></strong></dt>
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237 <dd>
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238 <div class="OptionsBox">
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239 $Status = $Bond->IsAromatic();</div>
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240 <p>Returns 1 or 0 based on whether it's an aromatic <em>Bond</em>.</p>
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241 </dd>
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242 <dt><strong><a name="isbondstereochemistryspecified" class="item"><strong>IsBondStereochemistrySpecified</strong></a></strong></dt>
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243 <dd>
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244 <div class="OptionsBox">
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245 $Status = $Bond->IsBondStereochemistrySpecified();</div>
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246 <p>Returns 1 or 0 based on whether <em>Bond</em>'s sterochemistry is specified.</p>
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247 </dd>
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248 <dt><strong><a name="isbondtypespecified" class="item"><strong>IsBondTypeSpecified</strong></a></strong></dt>
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249 <dd>
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250 <div class="OptionsBox">
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251 $Status = $Bond->IsBondTypeSpecified();</div>
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252 <p>Returns 1 or 0 based on whether <em>Bond</em>'s type is specified.</p>
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253 </dd>
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254 <dt><strong><a name="iscis" class="item"><strong>IsCis</strong></a></strong></dt>
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255 <dd>
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256 <div class="OptionsBox">
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257 $Status = $Bond->IsCis();</div>
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258 <p>Returns 1 or 0 based on whether it's a cis <em>Bond</em>.</p>
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259 </dd>
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260 <dt><strong><a name="iscisortrans" class="item"><strong>IsCisOrTrans</strong></a></strong></dt>
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261 <dd>
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262 <div class="OptionsBox">
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263 $Status = $Bond->IsCisOrTrans();</div>
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264 <p>Returns 1 or 0 based on whether it's a cis or trans <em>Bond</em>.</p>
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265 </dd>
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266 <dt><strong><a name="iscoordinate" class="item"><strong>IsCoordinate</strong></a></strong></dt>
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267 <dd>
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268 <div class="OptionsBox">
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269 $Status = $Bond->IsCoordinate();</div>
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270 <p>Returns 1 or 0 based on whether it's a coordinate or dative <em>Bond</em>.</p>
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271 </dd>
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272 <dt><strong><a name="isdative" class="item"><strong>IsDative</strong></a></strong></dt>
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273 <dd>
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274 <div class="OptionsBox">
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275 $Status = $Bond->IsDative();</div>
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276 <p>Returns 1 or 0 based on whether it's a coordinate or dative <em>Bond</em>.</p>
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277 </dd>
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278 <dt><strong><a name="isdouble" class="item"><strong>IsDouble</strong></a></strong></dt>
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279 <dd>
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280 <div class="OptionsBox">
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281 $Status =$Bond->IsDouble();</div>
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282 <p>Returns 1 or 0 based on whether it's a double <em>Bond</em>.</p>
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283 </dd>
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284 <dt><strong><a name="isdown" class="item"><strong>IsDown</strong></a></strong></dt>
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285 <dd>
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286 <div class="OptionsBox">
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287 $Status = $Bond->IsDown();</div>
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288 <p>Returns 1 or 0 based on whether it's a hash or down single <em>Bond</em>.</p>
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289 </dd>
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290 <dt><strong><a name="isdownward" class="item"><strong>IsDownward</strong></a></strong></dt>
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291 <dd>
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292 <div class="OptionsBox">
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293 $Return = $Bond->IsDownward();</div>
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294 <p>Returns 1 or 0 based on whether it's a downward <em>Bond</em>.</p>
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295 </dd>
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296 <dt><strong><a name="ishash" class="item"><strong>IsHash</strong></a></strong></dt>
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297 <dd>
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298 <div class="OptionsBox">
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299 $Status = $Bond->IsHash();</div>
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300 <p>Returns 1 or 0 based on whether it's a hash or down single <em>Bond</em>.</p>
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301 </dd>
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302 <dt><strong><a name="isinring" class="item"><strong>IsInRing</strong></a></strong></dt>
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303 <dd>
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304 <div class="OptionsBox">
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305 $Status = $Bond->IsInRing();</div>
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306 <p>Returns 1 or 0 based on whether <em>Bond</em> is present in a ring.</p>
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307 </dd>
