annotate mayachemtools/docs/modules/html/Atom.html @ 3:e420415a1799 draft

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date Wed, 20 Jan 2016 12:16:47 -0500
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1 <html>
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2 <head>
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3 <title>MayaChemTools:Documentation:Atom.pm</title>
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4 <meta http-equiv="content-type" content="text/html;charset=utf-8">
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5 <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css">
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6 </head>
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7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10">
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8 <br/>
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9 <center>
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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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11 </center>
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12 <br/>
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13 <div class="DocNav">
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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="./AminoAcids.html" title="AminoAcids.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./AtomicDescriptors.html" title="AtomicDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>Atom.pm</strong></td><td width="33%" align="right"><a href="././code/Atom.html" title="View source code">Code</a>&nbsp;|&nbsp;<a href="./../pdf/Atom.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/Atom.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/Atom.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/Atom.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>Atom</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 Atom;</p>
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26 <p>
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27 </p>
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28 <h2>DESCRIPTION</h2>
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29 <p><strong>Atom</strong> class provides the following methods:</p>
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30 <p> <a href="#new">new</a>, <a href="#addhydrogens">AddHydrogens</a>, <a href="#copy">Copy</a>, <a href="#deleteatom">DeleteAtom</a>, <a href="#deletehydrogens">DeleteHydrogens</a>, <a href="#doesatomneighborhoodmatch">DoesAtomNeighborhoodMatch</a>
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31 , <a href="#getatomicinvariantvalue">GetAtomicInvariantValue</a>, <a href="#getatomicweight">GetAtomicWeight</a>, <a href="#getbondtoatom">GetBondToAtom</a>, <a href="#getbonds">GetBonds</a>
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32 , <a href="#getbondstoheavyatoms">GetBondsToHeavyAtoms</a>, <a href="#getbondstohydrogenatoms">GetBondsToHydrogenAtoms</a>, <a href="#getbondstononhydrogenatoms">GetBondsToNonHydrogenAtoms</a>
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33 , <a href="#getexactmass">GetExactMass</a>, <a href="#getexplicithydrogens">GetExplicitHydrogens</a>, <a href="#getformalcharge">GetFormalCharge</a>, <a href="#getfreeradicalelectrons">GetFreeRadicalElectrons</a>
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34 , <a href="#getgroupnumber">GetGroupNumber</a>, <a href="#getheavyatomneighbors">GetHeavyAtomNeighbors</a>, <a href="#getheavyatomneighborsatominformation">GetHeavyAtomNeighborsAtomInformation</a>
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35 , <a href="#getheavyatomneighborsbondformation">GetHeavyAtomNeighborsBondformation</a>, <a href="#gethighestcommonvalence">GetHighestCommonValence</a>
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36 , <a href="#gethydrogenatomneighbors">GetHydrogenAtomNeighbors</a>, <a href="#gethydrogens">GetHydrogens</a>, <a href="#getimplicithydrogens">GetImplicitHydrogens</a>, <a href="#getlargestbondorder">GetLargestBondOrder</a>
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37 , <a href="#getlargestbondordertoheavyatoms">GetLargestBondOrderToHeavyAtoms</a>, <a href="#getlargestbondordertononhydrogenatoms">GetLargestBondOrderToNonHydrogenAtoms</a>
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38 , <a href="#getlargestring">GetLargestRing</a>, <a href="#getlowestcommonvalence">GetLowestCommonValence</a>, <a href="#getmassnumber">GetMassNumber</a>, <a href="#getmissinghydrogens">GetMissingHydrogens</a>
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39 , <a href="#getneighbors">GetNeighbors</a>, <a href="#getneighborsusingatomspecification">GetNeighborsUsingAtomSpecification</a>, <a href="#getnonhydrogenatomneighbors">GetNonHydrogenAtomNeighbors</a>
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40 , <a href="#getnonhydrogenatomneighborsatominformation">GetNonHydrogenAtomNeighborsAtomInformation</a>
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41 , <a href="#getnonhydrogenatomneighborsbondinformation">GetNonHydrogenAtomNeighborsBondInformation</a>, <a href="#getnonhydrogenneighborofhydrogenatom">GetNonHydrogenNeighborOfHydrogenAtom</a>
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42 , <a href="#getnumofaromaticbondstoheavyatoms">GetNumOfAromaticBondsToHeavyAtoms</a>, <a href="#getnumofaromaticbondstononhydrogenatoms">GetNumOfAromaticBondsToNonHydrogenAtoms</a>
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43 , <a href="#getnumofbondtypestoheavyatoms">GetNumOfBondTypesToHeavyAtoms</a>, <a href="#getnumofbondtypestononhydrogenatoms">GetNumOfBondTypesToNonHydrogenAtoms</a>, <a href="#getnumofbonds">GetNumOfBonds</a>
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44 , <a href="#getnumofbondstoheavyatoms">GetNumOfBondsToHeavyAtoms</a>, <a href="#getnumofbondstohydrogenatoms">GetNumOfBondsToHydrogenAtoms</a>
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45 , <a href="#getnumofbondstononhydrogenatoms">GetNumOfBondsToNonHydrogenAtoms</a>, <a href="#getnumofdoublebondstoheavyatoms">GetNumOfDoubleBondsToHeavyAtoms</a>
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46 , <a href="#getnumofbondsavailableforheavyatoms">GetNumOfBondsAvailableForHeavyAtoms</a>, <a href="#getnumofbondsavailablefornonhydrogenatoms">GetNumOfBondsAvailableForNonHydrogenAtoms</a>
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47 , <a href="#getnumofdoublebondstononhydrogenatoms">GetNumOfDoubleBondsToNonHydrogenAtoms</a>, <a href="#getnumofexplicithydrogens">GetNumOfExplicitHydrogens</a>
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48 , <a href="#getnumofheavyatomneighbors">GetNumOfHeavyAtomNeighbors</a>, <a href="#getnumofhydrogenatomneighbors">GetNumOfHydrogenAtomNeighbors</a>, <a href="#getnumofhydrogens">GetNumOfHydrogens</a>
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49 , <a href="#getnumofimplicithydrogens">GetNumOfImplicitHydrogens</a>, <a href="#getnumofmissinghydrogens">GetNumOfMissingHydrogens</a>, <a href="#getnumofneighbors">GetNumOfNeighbors</a>
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50 , <a href="#getnumofnonhydrogenatomneighbors">GetNumOfNonHydrogenAtomNeighbors</a>, <a href="#getnumofrings">GetNumOfRings</a>, <a href="#getnumofringswithevensize">GetNumOfRingsWithEvenSize</a>
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51 , <a href="#getnumofringswithoddsize">GetNumOfRingsWithOddSize</a>, <a href="#getnumofringswithsize">GetNumOfRingsWithSize</a>, <a href="#getnumofringswithsizegreaterthan">GetNumOfRingsWithSizeGreaterThan</a>
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52 , <a href="#getnumofringswithsizelessthan">GetNumOfRingsWithSizeLessThan</a>, <a href="#getnumofsigmaandpibondstoheavyatoms">GetNumOfSigmaAndPiBondsToHeavyAtoms</a>
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53 , <a href="#getnumofsigmaandpibondstononhydrogenatoms">GetNumOfSigmaAndPiBondsToNonHydrogenAtoms</a>, <a href="#getnumofsinglebondstoheavyatoms">GetNumOfSingleBondsToHeavyAtoms</a>
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54 , <a href="#getnumofsinglebondstononhydrogenatoms">GetNumOfSingleBondsToNonHydrogenAtoms</a>, <a href="#getnumoftriplebondstoheavyatoms">GetNumOfTripleBondsToHeavyAtoms</a>
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55 , <a href="#getnumoftriplebondstononhydrogenatoms">GetNumOfTripleBondsToNonHydrogenAtoms</a>, <a href="#getperiodnumber">GetPeriodNumber</a>
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56 , <a href="#getpotentialtotalcommonvalence">GetPotentialTotalCommonValence</a>, <a href="#getrings">GetRings</a>, <a href="#getringswithevensize">GetRingsWithEvenSize</a>
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57 , <a href="#getringswithoddsize">GetRingsWithOddSize</a>, <a href="#getringswithsize">GetRingsWithSize</a>, <a href="#getringswithsizegreaterthan">GetRingsWithSizeGreaterThan</a>
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58 , <a href="#getringswithsizelessthan">GetRingsWithSizeLessThan</a>, <a href="#getsizeoflargestring">GetSizeOfLargestRing</a>, <a href="#getsizeofsmallestring">GetSizeOfSmallestRing</a>
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59 , <a href="#getsmallestring">GetSmallestRing</a>, <a href="#getspinmultiplicity">GetSpinMultiplicity</a>, <a href="#getsumofbondorders">GetSumOfBondOrders</a>
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60 , <a href="#getsumofbondorderstoheavyatoms">GetSumOfBondOrdersToHeavyAtoms</a>, <a href="#getsumofbondorderstohydrogenatoms">GetSumOfBondOrdersToHydrogenAtoms</a>
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61 , <a href="#getsumofbondorderstononhydrogenatoms">GetSumOfBondOrdersToNonHydrogenAtoms</a>, <a href="#getvalence">GetValence</a>, <a href="#getvalenceelectrons">GetValenceElectrons</a>
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62 , <a href="#getvalencefreeelectrons">GetValenceFreeElectrons</a>, <a href="#getx">GetX</a>, <a href="#getxyz">GetXYZ</a>, <a href="#getxyzvector">GetXYZVector</a>, <a href="#gety">GetY</a>, <a href="#getz">GetZ</a>, <a href="#isamidecarbon">IsAmideCarbon</a>
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63 , <a href="#isamidenitrogen">IsAmideNitrogen</a>, <a href="#isaromatic">IsAromatic</a>, <a href="#isarsenic">IsArsenic</a>, <a href="#isbondedtoatom">IsBondedToAtom</a>, <a href="#isbromine">IsBromine</a>, <a href="#iscarbon">IsCarbon</a>, <a href="#iscarboxylcarbon">IsCarboxylCarbon</a>
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64 , <a href="#iscarboxyloxygen">IsCarboxylOxygen</a>, <a href="#iscarboxylatecarbon">IsCarboxylateCarbon</a>, <a href="#iscarboxylateoxygen">IsCarboxylateOxygen</a>, <a href="#ischlorine">IsChlorine</a>
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65 , <a href="#isfluorine">IsFluorine</a>, <a href="#isfunctionalclasstype">IsFunctionalClassType</a>, <a href="#isguadiniumcarbon">IsGuadiniumCarbon</a>, <a href="#isguadiniumnitrogen">IsGuadiniumNitrogen</a>
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66 , <a href="#ishbondacceptor">IsHBondAcceptor</a>, <a href="#ishbonddonor">IsHBondDonor</a>, <a href="#ishalogen">IsHalogen</a>, <a href="#isheteroatom">IsHeteroAtom</a>, <a href="#ishydrogen">IsHydrogen</a>
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67 , <a href="#ishydrogenbondacceptor">IsHydrogenBondAcceptor</a>, <a href="#ishydrogenbonddonor">IsHydrogenBondDonor</a>, <a href="#ishydrophobic">IsHydrophobic</a>, <a href="#isinring">IsInRing</a>
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68 , <a href="#isinringofsize">IsInRingOfSize</a>, <a href="#isiodine">IsIodine</a>, <a href="#isisotope">IsIsotope</a>, <a href="#islipophilic">IsLipophilic</a>, <a href="#ismetallic">IsMetallic</a>
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69 , <a href="#isnegativelyionizable">IsNegativelyIonizable</a>, <a href="#isnitrogen">IsNitrogen</a>, <a href="#isnoncarbonorhydrogen">IsNonCarbonOrHydrogen</a>, <a href="#isnotinring">IsNotInRing</a>
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70 , <a href="#isonlyinonering">IsOnlyInOneRing</a>, <a href="#isoxygen">IsOxygen</a>, <a href="#isphosphateoxygen">IsPhosphateOxygen</a>, <a href="#isphosphatephosphorus">IsPhosphatePhosphorus</a>, <a href="#isphosphorus">IsPhosphorus</a>
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71 , <a href="#ispolaratom">IsPolarAtom</a>, <a href="#ispolarhydrogen">IsPolarHydrogen</a>, <a href="#ispositivelyionizable">IsPositivelyIonizable</a>, <a href="#issaturated">IsSaturated</a>, <a href="#isselenium">IsSelenium</a>
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72 , <a href="#issilicon">IsSilicon</a>, <a href="#isstereocenter">IsStereoCenter</a>, <a href="#issulfur">IsSulfur</a>, <a href="#issulphur">IsSulphur</a>, <a href="#istellurium">IsTellurium</a>, <a href="#isterminal">IsTerminal</a>
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73 , <a href="#istopologicalpharmacophoretype">IsTopologicalPharmacophoreType</a>, <a href="#isunsaturated">IsUnsaturated</a>, <a href="#setatomsymbol">SetAtomSymbol</a>, <a href="#setatomicnumber">SetAtomicNumber</a>
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74 , <a href="#setexplicithydrogens">SetExplicitHydrogens</a>, <a href="#setmassnumber">SetMassNumber</a>, <a href="#setstereocenter">SetStereoCenter</a>, <a href="#setstereochemistry">SetStereochemistry</a>
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75 , <a href="#setx">SetX</a>, <a href="#setxyz">SetXYZ</a>, <a href="#sety">SetY</a>, <a href="#setz">SetZ</a>, <a href="#stringifyatom">StringifyAtom</a>
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76 </p><p><strong>Atom</strong> class is derived from <strong>ObjectProperty</strong> base class which provides methods not explicitly
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77 defined in <strong>Atom</strong> or <strong>ObjectProperty</strong> class using Perl's AUTOLOAD functionality. These methods
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78 are generated on-the-fly for a specified object property:</p>
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79 <div class="OptionsBox">
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80 Set&lt;PropertyName&gt;(&lt;PropertyValue&gt;);
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81 <br/> $PropertyValue = Get&lt;PropertyName&gt;();
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82 <br/> Delete&lt;PropertyName&gt;();</div>
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83 <p>
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84 </p>
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85 <h2>METHODS</h2>
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86 <dl>
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87 <dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt>
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88 <dd>
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89 <div class="OptionsBox">
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90 $NewAtom = new Atom([%PropertyNameAndValues]);</div>
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91 <p>Using specified <em>Atom</em> property names and values hash, <strong>new</strong> method creates a new object
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92 and returns a reference to newly created <strong>Atom</strong> object. By default, following properties are
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93 initialized:</p>
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94 <div class="OptionsBox">
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95 ID = SequentialObjectID
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96 <br/> Name = &quot;Atom &lt;SequentialObjectID&gt;&quot;
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97 <br/> AtomSymbol = &quot;&quot;
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98 <br/> AtomicNumber = 0
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99 <br/> XYZ = ZeroVector</div>
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100 <p>Except for <em>ID</em> property, all other default properties and other additional properties can
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101 be set during invocation of this method.</p>
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102 <p>Examples:</p>
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103 <div class="OptionsBox">
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104 $Atom = new Atom();
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105 <br/> $CarbonAtom = new Atom('AtomSymbol' =&gt; 'C', 'XYZ' =&gt; (0.0, 1.0,
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106 0.0));
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107 <br/> $OxygenAtom = new Atom('AtomName' =&gt; 'Oxygen', AtomSymbol' =&gt; 'O',
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108 'XYZ' =&gt; (1.0, 1.0, 1.0));</div>
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109 </dd>
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110 <dt><strong><a name="addhydrogens" class="item"><strong>AddHydrogens</strong></a></strong></dt>
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111 <dd>
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112 <div class="OptionsBox">
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113 $NumOfHydrogensAdded = $Atom-&gt;AddHydrogens();</div>
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114 <p>Adds hydrogens to an <strong>Atom</strong> present in a <strong>Molecule</strong> object and returns
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115 the number of added hydrogens. The current release of MayaChemTools doesn't
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116 assign hydrogen positions.</p>
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117 </dd>
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118 <dt><strong><a name="copy" class="item"><strong>Copy</strong></a></strong></dt>
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119 <dd>
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120 <div class="OptionsBox">
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121 $AtomCopy = $Atom-&gt;Copy();</div>
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122 <p>Copy <em>Atom</em> and its associated data using <strong>Storable::dclone</strong> and return a new
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123 <strong>Atom</strong> object.</p>
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124 </dd>
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125 <dt><strong><a name="deleteatom" class="item"><strong>DeleteAtom</strong></a></strong></dt>
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126 <dd>
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127 <div class="OptionsBox">
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128 $Atom-&gt;DeleteAtom();</div>
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129 <p>Delete <em>Atom</em> from a molecule.</p>
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130 </dd>
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131 <dt><strong><a name="doesatomneighborhoodmatch" class="item"><strong>DoesAtomNeighborhoodMatch</strong></a></strong></dt>
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132 <dd>
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133 <div class="OptionsBox">
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134 $Status = $Atom-&gt;DoesAtomNeighborhoodMatch($CentralAtomSpec);
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135 <br/> $Status = $Atom-&gt;DoesAtomNeighborhoodMatch($CentralAtomSpec,
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136 $NbrAtomSpecsRef);
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137 <br/> $Status = $Atom-&gt;DoesAtomNeighborhoodMatch($CentralAtomSpec,
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138 $NbrAtomSpecsRef, $AllowedNbrBondSpecsRef);
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139 <br/> $Status = $Atom-&gt;DoesAtomNeighborhoodMatch($CentralAtomSpec,
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140 $NbrAtomSpecsRef, $NbrBondSpecsRef,
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141 $AllowedNbrOfNbrAtomSpecsRef);</div>
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142 <p>Returns 1 or 0 based on whether atom matches central atom and its neighborhood
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143 using specified atom and bonds specifications. Neighborhood atom and bond specifications
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144 are specified as array references containing neighbor atom and bond specifications.</p>
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145 <p>Let:</p>
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146 <div class="OptionsBox">
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147 AS = Atom symbol corresponding to element symbol, atomic number (#n)
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148 or any atom (A)</div>
