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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/Bond.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,530 @@ +<html> +<head> +<title>MayaChemTools:Documentation:Bond.pm</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<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> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>Bond</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>use Bond;</p> +<p>use Bond qw(:all);</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p><strong>Bond</strong> class provides the following methods:</p> +<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> +, <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> +, <a href="#getnumofrings">GetNumOfRings</a>, <a href="#getnumofringswithevensize">GetNumOfRingsWithEvenSize</a>, <a href="#getnumofringswithoddsize">GetNumOfRingsWithOddSize</a> +, <a href="#getnumofringswithsize">GetNumOfRingsWithSize</a>, <a href="#getnumofringswithsizegreaterthan">GetNumOfRingsWithSizeGreaterThan</a> +, <a href="#getnumofringswithsizelessthan">GetNumOfRingsWithSizeLessThan</a>, <a href="#getrings">GetRings</a>, <a href="#getringswithevensize">GetRingsWithEvenSize</a> +, <a href="#getringswithoddsize">GetRingsWithOddSize</a>, <a href="#getringswithsize">GetRingsWithSize</a>, <a href="#getringswithsizegreaterthan">GetRingsWithSizeGreaterThan</a> +, <a href="#getringswithsizelessthan">GetRingsWithSizeLessThan</a>, <a href="#getsizeoflargestring">GetSizeOfLargestRing</a>, <a href="#getsizeofsmallestring">GetSizeOfSmallestRing</a> +, <a href="#getsmallestring">GetSmallestRing</a>, <a href="#isaromatic">IsAromatic</a>, <a href="#isbondstereochemistryspecified">IsBondStereochemistrySpecified</a>, <a href="#isbondtypespecified">IsBondTypeSpecified</a> +, <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> +, <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> +, <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> +, <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> +, <a href="#setbondstereochemistry">SetBondStereochemistry</a>, <a href="#setbondtype">SetBondType</a>, <a href="#stringifybond">StringifyBond</a>, <a href="#switchbondfromandtoatoms">SwitchBondFromAndToAtoms</a> +</p><p><strong>Bond</strong> class is derived from <strong>ObjectProperty</strong> base class which provides methods not explicitly +defined in <strong>Atom</strong> or <strong>ObjectProperty</strong> class using Perl's AUTOLOAD functionality. These methods +are generated on-the-fly for a specified object property:</p> +<div class="OptionsBox"> + Set<PropertyName>(<PropertyValue>); +<br/> $PropertyValue = Get<PropertyName>(); +<br/> Delete<PropertyName>();</div> +<p> +</p> +<h2>METHODS</h2> +<dl> +<dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NewBond = new Bond([%PropertyNameAndValues]);</div> +<p>Using specified <em>Bond</em> property names and values hash, <strong>new</strong> method creates a new object +and returns a reference to newly created <strong>Bond</strong> object. By default, following properties are +initialized:</p> +<div class="OptionsBox"> + ID = SequentialObjectID +<br/> @Atoms = (); +<br/> BondType = "" +<br/> BondOrder = ""</div> +<p>Except for <em>ID</em> property, all other default properties and other additional properties can +be set during invocation of this method.</p> +<p>Examples:</p> +<div class="OptionsBox"> + $Bond = new Bond(); +<br/> $DoubleBond = new Bond('Atoms' => [$Atom2, $Atom1], + 'BondOrder' => 2);</div> +</dd> +<dt><strong><a name="copy" class="item"><strong>Copy</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $BondCopy = $Bond->Copy();</div> +<p>Copy <em>Bond</em> and its associated data using <strong>Storable::dclone</strong> and return a new +<strong>Bond</strong> object.</p> +</dd> +<dt><strong><a name="deletebond" class="item"><strong>DeleteBond</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Bond->DeleteBond();</div> +<p>Delete <em>Bond</em> between atoms in from a molecule.</p> +</dd> +<dt><strong><a name="getatoms" class="item"><strong>GetAtoms</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @BondedAtoms = $Bond->GetAtoms();</div> +<p>Returns an array containing <em>Atoms</em> invoved in <em>Bond</em>.</p> +</dd> +<dt><strong><a name="getbondedatom" class="item"><strong>GetBondedAtom</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $BondedAtom = $Bond->GetBondedAtom($Atom);</div> +<p>Returns <strong>BondedAtom</strong> bonded to <em>Atom</em> in <em>Bond</em>.