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308 <dt><strong><a name="isinringofsize" class="item"><strong>IsInRingOfSize</strong></a></strong></dt>
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309 <dd>
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310 <div class="OptionsBox">
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311 $Status = $Bond->IsInRingOfSize($Size);</div>
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312 <p>Returns 1 or 0 based on whether <em>Bond</em> is present in a ring of specific <em>Size</em>.</p>
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313 </dd>
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314 <dt><strong><a name="isionic" class="item"><strong>IsIonic</strong></a></strong></dt>
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315 <dd>
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316 <div class="OptionsBox">
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317 $Status = $Bond->IsIonic();</div>
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318 <p>Returns 1 or 0 based on whether it's an ionic <em>Bond</em>.</p>
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319 </dd>
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320 <dt><strong><a name="isnotinring" class="item"><strong>IsNotInRing</strong></a></strong></dt>
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321 <dd>
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322 <div class="OptionsBox">
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323 $Status = $Bond->IsNotInRing();</div>
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324 <p>Returns 1 or 0 based on whether <em>Bond</em> is not present in a ring.</p>
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325 </dd>
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326 <dt><strong><a name="isonlyinonering" class="item"><strong>IsOnlyInOneRing</strong></a></strong></dt>
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327 <dd>
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328 <div class="OptionsBox">
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329 $Status = $Bond->IsOnlyInOneRing();</div>
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330 <p>Returns 1 or 0 based on whether <em>Bond</em> is only present in one ring.</p>
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331 </dd>
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332 <dt><strong><a name="isquadruple" class="item"><strong>IsQuadruple</strong></a></strong></dt>
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333 <dd>
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334 <div class="OptionsBox">
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335 $Status = $Bond->IsQuadruple();</div>
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336 <p>Returns 1 or 0 based on whether it's a quadruple <em>Bond</em>.</p>
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337 </dd>
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338 <dt><strong><a name="isquintuple" class="item"><strong>IsQuintuple</strong></a></strong></dt>
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339 <dd>
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340 <div class="OptionsBox">
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341 $Status = $Bond->IsQuintuple();</div>
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342 <p>Returns 1 or 0 based on whether it's a quintuple <em>Bond</em>.</p>
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343 </dd>
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344 <dt><strong><a name="issextuple" class="item"><strong>IsSextuple</strong></a></strong></dt>
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345 <dd>
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346 <div class="OptionsBox">
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347 $Status = $Bond->IsSextuple();</div>
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348 <p>Returns 1 or 0 based on whether it's a sextuple <em>Bond</em>.</p>
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349 </dd>
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350 <dt><strong><a name="issingle" class="item"><strong>IsSingle</strong></a></strong></dt>
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351 <dd>
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352 <div class="OptionsBox">
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353 $Status =$Bond->IsSingle();</div>
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354 <p>Returns 1 or 0 based on whether it's a single <em>Bond</em>.</p>
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355 </dd>
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356 <dt><strong><a name="istriple" class="item"><strong>IsTriple</strong></a></strong></dt>
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357 <dd>
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358 <div class="OptionsBox">
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359 $Status =$Bond->IsTriple();</div>
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360 <p>Returns 1 or 0 based on whether it's a triple <em>Bond</em>.</p>
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361 </dd>
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362 <dt><strong><a name="istautomeric" class="item"><strong>IsTautomeric</strong></a></strong></dt>
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363 <dd>
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364 <div class="OptionsBox">
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365 $Status = $Bond->IsTautomeric();</div>
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366 <p>Returns 1 or 0 based on whether it's a <em>Bond</em>.</p>
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367 </dd>
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368 <dt><strong><a name="istrans" class="item"><strong>IsTrans</strong></a></strong></dt>
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369 <dd>
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370 <div class="OptionsBox">
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371 $Status = $Bond->IsTrans();</div>
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372 <p>Returns 1 or 0 based on whether it's a trans <em>Bond</em>.</p>
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373 </dd>
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374 <dt><strong><a name="isup" class="item"><strong>IsUp</strong></a></strong></dt>
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375 <dd>
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376 <div class="OptionsBox">
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377 $Status = $Bond->IsUp();</div>
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378 <p>Returns 1 or 0 based on whether it's a up <em>Bond</em>.</p>