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149 <div class="OptionsBox">
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150 X&lt;n&gt; = Number of non-hydrogen atom neighbors or heavy atoms
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151 attached to atom
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152 <br/> T&lt;n&gt; = Total number of atom neighbors including implicit and explicit
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153 hydrogens
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154 <br/> BO&lt;n&gt; = Sum of bond orders to non-hydrogen atom neighbors or heavy
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155 atoms attached to atom
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156 <br/> LBO&lt;n&gt; = Largest bond order of non-hydrogen atom neighbors or heavy
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157 atoms attached to atom
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158 <br/> SB&lt;n&gt; = Number of single bonds to non-hydrogen atom neighbors or
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159 heavy atoms attached to atom
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160 <br/> TSB&lt;n&gt; = Total number of single bonds to atom neighbors including implicit
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161 and explicit hydrogens
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162 <br/> DB&lt;n&gt; = Number of double bonds to non-hydrogen atom neighbors or
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163 heavy atoms attached to atom
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164 <br/> TB&lt;n&gt; = Number of triple bonds to non-hydrogen atom neighbors or
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165 heavy atoms attached to atom
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166 <br/> AB&lt;n&gt; = Number of aromatic bonds to non-hydrogen atom neighbors or
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167 heavy atoms attached to atom
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168 <br/> H&lt;n&gt; = Number of implicit and explicit hydrogens for atom
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169 <br/> Ar = Aromatic annotation indicating whether atom is aromatic
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170 <br/> RA or RA&lt;n&gt; = Ring atom annotation indicating whether atom
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171 is a ring
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172 <br/> TR&lt;n&gt; = Total number of rings containing atom
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173 <br/> FC&lt;+n/-n&gt; = Formal charge assigned to atom
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174 <br/> MN&lt;n&gt; = Mass number indicating isotope other than most abundant isotope
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175 <br/> SM&lt;n&gt; = Spin multiplicity of atom. Possible values: 1 (singlet),
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176 2 (doublet) or 3 (triplet)</div>
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177 <p>Then, atom specification corresponds to:</p>
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178 <div class="OptionsBox">
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179 AS.X&lt;n&gt;.T&lt;n&gt;.BO&lt;n&gt;.LBO&lt;n&gt;.&lt;SB&gt;&lt;n&gt;.TSB&lt;n&gt;.&lt;DB&gt;&lt;n&gt;.&lt;TB&gt;&lt;n&gt;.AB&lt;n&gt;.H&lt;n&gt;.Ar.
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180 <br/> RA&lt;n&gt;.TR&lt;n&gt;FC&lt;+n/-n&gt;.MN&lt;n&gt;.SM&lt;n&gt;</div>
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181 <p>Except for AS which is a required atomic invariant in atom specification, all other atomic invariants are
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182 optional. For an atom specification to match an atom, the values of all specified atomic invariants must
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183 match. Exclamation in from of atomic invariant can be used to negate its effect during the match.</p>
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184 <p>For <em>FC</em> value matching, the following value operators are also supported:</p>
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185 <div class="OptionsBox">
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186 o +* : Any positive value
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187 <br/> o -* : Any negative value
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188 <br/> o &gt; ValidNumber or &gt;= ValidNumber
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189 <br/> o &lt; ValidNumber or &lt;= ValidNumber</div>
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190 <p>A comma delimited atom specification string is used to match any one of the specified atom specification.</p>
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191 <p>Notes:</p>
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192 <div class="OptionsBox">
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193 o During atom specification match to an atom, the first atomic invariant is always assumed to
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194 atom symbol.</div>
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195 <p>Examples:</p>
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196 <div class="OptionsBox">
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197 o ('N', 'N', 'N')
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198 <br/> o ('N.FC0', 'N.FC0', 'N,N.FC+1.H1')
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199 <br/> o ('N.H2', 'N.H2', 'N.H1')
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200 <br/> o ('C,N', '!N', '!H')
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201 <br/> o ('C,N', 'N.Ar', 'N.R5')</div>
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202 <p>Let:</p>
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203 <div class="OptionsBox">
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204 -|1|s|Single = Single bond
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205 <br/> =|2|d|Double = Double bond
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206 <br/> #|3|t|Triple = Triple bond
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207 <br/> :|1.5|a|Ar|Aromatic = Aromatic bond</div>
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208 <div class="OptionsBox">
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209 @|RB|Ring = Ring bond
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210 <br/> ~|*|Any = Any bond</div>
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211 <p>Then, bond specification corresponds to:</p>
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212 <div class="OptionsBox">
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213 -.:
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214 <br/> =.@
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215 <br/> Double.Aromatic</div>
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216 <p>For a bond specification to match bond between two atoms, the values of all specified bond symbols must
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217 match. Exclamation in from of bond symbol can be used to negate its effect during the match.</p>
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218 <p>A comma delimited bond specification string is used to match any one of the specified atom specification.</p>
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219 <p>Notes:</p>
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220 <div class="OptionsBox">
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221 o During atom neighborhood match for central atom neighborhood atom and bond specifications,
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222 implicit or missing hydrogens are automatically checked for any matches to unmatched
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223 specifications.</div>
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224 <p>Examples:</p>
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225 <div class="OptionsBox">
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226 Aromatic carbon in a 5 membered ring:
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227 $Atom-&gt;DoesAtomNeighborhoodMatch('C.Ar.RA5');</div>
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228 <div class="OptionsBox">
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229 AcetylenicCarbon: $Atom-&gt;DoesAtomNeighborhoodMatch('C.T2.TB1'); or
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230 $Atom-&gt;DoesAtomNeighborhoodMatch('C.T2.TB1',
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231 ['*', '*'], ['#', '-']);</div>
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232 <div class="OptionsBox">
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233 GuadiniumCarbon: $Atom-&gt;DoesAtomNeighborhoodMatch('C.X3.BO4',
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234 ['N.FC0', 'N.FC0', 'N.FC0,N.FC+1'],
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235 ['-', '-', '='],
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236 ['C,H', 'C,H', 'C,H']);</div>
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237 <div class="OptionsBox">
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238 AmideCarbon: $Atom-&gt;DoesAtomNeighborhoodMatch('C.X3.BO4,C.X2.BO3',
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239 ['C,H', 'O', 'N'],
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240 ['-', '=', '-'],
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241 ['C,H', 'C', 'C,H,N,O,S,P,F,Cl,Br,I']);</div>
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242 <div class="OptionsBox">
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243 CarboxylCarbon: $Atom-&gt;DoesAtomNeighborhoodMatch('C.X3.BO4,C.X2.BO3',
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244 ['C,H', 'O', 'O.X1.FC0'],
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245 ['-', '=', '-'],
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246 ['C,H', 'C', 'C']);</div>
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247 <div class="OptionsBox">
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248 CarboxylateCarbon: $Atom-&gt;DoesAtomNeighborhoodMatch('C.X3.BO4,C.X2.BO3',
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249 ['C,H', 'O', 'O.X1.FC-1'],
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250 ['-', '=', '-'],
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251 ['C,H', 'C', 'C']);</div>
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252 </dd>
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253 <dt><strong><a name="deletehydrogens" class="item"><strong>DeleteHydrogens</strong></a></strong></dt>
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254 <dd>
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255 <div class="OptionsBox">
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256 $NumOfHydrogensDeleted = $Atom-&gt;AddHydrogens();</div>
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257 <p>Delete hydrogens from an <strong>Atom</strong> present in a <strong>Molecule</strong> object and returns
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258 the number of deleted hydrogens.</p>
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259 </dd>
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260 <dt><strong><a name="getatomicinvariantvalue" class="item"><strong>GetAtomicInvariantValue</strong></a></strong></dt>
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261 <dd>
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262 <div class="OptionsBox">
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263 $Value = $Atom-&gt;GetAtomicInvariantValue($AtomicInvariant);</div>
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264 <p>Returns atomic invariant value for a specified <em>AtomicInvariant</em>. The current release
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265 of MayaChemTools supports following abbreviations and descriptive names for
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266 <em>AtomicInvarints</em>:</p>
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267 <div class="OptionsBox">
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268 AS : Atom or element symbol
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269 <br/> X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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270 <br/> T : TotalNumOfAtomNeighbors
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271 <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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272 <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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273 <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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274 <br/> TSB : TotalNumOfSingleBonds
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275 <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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276 <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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277 <br/> AB : NumOfAromaticBondsToNonHydrogenAtoms or NumOfAromaticBondsToHeavyAtoms
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278 <br/> H : NumOfImplicitAndExplicitHydrogens
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279 <br/> Ar : Aromatic
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280 <br/> Str : Stereochemistry
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281 <br/> RA : RingAtom
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282 <br/> FC : FormalCharge
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283 <br/> AN : AtomicNumber
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284 <br/> AM : AtomicMass
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285 <br/> MN : MassNumber
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286 <br/> SM : SpinMultiplicity</div>
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287 </dd>
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288 <dt><strong><a name="getatomicweight" class="item"><strong>GetAtomicWeight</strong></a></strong></dt>
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289 <dd>
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290 <div class="OptionsBox">
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291 $Value = $Aom-&gt;GetAtomicWeight();</div>
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292 <p>Returns atomic weight of an <strong>Atom</strong> which corresponds to either explicity set <em>AtomicWeight</em>
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293 atom property or atomic weight of the corresponding element in the periodic table available by
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294 <strong>PeriodicTable</strong> module.</p>
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295 </dd>
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296 <dt><strong><a name="getbondtoatom" class="item"><strong>GetBondToAtom</strong></a></strong></dt>
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297 <dd>
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298 <div class="OptionsBox">
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299 $Bond = $Atom-&gt;GetBondToAtom($OtherAtom);</div>
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300 <p>Returns a <strong>Bond</strong> object corresponding to bond between <em>Atom</em> and <em>OtherAtom</em> in
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301 a molecule.</p>
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302 </dd>
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303 <dt><strong><a name="getbonds" class="item"><strong>GetBonds</strong></a></strong></dt>
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304 <dd>
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305 <div class="OptionsBox">
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306 @Bonds = $Aoto-&gt;GetBonds();</div>
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307 <p>Returns an array of <strong>Bond</strong> objects corresponding to all bonds from <em>Atom</em> to other
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308 bonded atoms in a molecule.</p>
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309 </dd>
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310 <dt><strong><a name="getbondstoheavyatoms" class="item"><strong>GetBondsToHeavyAtoms</strong></a></strong></dt>
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311 <dd>
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312 <div class="OptionsBox">
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313 @Bonds = $Atom-&gt;GetBondsToHeavyAtoms();</div>
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314 <p>Returns an array of <strong>Bond</strong> objects corresponding to bonds from <em>Atom</em> to other bonded
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315 non-hydrogen atoms in a molecule.</p>
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316 </dd>
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317 <dt><strong><a name="getbondstohydrogenatoms" class="item"><strong>GetBondsToHydrogenAtoms</strong></a></strong></dt>
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318 <dd>
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319 <div class="OptionsBox">
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320 @Bonds = $Atom-&gt;GetBondsToHydrogenAtoms();</div>
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321 <p>Returns an array of <strong>Bond</strong> objects corresponding to bonds from <em>Atom</em> to any other
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322 hydrogen atom in a molecule.</p>
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323 </dd>
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324 <dt><strong><a name="getbondstononhydrogenatoms" class="item"><strong>GetBondsToNonHydrogenAtoms</strong></a></strong></dt>
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325 <dd>
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326 <div class="OptionsBox">
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327 @Bonds = $Atom-&gt;GetBondsToNonHydrogenAtoms();</div>
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328 <p>Returns an array of <strong>Bond</strong> objects corresponding to bonds from <em>Atom</em> to other bonded
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329 non-hydrogen atoms in a molecule.</p>
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330 </dd>
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331 <dt><strong><a name="getexactmass" class="item"><strong>GetExactMass</strong></a></strong></dt>
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332 <dd>
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333 <div class="OptionsBox">
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334 $ExactMass = $Atom-&gt;GetExactMass();</div>
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335 <p>Returns exact mass of an <em>Atom</em> which correspond to one of these three values: explicity set
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336 <em>ExactMass</em> property; mass of natural isotope for an explicty set value of <em>MassNumber</em>; most
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337 abundant natural isotope mass for <em>Atom</em> with valid atomic number value available by
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338 <strong>PerodicTable</strong> module.</p>
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339 </dd>
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340 <dt><strong><a name="getexplicithydrogens" class="item"><strong>GetExplicitHydrogens</strong></a></strong></dt>
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341 <dd>
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342 <div class="OptionsBox">
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343 $NumOfExplicitHydrogens = $Atom-&gt;GetExplicitHydrogens();</div>
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344 <p>Returns number of hydrogens explicity bonded to an <em>Atom</em> in a molecule.</p>
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345 </dd>
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346 <dt><strong><a name="getformalcharge" class="item"><strong>GetFormalCharge</strong></a></strong></dt>
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347 <dd>
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348 <div class="OptionsBox">
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349 $FormalCharge = $Atom-&gt;GetFormalCharge();</div>
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350 <p>Returns formal charge of an <em>Atom</em> in a molecule.</p>
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351 </dd>
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352 <dt><strong><a name="getfreeradicalelectrons" class="item"><strong>GetFreeRadicalElectrons</strong></a></strong></dt>
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353 <dd>