</p> +</dd> +<dt><strong><a name="getbondbeginatom" class="item"><strong>GetBondBeginAtom</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $BeginAtom = $Bond->GetBondBeginAtom();</div> +<p>Returns <strong>BeginAtom</strong> corresponding to bond starting atom in <em>Bond</em>.</p> +</dd> +<dt><strong><a name="getbondendatom" class="item"><strong>GetBondEndAtom</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $EndAtom = $Bond->GetBondEndAtom();</div> +<p>Returns <strong>EndAtom</strong> corresponding to bond ending atom in <em>Bond</em>.</p> +</dd> +<dt><strong><a name="getbondfromatom" class="item"><strong>GetBondFromAtom</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $FromAtom = $Bond->GetBondFromAtom();</div> +<p>Returns <strong>FromAtom</strong> corresponding to bond starting atom in <em>Bond</em>.</p> +</dd> +<dt><strong><a name="getbondtoatom" class="item"><strong>GetBondToAtom</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $ToAotm = $Bond->GetBondToAtom();</div> +<p>Returns <strong>ToAtom</strong> corresponding to bond ending atom in <em>Bond</em>.</p> +</dd> +<dt><strong><a name="getcommonatom" class="item"><strong>GetCommonAtom</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $CommonAtom = $Bond->GetCommonAtom($OtherBond);</div> +<p>Returns <strong>Atom</strong> common to both <em>Bond</em> and <em>$OtherBond</em>.</p> +</dd> +<dt><strong><a name="getlargestring" class="item"><strong>GetLargestRing</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @RingAtoms = $Bond->GetLargestRing();</div> +<p>Returns an array of ring <em>Atoms</em> corresponding to the largest ring containing <em>Bond</em>. +in a molecule</p> +</dd> +<dt><strong><a name="getnumofrings" class="item"><strong>GetNumOfRings</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NumOfRings = $Bond->GetNumOfRings();</div> +<p>Returns number of rings containing <em>Bond</em> in a molecule.</p> +</dd> +<dt><strong><a name="getnumofringswithevensize" class="item"><strong>GetNumOfRingsWithEvenSize</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NumOfRings = $Bond->GetNumOfRingsWithEvenSize();</div> +<p>Returns number of rings with even size containing <em>Bond</em> in a molecule.</p> +</dd> +<dt><strong><a name="getnumofringswithoddsize" class="item"><strong>GetNumOfRingsWithOddSize</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NumOfRings = $Bond->GetNumOfRingsWithOddSize();</div> +<p>Returns number of rings with odd size containing <em>Bond</em> in a molecule.</p> +</dd> +<dt><strong><a name="getnumofringswithsize" class="item"><strong>GetNumOfRingsWithSize</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NumOfRings = $Bond->GetNumOfRingsWithSize($RingSize);</div> +<p>Returns number of rings with specific <em>RingSize</em> containing <em>Bond</em> in a molecule.</p> +</dd> +<dt><strong><a name="getnumofringswithsizegreaterthan" class="item"><strong>GetNumOfRingsWithSizeGreaterThan</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NumOfRings = $Bond->GetNumOfRingsWithSizeGreaterThan($RingSize);</div> +<p>Returns number of rings with size greater than specific <em>RingSize</em> containing +<em>Bond</em> in a molecule.</p> +</dd> +<dt><strong><a name="getnumofringswithsizelessthan" class="item"><strong>GetNumOfRingsWithSizeLessThan</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NumOfRings = $Bond->GetNumOfRingsWithSizeLessThan($RingSize);</div> +<p>Returns number of rings with size less than specific <em>RingSize</em> containing <em>Bond</em> +in a molecule.</p> +</dd> +<dt><strong><a name="getrings" class="item"><strong>GetRings</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @Rings = $Bond->GetRings();</div> +<p>Returns an array of references to arrays containing ring atoms corressponding +to all rings containing <em>Bond</em> in a molecule.</p> +</dd> +<dt><strong><a name="getringswithevensize" class="item"><strong>GetRingsWithEvenSize</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @Rings = $Bond->GetRingsWithEvenSize();</div> +<p>Returns an array of references to arrays containing ring atoms corressponding to all rings with even size +containing <em>Bond</em> in a molecule.</p> +</dd> +<dt><strong><a name="getringswithoddsize" class="item"><strong>GetRingsWithOddSize</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @Rings = $Bond->GetRingsWithOddSize();</div> +<p>Returns an array of references to arrays containing ring atoms corressponding to all rings with odd size +containing <em>Bond</em> in a molecule.