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