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354 <div class="OptionsBox">
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355 $FreeRadicalElectrons = $Atom-&gt;GetFreeRadicalElectrons();</div>
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356 <p>Returns number of free radical electrons corresponding to to one of these
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357 three values: <em>FreeRadicalElectrons</em> property; <em>SpinMultiplicity</em> property; value
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358 of 0.</p>
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359 <p>For atoms with explicit assignment of <em>SpinMultiplicity</em> atom property values,</p>
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360 <div class="OptionsBox">
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361 Singlet - two unparied electrons corresponding to one spin state
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362 <br/> Doublet - free radical; an unpaired electron corresponding to two
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363 spin states
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364 <br/> Triplet - two unparied electrons corresponding to three spin states
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365 (divalent carbon atoms: carbenes)</div>
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366 <p><strong>FreeRadicalElectrons</strong> are calculated as follows:</p>
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367 <div class="OptionsBox">
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368 Doublet: 1 (one valence electron not available for bonding)
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369 <br/> Singlet: 2 (two valence electrons not available for bonding)
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370 <br/> Triplet: 2 (two valence electrons not available for bonding)</div>
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371 </dd>
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372 <dt><strong><a name="getgroupnumber" class="item"><strong>GetGroupNumber</strong></a></strong></dt>
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373 <dd>
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374 <div class="OptionsBox">
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375 $GroupNumber = $Atom-&gt;GetGroupNumber();</div>
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376 <p>Returns group number of an <em>Atom</em> in a molecule with a valid atomic number.</p>
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377 </dd>
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378 <dt><strong><a name="getheavyatomneighbors" class="item"><strong>GetHeavyAtomNeighbors</strong></a></strong></dt>
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379 <dd>
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380 <div class="OptionsBox">
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381 $NumOfHeavyAtoms = $Atom-&gt;GetHeavyAtomNeighbors();
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382 <br/> @HeavyAtoms = $Atom-&gt;GetHeavyAtomNeighbors();</div>
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383 <p>Return number of heavy atoms or an array of <strong>Atom</strong> objects corresponding to heavy atoms
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384 bonded to an <em>Atom</em> in a molecule.</p>
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385 </dd>
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386 <dt><strong><a name="getheavyatomneighborsatominformation" class="item"><strong>GetHeavyAtomNeighborsAtomInformation</strong></a></strong></dt>
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387 <dd>
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388 <div class="OptionsBox">
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389 ($NumOfAtomNeighbors, $AtomNeighborsRef,
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390 $NumOfAtomNeighborsType, $AtomNeighborsTypeMapRef) = $Atom-&gt;
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391 GetHeavyAtomNeighborsAtomInformation();</div>
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392 <p>Returns atoms information for all non-hydrogen atoms attached to an <em>Atom</em>
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393 in a molecule.</p>
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394 <p>The following values are returned:</p>
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395 <div class="OptionsBox">
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396 o Number of non-hydrogen atom neighbors
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397 <br/> o A reference to an array containing atom objects corresponding to
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398 non-hydrogen atom neighbors
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399 <br/> o Number of different types of non-hydrogen atom neighbors
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400 <br/> o A reference to a hash containing atom symbol as key with value
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401 corresponding to its count for non-hydrogen atom neighbors</div>
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402 </dd>
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403 <dt><strong><a name="getheavyatomneighborsbondformation" class="item"><strong>GetHeavyAtomNeighborsBondformation</strong></a></strong></dt>
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404 <dd>
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405 <div class="OptionsBox">
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406 ($NumOfBonds, $BondTypeCountMapRef,
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407 <br/> $AtomsBondTypesCountMapRef,
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408 <br/> $AtomsBondTypeAtomsMap) = $Atom-&gt;
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409 GetHeavyAtomNeighborsBondformation();</div>
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410 <p>Returns bonds information for all non-hydrogen atoms attached to an <em>Atom</em>
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411 in a molecule.</p>
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412 <p>The following values are returned:</p>
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413 <div class="OptionsBox">
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414 o Number of bonds to non-hydrogen atom neighbors
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415 <br/> o A reference to an array containing bond objects corresponding to
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416 non-hydrogen atom neighbors
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417 <br/> o A reference to a hash containing bond type as key with value
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418 corresponding to its count for non-hydrogen atom neighbors. Bond
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419 types are: Single, Double or Triple
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420 <br/> o A reference to a hash containing atom symbol as key pointing to bond
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421 type as second key with values corresponding to count of bond types for atom
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422 symbol for non-hydrogen atom neighbors
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423 <br/> o A reference to a hash containing atom symbol as key pointing to bond
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424 type as second key with values corresponding to atom objects array involved
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425 in corresponding bond type for atom symbol for non-hydrogen atom neighbors</div>
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426 </dd>
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427 <dt><strong><a name="gethighestcommonvalence" class="item"><strong>GetHighestCommonValence</strong></a></strong></dt>
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428 <dd>
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429 <div class="OptionsBox">
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430 $HighestCommonValence = $Atom-&gt;GetHighestCommonValence();</div>
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431 <p>Returns highest common valence of an <em>Atom</em> which corresponds to either explicity set
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432 <em>HighestCommonValence</em> atom property or highest common valence of the corresponding
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433 element in the periodic table available by <strong>PerodicTable</strong> module.</p>
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434 </dd>
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435 <dt><strong><a name="gethydrogens" class="item"><strong>GetHydrogens</strong></a></strong></dt>
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436 <dd>
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437 <div class="OptionsBox">
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438 $NumOfHydrogens = $Atom-&gt;GetHydrogens();</div>
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439 <p>Returns total number of hydrogens for an <em>Atom</em> in a molecule including both hydrogen atom
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440 neighbors and implicit hydrogens.</p>
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441 </dd>
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442 <dt><strong><a name="gethydrogenatomneighbors" class="item"><strong>GetHydrogenAtomNeighbors</strong></a></strong></dt>
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443 <dd>
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444 <div class="OptionsBox">
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445 $NumOfHydrogenAtomNeighbors = $Atom-&gt;GetHydrogenAtomNeighbors();
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446 <br/> @HydrogenAtomNeighbors = $Atom-&gt;GetHydrogenAtomNeighbors();</div>
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447 <p>Return number of hydrogen atoms or an array of <em>Atom</em> objects corresponding to hydrogen
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448 atoms bonded to an <em>Atom</em> in a molecule.</p>
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449 </dd>
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450 <dt><strong><a name="getimplicithydrogens" class="item"><strong>GetImplicitHydrogens</strong></a></strong></dt>
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451 <dd>
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452 <div class="OptionsBox">
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453 $NumOfImplicitHydrogens = $Atom-&gt;GetImplicitHydrogens();</div>
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454 <p>Returns number of implicit hydrogens for an <em>Atom</em> in a molecule. This value either
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455 corresponds to explicitly set <em>ImplicitHydrogens</em> atom property or calculated as the
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456 difference between the value of potential total valence and sum of bond orders to
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457 both hydrogen and non-hydrogen atom neighbors.</p>
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458 </dd>
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459 <dt><strong><a name="getpotentialtotalcommonvalence" class="item"><strong>GetPotentialTotalCommonValence</strong></a></strong></dt>
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460 <dd>
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461 <div class="OptionsBox">
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462 $PotentialTotalValence = $Atom-&gt;GetPotentialTotalCommonValence();</div>
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463 <p>Returns potential total common valence of an <em>Atom</em> in a molecule corresponding
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464 to a specific valence model set for the molecule using its <strong>SetValenceModel</strong> method
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465 or default internal valence model. It is used during the calculation of missing or
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466 implicit hydrogens.</p>
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467 <p>The current release of MayaChemTools supports three valence models: <em>MDLValenceModel,
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468 DaylightValenceModel, InternalValenceModel or MayaChemToolsValenceModel</em>.</p>
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469 <p>For <em>MDLValenceModel</em> and <em>DaylightValenceModel</em>, the following data files, distributed
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470 with the package, are used to calculate potential total valence:</p>
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471 <div class="OptionsBox">
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472 lib/data/MDLValenceModelData.csv
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473 <br/> lib/data/DaylightValenceModelData.csv</div>
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474 <p>The calculation of potential total common valence for these two models is performed as
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475 follows: Calculate current effective total valence of the <em>Atom</em> by adding up the bond
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476 order of its neighbors and number of free radical electrons; Find available common valence
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477 for the <em>Atom</em>, corresponding to any specified formal charge, higher than the effective
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478 total valence, and return it as <em>PotentialTotalValence</em>.</p>
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479 <p>The calculation of potential total common valence For <em>InternalValenceModel</em> or
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480 <em>MayaChenToolsValenceModel</em> doesn't uses <strong>PeriodicTable</strong> module to retrieve values
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481 for common valence, which in turn reads in PeriodicTableElements.csv file distributed with
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482 the package.</p>
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483 <p>For elements with one one common valence, potential total common valence corresponds
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484 to:</p>
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485 <div class="OptionsBox">
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486 CommonValence + FormalCharge - FreeRadicalElectrons</div>
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487 <p>For elements with multiple common valences, each common valence is used to
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488 calculate total potential common valence as shown above, and the first total potential
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489 common valence greater than the sum of bond orders to all neighbors is selected as
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490 the final total common valence.</p>
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491 <p>FormalCharge sign is reversed for electropositive elements with positive formal charge
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492 during common valence calculations. Electropositive elements, metals and transition elements,
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493 have usually plus formal charge and it leads to decrease in common valence; the negative
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deepakjadmin
parents:
diff changeset
494 formal charge should result in the decrease of common valence.</p>
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deepakjadmin
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495 <p>The sign of formal charge is adjusted as follows.</p>
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deepakjadmin
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496 <p>Group numbers &gt; 14 - Group numbers 15 (N), 16 (O), 17 (F), 18 (He):</p>
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deepakjadmin
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497 <p>Formal charge sign is not adjusted. Positive and negative values result in the
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diff changeset
498 increase and decrease of valence.</p>
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parents:
diff changeset
499 <p>Group 14 containing C, Si, Ge, Sn, Pb...:</p>
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deepakjadmin
parents:
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500 <p>Formal charge sign is reversed for positive values. Both positive and negative
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deepakjadmin
parents:
diff changeset
501 values result in the decrease of valence.</p>
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deepakjadmin
parents:
diff changeset
502 <p>Group 13 containing B, Al, Ga, In, Tl...:</p>
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deepakjadmin
parents:
diff changeset
503 <p>Formal charge sign is always reversed. Positive and negative values result in the
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deepakjadmin
parents:
diff changeset
504 decrease and increase of valence.</p>
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deepakjadmin
parents:
diff changeset
505 <p>Groups 1 (H) through 12 (Zn)...:</p>
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deepakjadmin
parents:
diff changeset
506 <p>Formal charge sign is reversed for positive values. Both positive and negative
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deepakjadmin
parents:
diff changeset
507 values result in the decrease of valence.</p>
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deepakjadmin
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508 <p>Lanthanides and actinides:</p>
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parents:
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509 <p>Formal charge sign is reversed for positive values. Both positive and negative
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deepakjadmin
parents:
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510 values result in the decrease of valence.</p>
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deepakjadmin
parents:
diff changeset
511 </dd>
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512 <dt><strong><a name="getlargestbondorder" class="item"><strong>GetLargestBondOrder</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
513 <dd>
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deepakjadmin
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514 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
515 $LargestBO =$Atom-&gt;GetLargestBondOrder();</div>
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deepakjadmin
parents:
diff changeset
516 <p>Returns largest bond order for an <em>Atom</em> among the bonds to other atoms in a molecule.</p>
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deepakjadmin
parents:
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517 </dd>
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518 <dt><strong><a name="getlargestbondordertoheavyatoms" class="item"><strong>GetLargestBondOrderToHeavyAtoms</strong></a></strong></dt>
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deepakjadmin
parents:
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519 <dd>
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deepakjadmin
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520 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
521 $LargestBO =$Atom-&gt;GetLargestBondOrderToHeavyAtoms();</div>
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deepakjadmin
parents:
diff changeset
522 <p>Returns largest bond order for an <em>Atom</em> among the bonds to other heavy atoms in a molecule.</p>
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deepakjadmin
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diff changeset
523 </dd>
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524 <dt><strong><a name="getlargestbondordertononhydrogenatoms" class="item"><strong>GetLargestBondOrderToNonHydrogenAtoms</strong></a></strong></dt>
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deepakjadmin
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diff changeset
525 <dd>
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deepakjadmin
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526 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
527 $LargestBO =$Atom-&gt;GetLargestBondOrderToNonHydrogenAtoms();</div>
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deepakjadmin