</p> +</dd> +<dt><strong><a name="getringswithsize" class="item"><strong>GetRingsWithSize</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @Rings = $Bond->GetRingsWithSize($RingSize);</div> +<p>Returns an array of references to arrays containing ring atoms corressponding to all rings with specific +<em>RingSize </em>containing <em>Bond</em> in a molecule.</p> +</dd> +<dt><strong><a name="getringswithsizegreaterthan" class="item"><strong>GetRingsWithSizeGreaterThan</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @Rings = $Bond->GetRingsWithSizeGreaterThan($RingSize);</div> +<p>Returns an array of references to arrays containing ring atoms corressponding to all rings with size +greater than specific <em>RingSize </em>containing <em>Bond</em> in a molecule.</p> +</dd> +<dt><strong><a name="getringswithsizelessthan" class="item"><strong>GetRingsWithSizeLessThan</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @Rings = $Bond->GetRingsWithSizeLessThan($RingSize);</div> +<p>Returns an array of references to arrays containing ring atoms corressponding to all rings with size +less than specific <em>RingSize </em>containing <em>Bond</em> in a molecule.</p> +</dd> +<dt><strong><a name="getsizeoflargestring" class="item"><strong>GetSizeOfLargestRing</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Size = $Bond->GetSizeOfLargestRing();</div> +<p>Returns size of the largest ring containing <em>Bond</em> in a molecule.</p> +</dd> +<dt><strong><a name="getsizeofsmallestring" class="item"><strong>GetSizeOfSmallestRing</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Size = $Bond->GetSizeOfSmallestRing();</div> +<p>Returns size of the smallest ring containing <em>Bond</em> in a molecule.</p> +</dd> +<dt><strong><a name="getsmallestring" class="item"><strong>GetSmallestRing</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @RingAtoms = $Bond->GetSmallestRing();</div> +<p>Returns an array of ring <em>Atoms</em> corresponding to the largest ring containing <em>Bond</em> +in a molecule.</p> +</dd> +<dt><strong><a name="isaromatic" class="item"><strong>IsAromatic</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsAromatic();</div> +<p>Returns 1 or 0 based on whether it's an aromatic <em>Bond</em>.</p> +</dd> +<dt><strong><a name="isbondstereochemistryspecified" class="item"><strong>IsBondStereochemistrySpecified</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsBondStereochemistrySpecified();</div> +<p>Returns 1 or 0 based on whether <em>Bond</em>'s sterochemistry is specified.</p> +</dd> +<dt><strong><a name="isbondtypespecified" class="item"><strong>IsBondTypeSpecified</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsBondTypeSpecified();</div> +<p>Returns 1 or 0 based on whether <em>Bond</em>'s type is specified.</p> +</dd> +<dt><strong><a name="iscis" class="item"><strong>IsCis</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsCis();</div> +<p>Returns 1 or 0 based on whether it's a cis <em>Bond</em>.</p> +</dd> +<dt><strong><a name="iscisortrans" class="item"><strong>IsCisOrTrans</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsCisOrTrans();</div> +<p>Returns 1 or 0 based on whether it's a cis or trans <em>Bond</em>.</p> +</dd> +<dt><strong><a name="iscoordinate" class="item"><strong>IsCoordinate</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsCoordinate();</div> +<p>Returns 1 or 0 based on whether it's a coordinate or dative <em>Bond</em>.</p> +</dd> +<dt><strong><a name="isdative" class="item"><strong>IsDative</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsDative();</div> +<p>Returns 1 or 0 based on whether it's a coordinate or dative <em>Bond</em>.</p> +</dd> +<dt><strong><a name="isdouble" class="item"><strong>IsDouble</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status =$Bond->IsDouble();</div> +<p>Returns 1 or 0 based on whether it's a double <em>Bond</em>.</p> +</dd> +<dt><strong><a name="isdown" class="item"><strong>IsDown</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsDown();</div> +<p>Returns 1 or 0 based on whether it's a hash or down single <em>Bond</em>.</p> +</dd> +<dt><strong><a name="isdownward" class="item"><strong>IsDownward</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Return = $Bond->IsDownward();</div> +<p>Returns 1 or 0 based on whether it's a downward <em>Bond</em>.