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379 </dd>
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380 <dt><strong><a name="isupordown" class="item"><strong>IsUpOrDown</strong></a></strong></dt>
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381 <dd>
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382 <div class="OptionsBox">
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383 $Status = $Bond->IsUpOrDown();</div>
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384 <p>Returns 1 or 0 based on whether it's an up or down <em>Bond</em>.</p>
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385 </dd>
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386 <dt><strong><a name="isupward" class="item"><strong>IsUpward</strong></a></strong></dt>
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387 <dd>
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388 <div class="OptionsBox">
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389 $Status = $Bond->IsUpward();</div>
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390 <p>Returns 1 or 0 based on whether it's an upward <em>Bond</em>.</p>
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391 </dd>
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392 <dt><strong><a name="iswedge" class="item"><strong>IsWedge</strong></a></strong></dt>
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393 <dd>
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394 <div class="OptionsBox">
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395 $Status = $Bond->IsWedge();</div>
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396 <p>Returns 1 or 0 based on whether it's a wedge <em>Bond</em>.</p>
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397 </dd>
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398 <dt><strong><a name="iswedgeorhash" class="item"><strong>IsWedgeOrHash</strong></a></strong></dt>
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399 <dd>
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400 <div class="OptionsBox">
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401 $Status = $Bond->IsWedgeOrHash();</div>
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402 <p>Returns 1 or 0 based on whether it's a wedge or hash <em>Bond</em>.</p>
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403 </dd>
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404 <dt><strong><a name="setatoms" class="item"><strong>SetAtoms</strong></a></strong></dt>
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405 <dd>
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406 <div class="OptionsBox">
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407 $Bond->SetAtoms($AtomsRef);
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408 <br/> $Bond->SetAtoms(@Atoms);</div>
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409 <p>Set atoms of <em>Bond</em> to atoms in <em>Atoms</em> array or in a reference to an array of atoms
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410 and return <em>Bond</em>.</p>
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411 </dd>
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412 <dt><strong><a name="setbondorder" class="item"><strong>SetBondOrder</strong></a></strong></dt>
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413 <dd>
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414 <div class="OptionsBox">
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415 $Bond->SetBondOrder($BondOrder);</div>
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416 <p>Sets bond order of <em>Bond</em> to specified <em>BondOrder</em> and returns <em>Bond</em>. Possible bond order
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417 values: 1 = Single, 1.5 = Aromatic, 2 = Double, 3 = Triple, 4 = Quadruple, 5 = Quintuple,
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418 6 = Sextuple, 7 = Septuple</p>
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419 <p>Notes:</p>
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420 <div class="OptionsBox">
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421 . BondType property is automatically assigned using default BondType
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422 values for specified BondOrder.
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423 <br/> . BondType values can also be explicit set.
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424 <br/> . To make bonds aromatic in a ring, explicitly set "Aromatic"
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425 property for bond/atoms and make sure appropriate BondOrder
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426 values are assigned.
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427 <br/> . Dative or coordinate bond types are treated as single bond types with
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428 explicit formal charge of + and - on first and second bond atoms.</div>
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429 </dd>
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430 <dt><strong><a name="setbondtype" class="item"><strong>SetBondType</strong></a></strong></dt>
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431 <dd>
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432 <div class="OptionsBox">
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433 $Bond->SetBondType($BondType);</div>
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434 <p>Sets bond type for <em>Bond</em> to specified <em>BondType</em> and returns <em>Bond</em>. Possible bond type
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435 values for different bond orders are:</p>
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436 <div class="OptionsBox">
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437 0: None, Ionic, Unspecified
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438 <br/> 1 : Single, Dative, Coordinate, SingleOrDouble, SingleOrAromatic, Tautomeric
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439 <br/> 2 : Double, SingleOrDouble, DoubleOrAromatic, Tautomeric
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440 <br/> 3 : Triple
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441 <br/> 4 : Quadruple
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442 <br/> 5 : Quintuple
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443 <br/> 6 : Sextuple
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444 <br/> 7 : Septuple
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445 <br/> 1.5 : Aromatic, Resonance, SingleOrAromatic, DoubleOrAromatic</div>
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446 <p>Notes:</p>
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447 <div class="OptionsBox">
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448 o BondType Any is valid for all BondOrders.