parents:
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528 <p>Returns largest bond order for an <em>Atom</em> among the bonds to other non-hydrogen atoms
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deepakjadmin
parents:
diff changeset
529 in a molecule.</p>
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deepakjadmin
parents:
diff changeset
530 </dd>
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deepakjadmin
parents:
diff changeset
531 <dt><strong><a name="getlargestring" class="item"><strong>GetLargestRing</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
532 <dd>
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533 <div class="OptionsBox">
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534 @RingAtoms = $Atom-&gt;GetLargestRing();</div>
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parents:
diff changeset
535 <p>Returns an array of ring <em>Atom</em> objects corresponding to the largest ring containing <em>Atom</em>
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parents:
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536 in a molecule.</p>
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deepakjadmin
parents:
diff changeset
537 </dd>
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diff changeset
538 <dt><strong><a name="getlowestcommonvalence" class="item"><strong>GetLowestCommonValence</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
539 <dd>
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deepakjadmin
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diff changeset
540 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
541 $LowestCommonValence = $Atom-&gt;GetLowestCommonValence();</div>
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deepakjadmin
parents:
diff changeset
542 <p>Returns lowest common valence of an <em>Atom</em> which corresponds to either explicity set
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deepakjadmin
parents:
diff changeset
543 <em>LowestCommonValence</em> atom property or highest common valence of the corresponding
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deepakjadmin
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diff changeset
544 element in the periodic table available by <strong>PerodicTable</strong> module.</p>
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deepakjadmin
parents:
diff changeset
545 </dd>
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deepakjadmin
parents:
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546 <dt><strong><a name="getmassnumber" class="item"><strong>GetMassNumber</strong></a></strong></dt>
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deepakjadmin
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547 <dd>
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548 <div class="OptionsBox">
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diff changeset
549 $MassNumber = $Aom-&gt;GetMassNumber();</div>
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parents:
diff changeset
550 <p>Returns atomic weight of an <strong>Atom</strong> which corresponds to either explicity set <em>MassNumber</em>
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deepakjadmin
parents:
diff changeset
551 atom property or mass number of the most abundant natural isotope of the corresponding element
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deepakjadmin
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552 in the periodic table available by <strong>PeriodicTable</strong> module.</p>
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deepakjadmin
parents:
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553 </dd>
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554 <dt><strong><a name="getmissinghydrogens" class="item"><strong>GetMissingHydrogens</strong></a></strong></dt>
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deepakjadmin
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555 <dd>
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deepakjadmin
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556 <div class="OptionsBox">
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557 $NumOfMissingHydrogens = $Atom-&gt;GetMissingHydrogens();</div>
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parents:
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558 <p>Returns number of missing hydrogens for an <em>Atom</em> in a molecule. This value either
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deepakjadmin
parents:
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559 corresponds to explicitly set <em>ImplicitHydrogens</em> atom property or calculated as the
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deepakjadmin
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560 difference between the value of potential total valence and sum of bond orders to
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deepakjadmin
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561 both hydrogen and non-hydrogen atom neighbors.</p>
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deepakjadmin
parents:
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562 </dd>
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563 <dt><strong><a name="getneighbors" class="item"><strong>GetNeighbors</strong></a></strong></dt>
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deepakjadmin
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564 <dd>
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deepakjadmin
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565 <div class="OptionsBox">
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566 $NumOfNeighbors = $Atom-&gt;GetNeighbors();
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diff changeset
567 <br/> @Neighbors = $Atom-&gt;GetNeighbors();</div>
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deepakjadmin
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568 <p>Returns number of neighbor atoms or an array of <em>Atom</em> objects corresponding to all
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deepakjadmin
parents:
diff changeset
569 atoms bonded to an <em>Atom</em> in a molecule.</p>
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deepakjadmin
parents:
diff changeset
570 </dd>
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571 <dt><strong><a name="getneighborsusingatomspecification" class="item"><strong>GetNeighborsUsingAtomSpecification</strong></a></strong></dt>
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deepakjadmin
parents:
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572 <dd>
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deepakjadmin
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diff changeset
573 <div class="OptionsBox">
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deepakjadmin
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574 @AtomNeighbors = $Atom-&gt;GetNeighborsUsingAtomSpecification($AtomSpec);
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575 <br/> $NumOfNeighbors = $Atom-&gt;GetNeighborsUsingAtomSpecification($AtomSpec);</div>
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576 <div class="OptionsBox">
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deepakjadmin
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577 @AtomNeighbors = $Atom-&gt;GetNeighborsUsingAtomSpecification($AtomSpec,
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578 @ExcludeNeighbors);</div>
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deepakjadmin
parents:
diff changeset
579 <p>Returns number of neighbor atoms or an array of <em>Atom</em> objects matching atom
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deepakjadmin
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580 specification corresponding to atom neighbors of an <em>Atom</em> in a molecule. Optionally,
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deepakjadmin
parents:
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581 <em>Atom</em> neighbors can be excluded from the neighbors list using <em>ExcludeNeighbors</em>.</p>
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deepakjadmin
parents:
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582 <p>Notes:</p>
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deepakjadmin
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583 <div class="OptionsBox">
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deepakjadmin
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584 o AtomSpecification correspond to any valid AtomicInvariant based atomic specifications
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parents:
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585 as supported by DoesAtomNeighborhoodMatch method
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deepakjadmin
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586 <br/> o Multiple atom specifications can be used in a string delimited by comma</div>
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deepakjadmin
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587 </dd>
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deepakjadmin
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588 <dt><strong><a name="getnonhydrogenatomneighbors" class="item"><strong>GetNonHydrogenAtomNeighbors</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
589 <dd>
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deepakjadmin
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590 <div class="OptionsBox">
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deepakjadmin
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591 $NumOfNeighbors = $Atom-&gt;GetNonHydrogenAtomNeighbors();
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deepakjadmin
parents:
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592 <br/> @Neighbors = $Atom-&gt;GetNonHydrogenAtomNeighbors();</div>
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deepakjadmin
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593 <p>Returns number of non-hydrogen atoms or an array of <strong>Atom</strong> objects corresponding to non-hydrogen
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deepakjadmin
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diff changeset
594 atoms bonded to an <em>Atom</em> in a molecule.</p>
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deepakjadmin
parents:
diff changeset
595 </dd>
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deepakjadmin
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diff changeset
596 <dt><strong><a name="getnonhydrogenatomneighborsatominformation" class="item"><strong>GetNonHydrogenAtomNeighborsAtomInformation</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
597 <dd>
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deepakjadmin
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diff changeset
598 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
599 ($NumOfAtomNeighbors, $AtomNeighborsRef,
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deepakjadmin
parents:
diff changeset
600 $NumOfAtomNeighborsType, $AtomNeighborsTypeMapRef) = $Atom-&gt;
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deepakjadmin
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diff changeset
601 GetNonHydrogenAtomNeighborsAtomInformation();</div>
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deepakjadmin
parents:
diff changeset
602 <p>Returns atoms information for all non-hydrogen atoms attached to an <em>Atom</em>
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deepakjadmin
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603 in a molecule.</p>
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deepakjadmin
parents:
diff changeset
604 <p>The following values are returned:</p>
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deepakjadmin
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diff changeset
605 <div class="OptionsBox">
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deepakjadmin
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606 o Number of non-hydrogen atom neighbors
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deepakjadmin
parents:
diff changeset
607 <br/> o A reference to an array containing atom objects corresponding to
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deepakjadmin
parents:
diff changeset
608 non-hydrogen atom neighbors
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deepakjadmin
parents:
diff changeset
609 <br/> o Number of different types of non-hydrogen atom neighbors
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deepakjadmin
parents:
diff changeset
610 <br/> o A reference to a hash containing atom symbol as key with value
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deepakjadmin
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611 corresponding to its count for non-hydrogen atom neighbors</div>
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deepakjadmin
parents:
diff changeset
612 </dd>
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deepakjadmin
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diff changeset
613 <dt><strong><a name="getnonhydrogenatomneighborsbondinformation" class="item"><strong>GetNonHydrogenAtomNeighborsBondInformation</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
614 <dd>
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deepakjadmin
parents:
diff changeset
615 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
616 ($NumOfBonds, $BondTypeCountMapRef,
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parents:
diff changeset
617 <br/> $AtomsBondTypesCountMapRef,
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deepakjadmin
parents:
diff changeset
618 <br/> $AtomsBondTypeAtomsMap) = $Atom-&gt;
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deepakjadmin
parents:
diff changeset
619 GetNonHydrogenAtomNeighborsBondInformation();</div>
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deepakjadmin
parents:
diff changeset
620 <p>Returns bonds information for all non-hydrogen atoms attached to an <em>Atom</em>
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deepakjadmin
parents:
diff changeset
621 in a molecule.</p>
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deepakjadmin
parents:
diff changeset
622 <p>The following values are returned:</p>
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diff changeset
623 <div class="OptionsBox">
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parents:
diff changeset
624 o Number of bonds to non-hydrogen atom neighbors
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deepakjadmin
parents:
diff changeset
625 <br/> o A reference to an array containing bond objects corresponding to
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deepakjadmin
parents:
diff changeset
626 non-hydrogen atom neighbors
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deepakjadmin
parents:
diff changeset
627 <br/> o A reference to a hash containing bond type as key with value
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deepakjadmin
parents:
diff changeset
628 corresponding to its count for non-hydrogen atom neighbors. Bond
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deepakjadmin
parents:
diff changeset
629 types are: Single, Double or Triple
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deepakjadmin
parents:
diff changeset
630 <br/> o A reference to a hash containing atom symbol as key pointing to bond
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deepakjadmin
parents:
diff changeset
631 type as second key with values corresponding to count of bond types for atom
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deepakjadmin
parents:
diff changeset
632 symbol for non-hydrogen atom neighbors
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deepakjadmin
parents:
diff changeset
633 <br/> o A reference to a hash containing atom symbol as key pointing to bond
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deepakjadmin
parents:
diff changeset
634 type as second key with values corresponding to atom objects array involved
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deepakjadmin
parents:
diff changeset
635 in corresponding bond type for atom symbol for non-hydrogen atom neighbors</div>
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deepakjadmin
parents:
diff changeset
636 </dd>
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diff changeset
637 <dt><strong><a name="getnonhydrogenneighborofhydrogenatom" class="item"><strong>GetNonHydrogenNeighborOfHydrogenAtom</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
638 <dd>
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deepakjadmin
parents:
diff changeset
639 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
640 $Atom = $Atom-&gt;GetNonHydrogenNeighborOfHydrogenAtom();</div>
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deepakjadmin
parents:
diff changeset
641 <p>Returns non-hydrogen or heavy atom neighbor of a hydrogen atom in a molecule..</p>
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deepakjadmin
parents:
diff changeset
642 </dd>
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deepakjadmin
parents:
diff changeset
643 <dt><strong><a name="getnumofaromaticbondstoheavyatoms" class="item"><strong>GetNumOfAromaticBondsToHeavyAtoms</strong></a></strong></dt>
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parents:
diff changeset
644 <dd>
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deepakjadmin
parents:
diff changeset
645 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
646 $NumOfBonds = $Atom-&gt;GetNumOfAromaticBondsToHeavyAtoms();</div>
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deepakjadmin
parents:
diff changeset
647 <p>Returns number of aromatic bonds from an <em>Atom</em> to other non-hydrogen or heavy atoms in
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deepakjadmin
parents:
diff changeset
648 a molecule.</p>
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deepakjadmin
parents:
diff changeset
649 </dd>
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deepakjadmin
parents:
diff changeset
650 <dt><strong><a name="getnumofaromaticbondstononhydrogenatoms" class="item"><strong>GetNumOfAromaticBondsToNonHydrogenAtoms</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
651 <dd>
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deepakjadmin
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diff changeset
652 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
653 $NumOfBonds = $Atom-&gt;GetNumOfAromaticBondsToNonHydrogenAtoms();</div>
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deepakjadmin
parents:
diff changeset
654 <p>Returns number of aromatic bonds from an <em>Atom</em> to other non-hydrogen or heavy atoms in
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deepakjadmin
parents:
diff changeset
655 a molecule.</p>
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deepakjadmin
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diff changeset
656 </dd>
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657 <dt><strong><a name="getnumofbonds" class="item"><strong>GetNumOfBonds</strong></a></strong></dt>
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diff changeset
658 <dd>
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deepakjadmin
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diff changeset
659 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
660 $NumOfBonds = $Atom-&gt;GetNumOfBonds();</div>
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deepakjadmin
parents:
diff changeset
661 <p>Returns number of bonds from an <em>Atom</em> to other atoms in a molecule.</p>
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deepakjadmin
parents:
diff changeset
662 </dd>
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deepakjadmin
parents:
diff changeset
663 <dt><strong><a name="getnumofbondsavailableforheavyatoms" class="item"><strong>GetNumOfBondsAvailableForHeavyAtoms</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
664 <dd>
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deepakjadmin
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diff changeset
665 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
666 $NumOfBonds = $Atom-&gt;GetNumOfBondsAvailableForHeavyAtoms();</div>
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deepakjadmin
parents:
diff changeset
667 <p>Get number of bonds available to form additional bonds with heavy atoms, excluding
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deepakjadmin
parents:
diff changeset
668 any implicit bonds to hydrogens set using <em>ImplicitHydrogens</em> property.</p>
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deepakjadmin
parents:
diff changeset
669 <p>It's different from number of implicit or missing hydrogens, both of which are equivalent.</p>
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deepakjadmin
parents:
diff changeset
670 <p>For example, in a SMILES string, [nH] ring atom corresponds to an aromatic nitrogen.