</p> +</dd> +<dt><strong><a name="ishash" class="item"><strong>IsHash</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsHash();</div> +<p>Returns 1 or 0 based on whether it's a hash or down single <em>Bond</em>.</p> +</dd> +<dt><strong><a name="isinring" class="item"><strong>IsInRing</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsInRing();</div> +<p>Returns 1 or 0 based on whether <em>Bond</em> is present in a ring.</p> +</dd> +<dt><strong><a name="isinringofsize" class="item"><strong>IsInRingOfSize</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsInRingOfSize($Size);</div> +<p>Returns 1 or 0 based on whether <em>Bond</em> is present in a ring of specific <em>Size</em>.</p> +</dd> +<dt><strong><a name="isionic" class="item"><strong>IsIonic</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsIonic();</div> +<p>Returns 1 or 0 based on whether it's an ionic <em>Bond</em>.</p> +</dd> +<dt><strong><a name="isnotinring" class="item"><strong>IsNotInRing</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsNotInRing();</div> +<p>Returns 1 or 0 based on whether <em>Bond</em> is not present in a ring.</p> +</dd> +<dt><strong><a name="isonlyinonering" class="item"><strong>IsOnlyInOneRing</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsOnlyInOneRing();</div> +<p>Returns 1 or 0 based on whether <em>Bond</em> is only present in one ring.</p> +</dd> +<dt><strong><a name="isquadruple" class="item"><strong>IsQuadruple</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsQuadruple();</div> +<p>Returns 1 or 0 based on whether it's a quadruple <em>Bond</em>.</p> +</dd> +<dt><strong><a name="isquintuple" class="item"><strong>IsQuintuple</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsQuintuple();</div> +<p>Returns 1 or 0 based on whether it's a quintuple <em>Bond</em>.</p> +</dd> +<dt><strong><a name="issextuple" class="item"><strong>IsSextuple</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsSextuple();</div> +<p>Returns 1 or 0 based on whether it's a sextuple <em>Bond</em>.</p> +</dd> +<dt><strong><a name="issingle" class="item"><strong>IsSingle</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status =$Bond->IsSingle();</div> +<p>Returns 1 or 0 based on whether it's a single <em>Bond</em>.</p> +</dd> +<dt><strong><a name="istriple" class="item"><strong>IsTriple</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status =$Bond->IsTriple();</div> +<p>Returns 1 or 0 based on whether it's a triple <em>Bond</em>.</p> +</dd> +<dt><strong><a name="istautomeric" class="item"><strong>IsTautomeric</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsTautomeric();</div> +<p>Returns 1 or 0 based on whether it's a <em>Bond</em>.</p> +</dd> +<dt><strong><a name="istrans" class="item"><strong>IsTrans</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsTrans();</div> +<p>Returns 1 or 0 based on whether it's a trans <em>Bond</em>.</p> +</dd> +<dt><strong><a name="isup" class="item"><strong>IsUp</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsUp();</div> +<p>Returns 1 or 0 based on whether it's a up <em>Bond</em>.</p> +</dd> +<dt><strong><a name="isupordown" class="item"><strong>IsUpOrDown</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsUpOrDown();</div> +<p>Returns 1 or 0 based on whether it's an up or down <em>Bond</em>.</p> +</dd> +<dt><strong><a name="isupward" class="item"><strong>IsUpward</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsUpward();</div> +<p>Returns 1 or 0 based on whether it's an upward <em>Bond</em>.</p> +</dd> +<dt><strong><a name="iswedge" class="item"><strong>IsWedge</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsWedge();</div> +<p>Returns 1 or 0 based on whether it's a wedge <em>Bond</em>.</p> +</dd> +<dt><strong><a name="iswedgeorhash" class="item"><strong>IsWedgeOrHash</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Bond->IsWedgeOrHash();</div> +<p>Returns 1 or 0 based on whether it's a wedge or hash <em>Bond</em>.</p> +</dd> +<dt><strong><a name="setatoms" class="item"><strong>SetAtoms</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Bond->SetAtoms($AtomsRef); +<br/> $Bond->SetAtoms(@Atoms);</div> +<p>Set atoms of <em>Bond</em> to atoms in <em>Atoms</em> array or in a reference to an array of atoms +and return <em>Bond</em>.