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449 <br/> o BondOrder property is automatically assigned using default BondOrder
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450 values for specified BondType.</div>
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451 <p>Possible bond stereochemistry values for different bond orders are:</p>
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452 <div class="OptionsBox">
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453 0 : None, Unspecified
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454 <br/> 1 : Wedge, Up, Hash, Down, Wavy, WedgeOrHash, UpOrDown, Upward, Downward,
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455 <br/> None, Unspecified
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456 <br/> 2 : Cis, Trans, Z, E, DoubleCross, CisOrTrans, None, Unspecified</div>
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457 </dd>
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458 <dt><strong><a name="setbondstereochemistry" class="item"><strong>SetBondStereochemistry</strong></a></strong></dt>
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459 <dd>
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460 <div class="OptionsBox">
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461 $Bond = $Bond->SetBondStereochemistry($BondStereochemistry);</div>
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462 <p>Sets bond stereochemistry of <em>Bond</em> to specified <em>BondStereochemistry</em> and
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463 returns <em>Bond</em>. Possible <em>BondStereoChemistry</em> values for different bond orders
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464 are:</p>
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465 <p>BondOrder: 1</p>
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466 <div class="OptionsBox">
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467 None, Unspecified: Not a stereo bond or unspecified</div>
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468 <div class="OptionsBox">
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469 Wedge, Up : Wedge end pointing up
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470 <br/> Hash, Down: Wedge end pointing down
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471 <br/> Wavy, WedgeOrHash, UpOrDown: Wedge end up or down</div>
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472 <div class="OptionsBox">
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473 Upward: Single bond around cis/trans double bonds pointing upward
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474 <br/> Downward: Single bond around cis/trans double bonds pointing upward</div>
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475 <p>Notes:</p>
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476 <div class="OptionsBox">
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477 o Wedge starts at begin atom of a bond making wedge pointed end always
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478 at this atom.
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479 <br/> o Upward/downward bonds start at atoms involved in cis/trans double bonds.</div>
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480 <p>BondOrder: 2</p>
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481 <div class="OptionsBox">
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482 None, Unspecified: Not a stereo bond or unspecified</div>
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483 <div class="OptionsBox">
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484 Z, cis: Similar groups on same side of double bond
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485 <br/> E, trans: Similar groups on different side of double bond</div>
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486 <div class="OptionsBox">
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487 CisOrTrans, DoubleCross: cis or trans</div>
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488 </dd>
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489 <dt><strong><a name="stringifybond" class="item"><strong>StringifyBond</strong></a></strong></dt>
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490 <dd>
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491 <div class="OptionsBox">
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492 $BondString = $Bond->StringifyBond();</div>
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493 <p>Returns a string containing information about <em>bond</em> object.</p>
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494 </dd>
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495 <dt><strong><a name="switchbondfromandtoatoms" class="item"><strong>SwitchBondFromAndToAtoms</strong></a></strong></dt>
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496 <dd>
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497 <div class="OptionsBox">
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498 $Bond = $Bond->SwitchBondFromAndToAtoms();</div>
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499 <p>Swaps bond from and to atoms in <em>Bond</em> and returns <em>Bond</em>.</p>
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500 </dd>
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501 </dl>
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502 <p>
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503 </p>
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504 <h2>AUTHOR</h2>
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505 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
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506 <p>
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507 </p>
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508 <h2>SEE ALSO</h2>
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509 <p><a href="./Atom.html">Atom.pm</a>, <a href="./Molecule.html">Molecule.pm</a>
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510 </p>
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511 <p>
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512 </p>
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513 <h2>COPYRIGHT</h2>
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514 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
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515 <p>This file is part of MayaChemTools.</p>
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516 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
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517 the terms of the GNU Lesser General Public License as published by the Free
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518 Software Foundation; either version 3 of the License, or (at your option)
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519 any later version.</p>
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520 <p> </p><p> </p><div class="DocNav">
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521 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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522 <tr align="left" valign="top"><td width="33%" align="left"><a href="./BitVector.html" title="BitVector.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./Constants.html" title="Constants.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Bond.pm</strong></td></tr>
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523 </table>
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524 </div>
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525 <br />
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526 <center>
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527 <img src="../../images/h2o2.png">
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528 </center>
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529 </body>
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530 </html>
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