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deepakjadmin
parents:
diff changeset
671 Although the hydrogen specified for n is treated internally as implicit hydrogen and shows
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deepakjadmin
parents:
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672 up in missing hydrogen count, it's not available to participate in double bonds to additional
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deepakjadmin
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673 heavy atoms.</p>
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deepakjadmin
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diff changeset
674 </dd>
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deepakjadmin
parents:
diff changeset
675 <dt><strong><a name="getnumofbondsavailablefornonhydrogenatoms" class="item"><strong>GetNumOfBondsAvailableForNonHydrogenAtoms</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
676 <dd>
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deepakjadmin
parents:
diff changeset
677 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
678 $NumOfBonds = $Atom-&gt;GetNumOfBondsAvailableForNonHydrogenAtoms();</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
679 <p>Get number of bonds available to form additional bonds with heavy atoms, excluding
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
680 any implicit bonds to hydrogens set using ImplicitHydrogens property.</p>
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deepakjadmin
parents:
diff changeset
681 </dd>
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deepakjadmin
parents:
diff changeset
682 <dt><strong><a name="getnumofbondstoheavyatoms" class="item"><strong>GetNumOfBondsToHeavyAtoms</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
683 <dd>
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deepakjadmin
parents:
diff changeset
684 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
685 $NumOfBondsToHeavyAtoms = $Atom-&gt;GetNumOfBondsToHeavyAtoms();</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
686 <p>Returns number of bonds from an <em>Atom</em> to other heavy atoms in a molecule.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
687 </dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
688 <dt><strong><a name="getnumofbondstohydrogenatoms" class="item"><strong>GetNumOfBondsToHydrogenAtoms</strong></a></strong></dt>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
689 <dd>
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deepakjadmin
parents:
diff changeset
690 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
691 $NumOfBonds = $Atom-&gt;GetNumOfBondsToHydrogenAtoms();</div>
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deepakjadmin
parents:
diff changeset
692 <p>Returns number of bonds from an <em>Atom</em> to other hydrogen atoms in a molecule.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
693 </dd>
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deepakjadmin
parents:
diff changeset
694 <dt><strong><a name="getnumofbondstononhydrogenatoms" class="item"><strong>GetNumOfBondsToNonHydrogenAtoms</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
695 <dd>
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deepakjadmin
parents:
diff changeset
696 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
697 $NumOfBonds = $Atom-&gt;GetNumOfBondsToNonHydrogenAtoms();</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
698 <p>Returns number of bonds from an <em>Atom</em> to other non-hydrogen atoms in a molecule.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
699 </dd>
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deepakjadmin
parents:
diff changeset
700 <dt><strong><a name="getnumofbondtypestoheavyatoms" class="item"><strong>GetNumOfBondTypesToHeavyAtoms</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
701 <dd>
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deepakjadmin
parents:
diff changeset
702 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
703 ($NumOfSingleBonds, $NumOfDoubleBonds,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
704 $NumOfTripleBonds, $NumOfAromaticBonds) = $Atom-&gt;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
705 GetNumOfBondTypesToHeavyAtoms($CountAromaticBonds);</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
706 <p>Get number of single, double, triple, and aromatic bonds from an <em>Atom</em> to all other
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
707 non-hydrogen atoms in a molecule.</p>
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deepakjadmin
parents:
diff changeset
708 <p>Value of <em>CountAtomaticBonds</em> parameter controls whether number of aromatic
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
709 bonds is returned; default is not to count aromatic bonds. During counting of
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
710 aromatic bonds, the bond marked aromatic is not included in the count
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
711 of other bond types.</p>
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deepakjadmin
parents:
diff changeset
712 </dd>
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deepakjadmin
parents:
diff changeset
713 <dt><strong><a name="getnumofbondtypestononhydrogenatoms" class="item"><strong>GetNumOfBondTypesToNonHydrogenAtoms</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
714 <dd>
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deepakjadmin
parents:
diff changeset
715 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
716 ($NumOfSingleBonds, $NumOfDoubleBonds,
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
717 $NumOfTripleBonds, $NumOfAromaticBonds) = $Atom-&gt;
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
718 GetNumOfBondTypesToNonHydrogenAtoms($CountAromaticBonds);</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
719 <p>Get number of single, double, triple, and aromatic bonds from an <em>Atom</em> to all other
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
720 non-hydrogen atoms in a molecule.</p>
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deepakjadmin
parents:
diff changeset
721 <p>Value of <em>CountAtomaticBonds</em> parameter controls whether number of aromatic
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
722 bonds is returned; default is not to count aromatic bonds. During counting of
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
723 aromatic bonds, the bond marked aromatic is not included in the count
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
724 of other bond types.</p>
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deepakjadmin
parents:
diff changeset
725 </dd>
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deepakjadmin
parents:
diff changeset
726 <dt><strong><a name="getnumofdoublebondstoheavyatoms" class="item"><strong>GetNumOfDoubleBondsToHeavyAtoms</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
727 <dd>
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deepakjadmin
parents:
diff changeset
728 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
729 $NumOfDoubleBonds = $Atom-&gt;GetNumOfDoubleBondsToHeavyAtoms();</div>
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deepakjadmin
parents:
diff changeset
730 <p>Returns number of double bonds from an <em>Atom</em> to other heavy atoms or non-hydrogen
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
731 atoms in a molecule.</p>
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deepakjadmin
parents:
diff changeset
732 </dd>
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deepakjadmin
parents:
diff changeset
733 <dt><strong><a name="getnumofdoublebondstononhydrogenatoms" class="item"><strong>GetNumOfDoubleBondsToNonHydrogenAtoms</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
734 <dd>
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deepakjadmin
parents:
diff changeset
735 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
736 $NumOfDoubleBonds =$Atom-&gt;GetNumOfDoubleBondsToNonHydrogenAtoms();</div>
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deepakjadmin
parents:
diff changeset
737 <p>Returns number of double bonds from an <em>Atom</em> to other heavy atoms or non-hydrogen
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
738 atoms in a molecule.</p>
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deepakjadmin
parents:
diff changeset
739 </dd>
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deepakjadmin
parents:
diff changeset
740 <dt><strong><a name="getnumofheavyatomneighbors" class="item"><strong>GetNumOfHeavyAtomNeighbors</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
741 <dd>
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deepakjadmin
parents:
diff changeset
742 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
743 $NumOfNeighbors = $Atom-&gt;GetNumOfHeavyAtomNeighbors();</div>
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deepakjadmin
parents:
diff changeset
744 <p>Returns number heavy atom neighbors for an <em>Atom</em> in a molecule.</p>
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deepakjadmin
parents:
diff changeset
745 </dd>
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deepakjadmin
parents:
diff changeset
746 <dt><strong><a name="getnumofhydrogenatomneighbors" class="item"><strong>GetNumOfHydrogenAtomNeighbors</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
747 <dd>
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deepakjadmin
parents:
diff changeset
748 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
749 $NumOfNeighbors = $Atom-&gt;GetNumOfHydrogenAtomNeighbors();</div>
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deepakjadmin
parents:
diff changeset
750 <p>Returns number hydrogens atom neighbors for an <em>Atom</em> in a molecule.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
751 </dd>
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deepakjadmin
parents:
diff changeset
752 <dt><strong><a name="getnumofmissinghydrogens" class="item"><strong>GetNumOfMissingHydrogens</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
753 <dd>
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deepakjadmin
parents:
diff changeset
754 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
755 $NumOfMissingHydrogens = $Atom-&gt;GetNumOfMissingHydrogens();</div>
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deepakjadmin
parents:
diff changeset
756 <p>Returns number of implicit hydrogens for an <em>Atom</em> in a molecule. This value either
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
757 corresponds to explicitly set <em>ImplicitHydrogens</em> atom property or calculated as the
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
758 difference between the value of potential total valence and sum of bond orders to
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
759 both hydrogen and non-hydrogen atom neighbors.</p>
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deepakjadmin
parents:
diff changeset
760 </dd>
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deepakjadmin
parents:
diff changeset
761 <dt><strong><a name="getnumofexplicithydrogens" class="item"><strong>GetNumOfExplicitHydrogens</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
762 <dd>
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deepakjadmin
parents:
diff changeset
763 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
764 $NumOfExplicitHydrogens = $Atom-&gt;GetNumOfExplicitHydrogens();</div>
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deepakjadmin
parents:
diff changeset
765 <p>Returns number hydrogens atom neighbors for an <em>Atom</em> in a molecule.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
766 </dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
767 <dt><strong><a name="getnumofhydrogens" class="item"><strong>GetNumOfHydrogens</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
768 <dd>
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deepakjadmin
parents:
diff changeset
769 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
770 $NumOfHydrogens = $Atom-&gt;GetNumOfHydrogens();</div>
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deepakjadmin
parents:
diff changeset
771 <p>Returns total number of hydrogens for an <em>Atom</em> in a molecule including both hydrogen atom
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
772 neighbors and implicit hydrogens.</p>
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deepakjadmin
parents:
diff changeset
773 </dd>
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deepakjadmin
parents:
diff changeset
774 <dt><strong><a name="getnumofimplicithydrogens" class="item"><strong>GetNumOfImplicitHydrogens</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
775 <dd>
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deepakjadmin
parents:
diff changeset
776 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
777 $NumOfImplicitHydrogens = $Atom-&gt;GetNumOfImplicitHydrogens();</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
778 <p>Returns number of implicit hydrogens for an <em>Atom</em> in a molecule. This value either
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
779 corresponds to explicitly set <em>ImplicitHydrogens</em> atom property or calculated as the
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
780 difference between the value of potential total valence and sum of bond orders to
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
781 both hydrogen and non-hydrogen atom neighbors.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
782 </dd>
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deepakjadmin
parents:
diff changeset
783 <dt><strong><a name="getnumofneighbors" class="item"><strong>GetNumOfNeighbors</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
784 <dd>
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deepakjadmin
parents:
diff changeset
785 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
786 $NumOfNeighbors = $Atom-&gt;GetNumOfNeighbors();</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
787 <p>Returns number atom neighbors for an <em>Atom</em> in a molecule.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
788 </dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
789 <dt><strong><a name="getnumofnonhydrogenatomneighbors" class="item"><strong>GetNumOfNonHydrogenAtomNeighbors</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
790 <dd>
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deepakjadmin
parents:
diff changeset
791 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
792 $NumNeighbors = $This-&gt;GetNumOfNonHydrogenAtomNeighbors();</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
793 <p>Returns number non-hydrogens atom neighbors for an <em>Atom</em> in a molecule.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
794 </dd>
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deepakjadmin
parents:
diff changeset
795 <dt><strong><a name="getnumofrings" class="item"><strong>GetNumOfRings</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
796 <dd>
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deepakjadmin
parents:
diff changeset
797 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
798 $NumOfRings = $Atom-&gt;GetNumOfRings();</div>
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deepakjadmin
parents:
diff changeset
799 <p>Returns number of rings containing <em>Atom</em> in a molecule.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
800 </dd>
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deepakjadmin
parents:
diff changeset
801 <dt><strong><a name="getnumofringswithevensize" class="item"><strong>GetNumOfRingsWithEvenSize</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
802 <dd>
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deepakjadmin
parents:
diff changeset
803 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
804 $NumOfRings = $Atom-&gt;GetNumOfRingsWithEvenSize();</div>
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deepakjadmin
parents:
diff changeset
805 <p>Returns number of rings with even size containing <em>Atom</em> in a molecule.</p>
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deepakjadmin
parents:
diff changeset
806 </dd>
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deepakjadmin
parents:
diff changeset
807 <dt><strong><a name="getnumofringswithoddsize" class="item"><strong>GetNumOfRingsWithOddSize</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
808 <dd>
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deepakjadmin
parents:
diff changeset
809 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
810 $NumOfRings = $Atom-&gt;GetNumOfRingsWithOddSize();</div>
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deepakjadmin
parents:
diff changeset
811 <p>Returns number of rings with odd size containing <em>Atom</em> in a molecule.</p>
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deepakjadmin
parents:
diff changeset
812 </dd>
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deepakjadmin
parents:
diff changeset
813 <dt><strong><a name="getnumofringswithsize" class="item"><strong>GetNumOfRingsWithSize</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
814 <dd>
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deepakjadmin
parents:
diff changeset
815 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
816 $NumOfRings = $Atom-&gt;GetNumOfRingsWithSize($RingSize);</div>
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deepakjadmin
parents:
diff changeset
817 <p>Returns number of rings with specific <em>RingSize</em> containing <em>Atom</em> in a molecule.</p>
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deepakjadmin
parents:
diff changeset
818 </dd>
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deepakjadmin
parents:
diff changeset
819 <dt><strong><a name="getnumofringswithsizegreaterthan" class="item"><strong>GetNumOfRingsWithSizeGreaterThan</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
820 <dd>
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deepakjadmin
parents:
diff changeset
821 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
822 $NumOfRings = $Atom-&gt;GetNumOfRingsWithSizeGreaterThan($RingSize);</div>
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deepakjadmin
parents:
diff changeset
823 <p>Returns number of rings with size greater than specific <em>RingSize</em> containing <em>Atom</em>
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deepakjadmin
parents:
diff changeset
824 in a molecule.</p>
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deepakjadmin
parents:
diff changeset
825 </dd>
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deepakjadmin
parents:
diff changeset
826 <dt><strong><a name="getnumofringswithsizelessthan" class="item"><strong>GetNumOfRingsWithSizeLessThan</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
827 <dd>
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deepakjadmin
parents:
diff changeset
828 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
829 $NumOfRings = $Atom-&gt;GetNumOfRingsWithSizeLessThan($RingSize);</div>
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deepakjadmin
parents:
diff changeset
830 <p>Returns number of rings with size less than specific <em>RingSize</em> containing <em>Atom</em> in a molecule.</p>
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deepakjadmin
parents:
diff changeset
831 </dd>
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deepakjadmin
parents:
diff changeset
832 <dt><strong><a name="getnumofsigmaandpibondstoheavyatoms" class="item"><strong>GetNumOfSigmaAndPiBondsToHeavyAtoms</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
833 <dd>