</p> +</dd> +<dt><strong><a name="setbondorder" class="item"><strong>SetBondOrder</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Bond->SetBondOrder($BondOrder);</div> +<p>Sets bond order of <em>Bond</em> to specified <em>BondOrder</em> and returns <em>Bond</em>. Possible bond order +values: 1 = Single, 1.5 = Aromatic, 2 = Double, 3 = Triple, 4 = Quadruple, 5 = Quintuple, +6 = Sextuple, 7 = Septuple</p> +<p>Notes:</p> +<div class="OptionsBox"> + . BondType property is automatically assigned using default BondType + values for specified BondOrder. +<br/> . BondType values can also be explicit set. +<br/> . To make bonds aromatic in a ring, explicitly set "Aromatic" + property for bond/atoms and make sure appropriate BondOrder + values are assigned. +<br/> . Dative or coordinate bond types are treated as single bond types with + explicit formal charge of + and - on first and second bond atoms.</div> +</dd> +<dt><strong><a name="setbondtype" class="item"><strong>SetBondType</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Bond->SetBondType($BondType);</div> +<p>Sets bond type for <em>Bond</em> to specified <em>BondType</em> and returns <em>Bond</em>. Possible bond type +values for different bond orders are:</p> +<div class="OptionsBox"> + 0: None, Ionic, Unspecified +<br/> 1 : Single, Dative, Coordinate, SingleOrDouble, SingleOrAromatic, Tautomeric +<br/> 2 : Double, SingleOrDouble, DoubleOrAromatic, Tautomeric +<br/> 3 : Triple +<br/> 4 : Quadruple +<br/> 5 : Quintuple +<br/> 6 : Sextuple +<br/> 7 : Septuple +<br/> 1.5 : Aromatic, Resonance, SingleOrAromatic, DoubleOrAromatic</div> +<p>Notes:</p> +<div class="OptionsBox"> + o BondType Any is valid for all BondOrders. +<br/> o BondOrder property is automatically assigned using default BondOrder + values for specified BondType.</div> +<p>Possible bond stereochemistry values for different bond orders are:</p> +<div class="OptionsBox"> + 0 : None, Unspecified +<br/> 1 : Wedge, Up, Hash, Down, Wavy, WedgeOrHash, UpOrDown, Upward, Downward, +<br/> None, Unspecified +<br/> 2 : Cis, Trans, Z, E, DoubleCross, CisOrTrans, None, Unspecified</div> +</dd> +<dt><strong><a name="setbondstereochemistry" class="item"><strong>SetBondStereochemistry</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Bond = $Bond->SetBondStereochemistry($BondStereochemistry);</div> +<p>Sets bond stereochemistry of <em>Bond</em> to specified <em>BondStereochemistry</em> and +returns <em>Bond</em>. Possible <em>BondStereoChemistry</em> values for different bond orders +are:</p> +<p>BondOrder: 1</p> +<div class="OptionsBox"> + None, Unspecified: Not a stereo bond or unspecified</div> +<div class="OptionsBox"> + Wedge, Up : Wedge end pointing up +<br/> Hash, Down: Wedge end pointing down +<br/> Wavy, WedgeOrHash, UpOrDown: Wedge end up or down</div> +<div class="OptionsBox"> + Upward: Single bond around cis/trans double bonds pointing upward +<br/> Downward: Single bond around cis/trans double bonds pointing upward</div> +<p>Notes:</p> +<div class="OptionsBox"> + o Wedge starts at begin atom of a bond making wedge pointed end always + at this atom. +<br/> o Upward/downward bonds start at atoms involved in cis/trans double bonds.</div> +<p>BondOrder: 2</p> +<div class="OptionsBox"> + None, Unspecified: Not a stereo bond or unspecified</div> +<div class="OptionsBox"> + Z, cis: Similar groups on same side of double bond +<br/> E, trans: Similar groups on different side of double bond</div> +<div class="OptionsBox"> + CisOrTrans, DoubleCross: cis or trans</div> +</dd> +<dt><strong><a name="stringifybond" class="item"><strong>StringifyBond</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $BondString = $Bond->StringifyBond();</div> +<p>Returns a string containing information about <em>bond</em> object.</p> +</dd> +<dt><strong><a name="switchbondfromandtoatoms" class="item"><strong>SwitchBondFromAndToAtoms</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Bond = $Bond->SwitchBondFromAndToAtoms();</div> +<p>Swaps bond from and to atoms in <em>Bond</em> and returns <em>Bond</em>.</p> +</dd> +</dl> +<p> +</p> +<h2>AUTHOR</h2> +<p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> +<p> +</p> +<h2>SEE ALSO</h2> +<p><a href="./Atom.html">Atom.pm</a>, <a href="./Molecule.html">Molecule.pm</a> +</p> +<p> +</p> +<h2>COPYRIGHT</h2> +<p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> +<p>This file is part of MayaChemTools.</p> +<p>MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the GNU Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.</p> +<p> </p><p> </p><div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<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> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>