|
1
|
1 <html>
|
|
|
2 <head>
|
|
|
3 <title>MayaChemTools:Documentation:Bond.pm</title>
|
|
|
4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
|
|
|
5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css">
|
|
|
6 </head>
|
|
|
7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
|
|
|
8 <br/>
|
|
|
9 <center>
|
|
|
10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a>
|
|
|
11 </center>
|
|
|
12 <br/>
|
|
|
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> <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>
|
|
|
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<PropertyName>(<PropertyValue>);
|
|
|
49 <br/> $PropertyValue = Get<PropertyName>();
|
|
|
50 <br/> Delete<PropertyName>();</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 = ""
|
|
|
66 <br/> BondOrder = ""</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/> $DoubleBond = new Bond('Atoms' => [$Atom2, $Atom1],
|
|
|
73 'BondOrder' => 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->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->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->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 = $Bond->GetBondedAtom($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->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->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->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->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 = $Bond->GetCommonAtom($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->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->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->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->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 = $Bond->GetNumOfRingsWithSize($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 = $Bond->GetNumOfRingsWithSizeGreaterThan($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 = $Bond->GetNumOfRingsWithSizeLessThan($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->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->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->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 = $Bond->GetRingsWithSize($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 = $Bond->GetRingsWithSizeGreaterThan($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 = $Bond->GetRingsWithSizeLessThan($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->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->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->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->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->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->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->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->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->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->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->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->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->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->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->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 = $Bond->IsInRingOfSize($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->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->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->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->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->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->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->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->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->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->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->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->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->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->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->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 $Bond->SetAtoms($AtomsRef);
|
|
|
408 <br/> $Bond->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 $Bond->SetBondOrder($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 "Aromatic"
|
|
|
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 $Bond->SetBondType($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/> 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 = $Bond->SetBondStereochemistry($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->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->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>, <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> </p><p> </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> <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>
|
|
|
523 </table>
|
|
|
524 </div>
|
|
|
525 <br />
|
|
|
526 <center>
|
|
|
527 <img src="../../images/h2o2.png">
|
|
|
528 </center>
|
|
|
529 </body>
|
|
|
530 </html>
|