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deepakjadmin
parents:
diff changeset
834 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
835 ($NumOfSigmaBonds, $NumOfPiBonds) = $Atom-&gt;
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deepakjadmin
parents:
diff changeset
836 GetNumOfSigmaAndPiBondsToHeavyAtoms();</div>
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deepakjadmin
parents:
diff changeset
837 <p>Get number of sigma and pi bonds from an <em>Atom</em> to all other non-hydrogen
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
838 atoms in a molecule.</p>
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deepakjadmin
parents:
diff changeset
839 <p>Sigma and pi bonds are counted using the following methodology: a single bond
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deepakjadmin
parents:
diff changeset
840 correspond to one sigma bond; a double bond contributes one to sigma bond count
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deepakjadmin
parents:
diff changeset
841 and one to pi bond count; a triple bond contributes one to sigma bond count and
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deepakjadmin
parents:
diff changeset
842 two to pi bond count.</p>
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deepakjadmin
parents:
diff changeset
843 </dd>
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deepakjadmin
parents:
diff changeset
844 <dt><strong><a name="getnumofsigmaandpibondstononhydrogenatoms" class="item"><strong>GetNumOfSigmaAndPiBondsToNonHydrogenAtoms</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
845 <dd>
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deepakjadmin
parents:
diff changeset
846 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
847 ($NumOfSigmaBonds, $NumOfPiBonds) = $Atom-&gt;
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deepakjadmin
parents:
diff changeset
848 GetNumOfSigmaAndPiBondsToNonHydrogenAtoms();</div>
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deepakjadmin
parents:
diff changeset
849 <p>Get number of sigma and pi bonds from an <em>Atom</em> to all other non-hydrogen
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
850 atoms in a molecule.</p>
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851 <p>Sigma and pi bonds are counted using the following methodology: a single bond
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852 correspond to one sigma bond; a double bond contributes one to sigma bond count
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853 and one to pi bond count; a triple bond contributes one to sigma bond count and
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854 two to pi bond count.</p>
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diff changeset
855 </dd>
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diff changeset
856 <dt><strong><a name="getnumofsinglebondstononhydrogenatoms" class="item"><strong>GetNumOfSingleBondsToNonHydrogenAtoms</strong></a></strong></dt>
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857 <dd>
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858 <div class="OptionsBox">
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parents:
diff changeset
859 $NumOfSingleBonds =$Atom-&gt;GetNumOfSingleBondsToNonHydrogenAtoms();</div>
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diff changeset
860 <p>Returns number of single bonds from an <em>Atom</em> to other heavy atoms or non-hydrogen
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861 atoms in a molecule.</p>
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diff changeset
862 </dd>
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863 <dt><strong><a name="getnumofsinglebondstoheavyatoms" class="item"><strong>GetNumOfSingleBondsToHeavyAtoms</strong></a></strong></dt>
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diff changeset
864 <dd>
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diff changeset
865 <div class="OptionsBox">
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parents:
diff changeset
866 $NumOfSingleBonds = $Atom-&gt;GetNumOfSingleBondsToHeavyAtoms();</div>
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867 <p>Returns number of single bonds from an <em>Atom</em> to other heavy atoms or non-hydrogen
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868 atoms in a molecule.</p>
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869 </dd>
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parents:
diff changeset
870 <dt><strong><a name="getnumoftriplebondstononhydrogenatoms" class="item"><strong>GetNumOfTripleBondsToNonHydrogenAtoms</strong></a></strong></dt>
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parents:
diff changeset
871 <dd>
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872 <div class="OptionsBox">
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diff changeset
873 $NumOfTripleBonds =$Atom-&gt;GetNumOfTripleBondsToNonHydrogenAtoms();</div>
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874 <p>Returns number of triple bonds from an <em>Atom</em> to other heavy atoms or non-hydrogen
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875 atoms in a molecule.</p>
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876 </dd>
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877 <dt><strong><a name="getnumoftriplebondstoheavyatoms" class="item"><strong>GetNumOfTripleBondsToHeavyAtoms</strong></a></strong></dt>
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parents:
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878 <dd>
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diff changeset
879 <div class="OptionsBox">
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880 $NumOfTripleBonds = $Atom-&gt;GetNumOfTripleBondsToHeavyAtoms();</div>
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881 <p>Returns number of triple bonds from an <em>Atom</em> to other heavy atoms or non-hydrogen
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882 atoms in a molecule.</p>
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883 </dd>
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884 <dt><strong><a name="getperiodnumber" class="item"><strong>GetPeriodNumber</strong></a></strong></dt>
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885 <dd>
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886 <div class="OptionsBox">
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887 $PeriodNumber = $Atom-&gt;GetPeriodNumber();</div>
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parents:
diff changeset
888 <p>Returns periodic table period number for an <em>Atom</em> in a molecule with a valid atomic number .</p>
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889 </dd>
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890 <dt><strong><a name="getrings" class="item"><strong>GetRings</strong></a></strong></dt>
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891 <dd>
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892 <div class="OptionsBox">
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893 @Rings = $Aotm-&gt;GetRings();</div>
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894 <p>Returns an array of references to arrays containing ring atoms corressponding to all rings containing
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895 <em>Atom</em> in a molecule.</p>
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896 </dd>
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897 <dt><strong><a name="getringswithevensize" class="item"><strong>GetRingsWithEvenSize</strong></a></strong></dt>
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898 <dd>
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899 <div class="OptionsBox">
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900 @Rings = $Aotm-&gt;GetRingsWithEvenSize();</div>
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901 <p>Returns an array of references to arrays containing ring atoms corressponding to all rings with even size
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902 containing <em>Atom</em> in a molecule.</p>
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903 </dd>
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904 <dt><strong><a name="getringswithoddsize" class="item"><strong>GetRingsWithOddSize</strong></a></strong></dt>
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905 <dd>
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906 <div class="OptionsBox">
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907 @Rings = $Aotm-&gt;GetRingsWithOddSize();</div>
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908 <p>Returns an array of references to arrays containing ring atoms corressponding to all rings with odd size
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909 containing <em>Atom</em> in a molecule.</p>
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910 </dd>
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911 <dt><strong><a name="getringswithsize" class="item"><strong>GetRingsWithSize</strong></a></strong></dt>
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912 <dd>
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913 <div class="OptionsBox">
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914 @Rings = $Aotm-&gt;GetRingsWithSize($RingSize);</div>
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915 <p>Returns an array of references to arrays containing ring atoms corressponding to all rings with specific
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916 <em>RingSize </em>containing <em>Atom</em> in a molecule.</p>
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917 </dd>
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918 <dt><strong><a name="getringswithsizegreaterthan" class="item"><strong>GetRingsWithSizeGreaterThan</strong></a></strong></dt>
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919 <dd>
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920 <div class="OptionsBox">
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diff changeset
921 @Rings = $Aotm-&gt;GetRingsWithSizeGreaterThan($RingSize);</div>
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922 <p>Returns an array of references to arrays containing ring atoms corressponding to all rings with size
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923 greater than specific <em>RingSize </em>containing <em>Atom</em> in a molecule.</p>
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924 </dd>
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925 <dt><strong><a name="getringswithsizelessthan" class="item"><strong>GetRingsWithSizeLessThan</strong></a></strong></dt>
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926 <dd>
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927 <div class="OptionsBox">
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928 @Rings = $Aotm-&gt;GetRingsWithSizeLessThan($RingSize);</div>
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929 <p>Returns an array of references to arrays containing ring atoms corressponding to all rings with size
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930 less than specific <em>RingSize </em>containing <em>Atom</em> in a molecule.</p>
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931 </dd>
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932 <dt><strong><a name="getsizeoflargestring" class="item"><strong>GetSizeOfLargestRing</strong></a></strong></dt>
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933 <dd>
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934 <div class="OptionsBox">
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935 $Size = $Atom-&gt;GetSizeOfLargestRing();</div>
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936 <p>Returns size of the largest ring containing <em>Atom</em> in a molecule.</p>
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937 </dd>
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938 <dt><strong><a name="getsizeofsmallestring" class="item"><strong>GetSizeOfSmallestRing</strong></a></strong></dt>
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939 <dd>
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940 <div class="OptionsBox">
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941 $Size = $Atom-&gt;GetSizeOfSmallestRing();</div>
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942 <p>Returns size of the smallest ring containing <em>Atom</em> in a molecule.</p>
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943 </dd>
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944 <dt><strong><a name="getsmallestring" class="item"><strong>GetSmallestRing</strong></a></strong></dt>
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945 <dd>
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946 <div class="OptionsBox">
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947 @RingAtoms = $Atom-&gt;GetSmallestRing();</div>
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948 <p>Returns an array of ring <em>Atom</em> objects corresponding to the largest ring containing <em>Atom</em>
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949 in a molecule.</p>
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950 </dd>
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951 <dt><strong><a name="getspinmultiplicity" class="item"><strong>GetSpinMultiplicity</strong></a></strong></dt>
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952 <dd>
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953 <div class="OptionsBox">
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954 $SpinMultiplicity = $Atom-&gt;GetSpinMultiplicity();</div>
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955 <p>Returns spin multiplicity of an <em>Atom</em> corresponding to one of these three
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956 values: explicitly set <strong>SpinMultiplicity</strong> property value; calculated from
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957 <strong>FreeRadicalElectrons</strong> property; value of 0.</p>
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958 <p>The <strong>SpinMultiplicity</strong> is calculate from <em>FreeRadicalElectrons</em> property as
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959 follows:</p>
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960 <div class="OptionsBox">
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961 FreeRadicalElectrons: 1; SpinMultiplicity: 2
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962 <br/> FreeRadicalElectrons: 2; SpinMultiplicity: 1
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963 <br/> FreeRadicalElectrons: other; SpinMultiplicity: 0</div>
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964 </dd>
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965 <dt><strong><a name="getsumofbondorders" class="item"><strong>GetSumOfBondOrders</strong></a></strong></dt>
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966 <dd>
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967 <div class="OptionsBox">
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968 $SumBondOrders = $Atom-&gt;GetSumOfBondOrders();</div>
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969 <p>Returns sum of bond orders corresponding to all atoms bonded to an <em>Atom</em> in a molecule.</p>
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970 </dd>
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971 <dt><strong><a name="getsumofbondorderstoheavyatoms" class="item"><strong>GetSumOfBondOrdersToHeavyAtoms</strong></a></strong></dt>
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972 <dd>
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973 <div class="OptionsBox">
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974 $SumBondOrders = $Atom-&gt;GetSumOfBondOrdersToHeavyAtoms();</div>
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975 <p>Returns sum of bond orders corresponding to all heavy atoms bonded to an <em>Atom</em> in a molecule.</p>
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976 </dd>
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977 <dt><strong><a name="getsumofbondorderstohydrogenatoms" class="item"><strong>GetSumOfBondOrdersToHydrogenAtoms</strong></a></strong></dt>
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978 <dd>
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979 <div class="OptionsBox">
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980 $SumBondOrders = $Atom-&gt;GetSumOfBondOrdersToHydrogenAtoms();</div>
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981 <p>Returns sum of bond orders corresponding to all hydrogen atoms bonded to an <em>Atom</em> in a molecule.</p>
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982 </dd>
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983 <dt><strong><a name="getsumofbondorderstononhydrogenatoms" class="item"><strong>GetSumOfBondOrdersToNonHydrogenAtoms</strong></a></strong></dt>
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984 <dd>
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985 <div class="OptionsBox">
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986 $SumBondOrders = $Atom-&gt;GetSumOfBondOrdersToNonHydrogenAtoms();</div>
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987 <p>Returns sum of bond orders corresponding to all non-hydrogen atoms bonded to an <em>Atom</em>
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988 in a molecule.</p>
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989 </dd>
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990 <dt><strong><a name="getvalence" class="item"><strong>GetValence</strong></a></strong></dt>
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991 <dd>
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992 <div class="OptionsBox">
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993 $Valence = $Atom-&gt;GetValence();</div>
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994 <p>Returns valence of an <em>Atom</em> in a molecule. Valence corresponds to number of electrons used
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995 by an atom in bonding:</p>
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996 <div class="OptionsBox">
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997 Valence = ValenceElectrons - ValenceFreeElectrons = BondingElectrons</div>
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998 <p>Single, double and triple bonds with bond orders of 1, 2, and 3 correspond to
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999 contribution of 1, 2, and 3 bonding electrons. So:</p>
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1000 <div class="OptionsBox">
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1001 Valence = SumOfBondOrders + NumOfMissingHydrogens + FormalCharge</div>
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1002 <p>where positive and negative values of FormalCharge increase and decrease the number of bonding
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1003 electrons, respectively.</p>
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1004 <p>The current release of MayaChemTools supports the following three valence models, which
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1005 are used during calculation of implicit hydrogens: MDLValenceModel, DaylightValenceModel,
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1006 InternalValenceModel or MayaChemToolsValenceModel.</p>
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1007 <p>Notes:</p>
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1008 <div class="OptionsBox">
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1009 . Missing hydrogens are included in the valence.
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1010 <br/> . For neutral molecules, valence and sum of bond orders are equal.
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1011 <br/> . For molecules containing only single bonds, SumOfBondOrders and
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1012 NumOfBonds are equal.
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1013 <br/> . Free radical electrons lead to the decrease in valence. For atoms with
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1014 explicit assignment of SpinMultiplicity property values corresponding to
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1015 Singlet (two unparied electrons corresponding to one spin state), Doublet
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1016 (free radical; an unpaired electron corresponding to two spin states),
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1017 and Triplet (two unparied electrons corresponding to three spin states;
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1018 divalent carbon atoms (carbenes)), FreeRadicalElectrons are calculated as follows:</div>
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1019 <div class="OptionsBox">
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1020 &nbsp;&nbsp;&nbsp; SpinMultiplicity: Doublet(2); FreeRadicalElectrons: 1 (one valence
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1021 <br/>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; electron not available for bonding)
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1022 <br/>&nbsp;&nbsp;&nbsp; SpinMultiplicity: Singlet(1)/Triplet(3); FreeRadicalElectrons: 2 (two
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1023 <br/>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; valence electrons not available for bonding)</div>
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1024 </dd>
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1025 <dt><strong><a name="getvalenceelectrons" class="item"><strong>GetValenceElectrons</strong></a></strong></dt>
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1026 <dd>
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1027 <div class="OptionsBox">
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1028 $ValenceElectrons = $Atom-&gt;GetValenceElectrons();</div>
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parents:
diff changeset
1029 <p>Returns valence electrons for an <strong>Atom</strong> which corresponds to either explicity set <em>ValenceElectrons</em>
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parents:
diff changeset
1030 atom property or valence electrons for the corresponding element in the periodic table available by
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parents:
diff changeset
1031 <strong>PeriodicTable</strong> module.</p>
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deepakjadmin
parents:
diff changeset
1032 </dd>
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deepakjadmin
parents:
diff changeset
1033 <dt><strong><a name="getvalencefreeelectrons" class="item"><strong>GetValenceFreeElectrons</strong></a></strong></dt>
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parents:
diff changeset
1034 <dd>
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parents:
diff changeset
1035 <div class="OptionsBox">
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parents:
diff changeset
1036 $ValenceFreeElectrons = $Atom-&gt;GetValenceFreeElectrons();
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deepakjadmin
parents:
diff changeset
1037 <br/> $ValenceFreeElectrons = $Atom-&gt;GetValenceFreeElectrons(
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deepakjadmin
parents:
diff changeset
1038 $ExcludeFreeRadicalElectrons);</div>
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deepakjadmin
parents:
diff changeset
1039 <p>Returns valence frees electrons for an <strong>Atom</strong> in a molecule. It corresponds to:</p>
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parents:
diff changeset
1040 <div class="OptionsBox">
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parents:
diff changeset
1041 ValenceElectrons - Valence
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parents:
diff changeset
1042 <br/> or
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parents:
diff changeset
1043 <br/> ValenceElectrons - NumOfMissingHydrogens - SumOfBondOrders - FormalCharge</div>
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deepakjadmin
parents:
diff changeset
1044 <p>Free radical electrons are included in the valence free electrons count by default.</p>
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parents:
diff changeset
1045 <p>Examples:</p>
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parents:
diff changeset
1046 <div class="OptionsBox">
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parents:
diff changeset
1047 NH3: ValenceFreeElectrons = 5 - 3 = 5 - 3 - 0 - 0 = 2
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parents:
diff changeset
1048 <br/> NH2: ValenceFreeElectrons = 5 - 3 = 5 - 2 - 1 - 0 = 2
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parents:
diff changeset
1049 <br/> NH4+; ValenceFreeElectrons = 5 - 5 = 5 - 4 - 0 - 1 = 0
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deepakjadmin
parents:
diff changeset
1050 <br/> NH3+; ValenceFreeElectrons = 5 - 5 = 5 - 3 - 1 - 1 = 0
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deepakjadmin
parents:
diff changeset
1051 <br/> C(=O)O- : ValenceFreeElectrons on O- = 6 - 0 = 6 - 1 - 0 - (-1) = 6
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parents:
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1052 <br/> C(=O)O- : ValenceFreeElectrons on =O = 6 - 2 = 6 - 2 - 0 - 0 = 4</div>
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deepakjadmin
parents:
diff changeset
1053 </dd>
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parents:
diff changeset
1054 <dt><strong><a name="getx" class="item"><strong>GetX</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1055 <dd>
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deepakjadmin
parents:
diff changeset
1056 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1057 $X = $Atom-&gt;GetX();</div>
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deepakjadmin
parents:
diff changeset
1058 <p>Returns value of X-coordinate for an <em>Atom</em>.</p>
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parents:
diff changeset
1059 </dd>
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parents:
diff changeset
1060 <dt><strong><a name="getxyz" class="item"><strong>GetXYZ</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1061 <dd>
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deepakjadmin
parents:
diff changeset
1062 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1063 @XYZ = $Atom-&gt;GetXYZ();
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parents:
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1064 <br/> $XYZRef = $Atom-&gt;GetXYZ();</div>
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parents:
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1065 <p>Returns an array or a reference to an array containing values for <em>Atom</em> coordinates.</p>
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parents:
diff changeset
1066 </dd>
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parents:
diff changeset
1067 <dt><strong><a name="getxyzvector" class="item"><strong>GetXYZVector</strong></a></strong></dt>
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parents:
diff changeset
1068 <dd>
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1069 <div class="OptionsBox">
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parents:
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1070 $XYZVector = $Atom-&gt;GetXYZVector();</div>
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parents:
diff changeset
1071 <p>Returns a <em>Vector</em> object containing values for <em>Atom</em> coordinates</p>
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parents:
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1072 </dd>
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1073 <dt><strong><a name="gety" class="item"><strong>GetY</strong></a></strong></dt>
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1074 <dd>
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1075 <div class="OptionsBox">
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parents:
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1076 $Y = $Atom-&gt;GetY();</div>
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parents:
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1077 <p>Returns value of Y-coordinate for an <em>Atom</em>.</p>
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parents:
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1078 </dd>
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parents:
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1079 <dt><strong><a name="getz" class="item"><strong>GetZ</strong></a></strong></dt>
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parents:
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1080 <dd>
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parents:
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1081 <div class="OptionsBox">
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parents:
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1082 $Z = $Atom-&gt;GetZ();</div>
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parents:
diff changeset
1083 <p>Returns value of Z-coordinate for an <em>Atom</em>.</p>
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parents:
diff changeset
1084 </dd>
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parents:
diff changeset
1085 <dt><strong><a name="isamidecarbon" class="item"><strong>IsAmideCarbon</strong></a></strong></dt>
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parents:
diff changeset
1086 <dd>
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parents:
diff changeset
1087 <div class="OptionsBox">
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parents:
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1088 $Status = $Atom-&gt;IsAmideCarbon();</div>
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parents:
diff changeset
1089 <p>Returns 1 or 0 based on whether it's amide carbon <em>Atom</em>.</p>
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parents:
diff changeset
1090 <p>An amide group is defineds as:</p>
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parents:
diff changeset
1091 <div class="OptionsBox">
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diff changeset
1092 R-C(=O)-N(-R')-R''</div>
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1093 <p>where:</p>
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parents:
diff changeset
1094 <div class="OptionsBox">
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parents:
diff changeset
1095 o R = Hydrogen or groups of atoms attached through carbon
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parents:
diff changeset
1096 <br/> o R' = Hydrogens or groups of atoms attached through carbon or
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parents:
diff changeset
1097 hetro atoms
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parents:
diff changeset
1098 <br/> o R'' = Hydrogens or groups of atoms attached through carbon or
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parents:
diff changeset
1099 hetro atoms</div>
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parents:
diff changeset
1100 </dd>
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parents:
diff changeset
1101 <dt><strong><a name="isamidenitrogen" class="item"><strong>IsAmideNitrogen</strong></a></strong></dt>
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diff changeset
1102 <dd>
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parents:
diff changeset
1103 <div class="OptionsBox">
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parents:
diff changeset
1104 $Status = $Atom-&gt;IsAmideNitrogen();</div>
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parents:
diff changeset
1105 <p>Returns 1 or 0 based on whether it's amide nitrogen <em>Atom</em>.</p>
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parents:
diff changeset
1106 </dd>
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parents:
diff changeset
1107 <dt><strong><a name="isaromatic" class="item"><strong>IsAromatic</strong></a></strong></dt>
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parents:
diff changeset
1108 <dd>
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parents:
diff changeset
1109 <div class="OptionsBox">
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parents:
diff changeset
1110 $Status = $Atom-&gt;IsAromatic();</div>
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parents:
diff changeset
1111 <p>Returns 1 or 0 based on whether it's an aromatic <em>Atom</em>.</p>
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parents:
diff changeset
1112 </dd>
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parents:
diff changeset
1113 <dt><strong><a name="isarsenic" class="item"><strong>IsArsenic</strong></a></strong></dt>
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parents:
diff changeset
1114 <dd>
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parents:
diff changeset
1115 <div class="OptionsBox">
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parents:
diff changeset
1116 $Status = $Atom-&gt;IsArsenic();</div>
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parents:
diff changeset
1117 <p>Returns 1 or 0 based on whether it's an arsenic <em>Atom</em>.</p>
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parents:
diff changeset
1118 </dd>
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diff changeset
1119 <dt><strong><a name="isbondedtoatom" class="item"><strong>IsBondedToAtom</strong></a></strong></dt>
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parents:
diff changeset
1120 <dd>
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parents:
diff changeset
1121 <div class="OptionsBox">
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parents:
diff changeset
1122 $Status = $Atom-&gt;IsBondedToAtom($OtherAtom);</div>
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parents:
diff changeset
1123 <p>Returns 1 or 0 based on whether <em>Atom</em> is bonded to <em>OtherAtom</em>.</p>
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parents:
diff changeset
1124 </dd>
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diff changeset
1125 <dt><strong><a name="isbromine" class="item"><strong>IsBromine</strong></a></strong></dt>
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diff changeset
1126 <dd>
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parents:
diff changeset
1127 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1128 $Status = $Atom-&gt;IsBromine();</div>
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parents:
diff changeset
1129 <p>Returns 1 or 0 based on whether it's a bromine <em>Atom</em>.</p>
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parents:
diff changeset
1130 </dd>
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parents:
diff changeset
1131 <dt><strong><a name="iscarbon" class="item"><strong>IsCarbon</strong></a></strong></dt>
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parents:
diff changeset
1132 <dd>
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deepakjadmin
parents:
diff changeset
1133 <div class="OptionsBox">
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parents:
diff changeset
1134 $Status = $Atom-&gt;IsCarbon();</div>
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parents:
diff changeset
1135 <p>Returns 1 or 0 based on whether it's a carbon <em>Atom</em>.</p>
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parents:
diff changeset
1136 </dd>
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parents:
diff changeset
1137 <dt><strong><a name="iscarboxylcarbon" class="item"><strong>IsCarboxylCarbon</strong></a></strong></dt>
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parents:
diff changeset
1138 <dd>
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parents:
diff changeset
1139 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1140 $Status = $Atom-&gt;IsCarboxylCarbon();</div>
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parents:
diff changeset
1141 <p>Returns 1 or 0 based on whether it's a carboxyl carbon atom in carboxyl group:
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deepakjadmin
parents:
diff changeset
1142 R-C(=O)-OH.</p>
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deepakjadmin
parents:
diff changeset
1143 </dd>
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parents:
diff changeset
1144 <dt><strong><a name="iscarboxyloxygen" class="item"><strong>IsCarboxylOxygen</strong></a></strong></dt>
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parents:
diff changeset
1145 <dd>
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parents:
diff changeset
1146 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1147 $Status = $Atom-&gt;IsCarboxylOxygen();</div>
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deepakjadmin
parents:
diff changeset
1148 <p>Returns 1 or 0 based on whether it's a carboxyl oxygen atom in carboxyl group:
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deepakjadmin
parents:
diff changeset
1149 R-C(=O)-OH.</p>
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deepakjadmin
parents:
diff changeset
1150 </dd>
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deepakjadmin
parents:
diff changeset
1151 <dt><strong><a name="iscarboxylatecarbon" class="item"><strong>IsCarboxylateCarbon</strong></a></strong></dt>
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parents:
diff changeset
1152 <dd>
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deepakjadmin
parents:
diff changeset
1153 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1154 $Status = $Atom-&gt;IsCarboxylateCarbon();</div>
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deepakjadmin
parents:
diff changeset
1155 <p>Returns 1 or 0 based on whether it's a carboxylate carbon atom in carboxyl group:
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deepakjadmin
parents:
diff changeset
1156 R-C(=O)-O-.</p>
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deepakjadmin
parents:
diff changeset
1157 </dd>
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deepakjadmin
parents:
diff changeset
1158 <dt><strong><a name="iscarboxylateoxygen" class="item"><strong>IsCarboxylateOxygen</strong></a></strong></dt>
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parents:
diff changeset
1159 <dd>
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deepakjadmin
parents:
diff changeset
1160 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1161 $Status = $Atom-&gt;IsCarboxylateOxygen();</div>
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deepakjadmin
parents:
diff changeset
1162 <p>Returns 1 or 0 based on whether it's a carboxylate oxygen atom in carboxyl group:
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deepakjadmin
parents:
diff changeset
1163 R-C(=O)-O-.</p>
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deepakjadmin
parents:
diff changeset
1164 </dd>
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parents:
diff changeset
1165 <dt><strong><a name="ischlorine" class="item"><strong>IsChlorine</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1166 <dd>
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deepakjadmin
parents:
diff changeset
1167 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1168 $Status = $Atom-&gt;IsChlorine();</div>
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deepakjadmin
parents:
diff changeset
1169 <p>Returns 1 or 0 based on whether it's a chlorine <em>Atom</em>.</p>
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deepakjadmin
parents:
diff changeset
1170 </dd>
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parents:
diff changeset
1171 <dt><strong><a name="isfluorine" class="item"><strong>IsFluorine</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1172 <dd>
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deepakjadmin
parents:
diff changeset
1173 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1174 $Status = $Atom-&gt;IsFluorine();</div>
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deepakjadmin
parents:
diff changeset
1175 <p>Returns 1 or 0 based on whether it's a fluorine <em>Atom</em>.</p>
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deepakjadmin
parents:
diff changeset
1176 </dd>
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deepakjadmin
parents:
diff changeset
1177 <dt><strong><a name="isfunctionalclasstype" class="item"><strong>IsFunctionalClassType</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1178 <dd>
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deepakjadmin
parents:
diff changeset
1179 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1180 $Status =$Atom-&gt;IsFunctionalClassType($Type);</div>
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deepakjadmin
parents:
diff changeset
1181 <p>Returns 1 or 0 based on whether it's a specified functional class <em>Type</em>.</p>
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deepakjadmin
parents:
diff changeset
1182 <p>The current release of MayaChemTools supports following abbreviations and descriptive
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deepakjadmin
parents:
diff changeset
1183 names for <em>FunctionalClassType</em>:</p>
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deepakjadmin
parents:
diff changeset
1184 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1185 HBD: HydrogenBondDonor
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deepakjadmin
parents:
diff changeset
1186 <br/> HBA: HydrogenBondAcceptor
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deepakjadmin
parents:
diff changeset
1187 <br/> PI : PositivelyIonizable
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deepakjadmin
parents:
diff changeset
1188 <br/> NI : NegativelyIonizable
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deepakjadmin
parents:
diff changeset
1189 <br/> Ar : Aromatic
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deepakjadmin
parents:
diff changeset
1190 <br/> Hal : Halogen
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deepakjadmin
parents:
diff changeset
1191 <br/> H : Hydrophobic
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deepakjadmin
parents:
diff changeset
1192 <br/> RA : RingAtom
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deepakjadmin
parents:
diff changeset
1193 <br/> CA : ChainAtom</div>
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deepakjadmin
parents:
diff changeset
1194 <p>The following definitions are used to determine functional class types: [ Ref 60-61, Ref 65-66 ]:</p>
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parents:
diff changeset
1195 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1196 HydrogenBondDonor: NH, NH2, OH
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deepakjadmin
parents:
diff changeset
1197 <br/> HydrogenBondAcceptor: N[!H], O
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deepakjadmin
parents:
diff changeset
1198 <br/> PositivelyIonizable: +, NH2
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parents:
diff changeset
1199 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div>
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deepakjadmin
parents:
diff changeset
1200 </dd>
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parents:
diff changeset
1201 <dt><strong><a name="isguadiniumcarbon" class="item"><strong>IsGuadiniumCarbon</strong></a></strong></dt>
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parents:
diff changeset
1202 <dd>
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deepakjadmin
parents:
diff changeset
1203 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1204 $Status = $Atom-&gt;IsGuadiniumCarbon();</div>
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deepakjadmin
parents:
diff changeset
1205 <p>Returns 1 or 0 based on whether it's a guadinium carbon in guadinium group by
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deepakjadmin
parents:
diff changeset
1206 checking its neighbors for a nitrogen in guadinium group.</p>
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deepakjadmin
parents:
diff changeset
1207 </dd>
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deepakjadmin
parents:
diff changeset
1208 <dt><strong><a name="isguadiniumnitrogen" class="item"><strong>IsGuadiniumNitrogen</strong></a></strong></dt>
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parents:
diff changeset
1209 <dd>
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deepakjadmin
parents:
diff changeset
1210 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1211 $Status = $Atom-&gt;IsGuadiniumNitrogen();</div>
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deepakjadmin
parents:
diff changeset
1212 <p>Returns 1 or 0 based on whether it's a guadinium nitrogen in guadinium group.</p>
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deepakjadmin
parents:
diff changeset
1213 <p>A guadinium group is defined as:</p>
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deepakjadmin
parents:
diff changeset
1214 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1215 R2N-C(=NR)-(NR2) or R2N-C(=NR2+)-(NR2)</div>
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deepakjadmin
parents:
diff changeset
1216 <p>where:</p>
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deepakjadmin
parents:
diff changeset
1217 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1218 o R = Hydrogens or group of atoms attached through carbon
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deepakjadmin
parents:
diff changeset
1219 <br/> o Only one of the three nitrogens has a double bond to carbon
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deepakjadmin
parents:
diff changeset
1220 and has optional formal charge allowing it to be neutral or charged state</div>
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deepakjadmin
parents:
diff changeset
1221 </dd>
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deepakjadmin
parents:
diff changeset
1222 <dt><strong><a name="ishbondacceptor" class="item"><strong>IsHBondAcceptor</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1223 <dd>
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deepakjadmin
parents:
diff changeset
1224 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1225 $Status =$Atom-&gt;IsHBondAcceptor();
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deepakjadmin
parents:
diff changeset
1226 <br/> $Status =$Atom-&gt;IsHBondAcceptor($HydrogenBondsType);</div>
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deepakjadmin
parents:
diff changeset
1227 <p>Returns 1 or 0 based on whether it's a hydrogen bond acceptor <em>Atom</em>.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1228 </dd>
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deepakjadmin
parents:
diff changeset
1229 <dt><strong><a name="ishbonddonor" class="item"><strong>IsHBondDonor</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1230 <dd>
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deepakjadmin
parents:
diff changeset
1231 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1232 $Status =$Atom-&gt;IsHBondDonor();
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deepakjadmin
parents:
diff changeset
1233 <br/> $Status =$Atom-&gt;IsHBondDonor($HydrogenBondsType);</div>
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deepakjadmin
parents:
diff changeset
1234 <p>Returns 1 or 0 based on whether it's a hydrogen bond donor <em>Atom</em>.</p>
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deepakjadmin
parents:
diff changeset
1235 </dd>
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deepakjadmin
parents:
diff changeset
1236 <dt><strong><a name="ishydrogenbondacceptor" class="item"><strong>IsHydrogenBondAcceptor</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1237 <dd>
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deepakjadmin
parents:
diff changeset
1238 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1239 $Status =$Atom-&gt;IsHydrogenBondAcceptor();
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deepakjadmin
parents:
diff changeset
1240 <br/> $Status =$Atom-&gt;IsHydrogenBondAcceptor($HydrogenBondsType);</div>
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deepakjadmin
parents:
diff changeset
1241 <p>Returns 1 or 0 based on whether it's a hydrogen bond acceptor <em>Atom</em>.</p>
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deepakjadmin
parents:
diff changeset
1242 </dd>
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deepakjadmin
parents:
diff changeset
1243 <dt><strong><a name="ishydrogenbonddonor" class="item"><strong>IsHydrogenBondDonor</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1244 <dd>
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deepakjadmin
parents:
diff changeset
1245 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1246 $Status =$Atom-&gt;IsHydrogenBondDonor();
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deepakjadmin
parents:
diff changeset
1247 <br/> $Status =$Atom-&gt;IsHydrogenBondDonor($HydrogenBondsType);</div>
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deepakjadmin
parents:
diff changeset
1248 <p>Returns 1 or 0 based on whether it's a hydrogen bond donor <em>Atom</em>.</p>
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deepakjadmin
parents:
diff changeset
1249 <p>The current release of MayaChemTools supports identification of two types of hydrogen bond
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deepakjadmin
parents:
diff changeset
1250 donor and acceptor atoms with these names:</p>
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deepakjadmin
parents:
diff changeset
1251 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1252 HBondsType1 or HydrogenBondsType1
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deepakjadmin
parents:
diff changeset
1253 <br/> HBondsType2 or HydrogenBondsType2</div>
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deepakjadmin
parents:
diff changeset
1254 <p>The names of these hydrogen bond types are rather arbitrary. However, their definitions have
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deepakjadmin
parents:
diff changeset
1255 specific meaning and are as follows:</p>
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deepakjadmin
parents:
diff changeset
1256 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1257 HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:</div>
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deepakjadmin
parents:
diff changeset
1258 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1259 &nbsp;&nbsp;&nbsp;&nbsp; Donor: NH, NH2, OH - Any N and O with available H
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deepakjadmin
parents:
diff changeset
1260 Acceptor: N[!H], O - Any N without available H and any O</div>
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deepakjadmin
parents:
diff changeset
1261 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1262 HydrogenBondsType2 [ Ref 91 ]:</div>
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deepakjadmin
parents:
diff changeset
1263 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1264 &nbsp;&nbsp;&nbsp;&nbsp; Donor: NH, NH2, OH - N and O with available H
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deepakjadmin
parents:
diff changeset
1265 Acceptor: N, O - And N and O</div>
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deepakjadmin
parents:
diff changeset
1266 <p>By default, <em>HydrogenBondsType1</em> is used to calculate number hydrogen bond donor
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1267 and acceptor atoms. <em>HydrogenBondsType2</em> corresponds to <strong>RuleOf5</strong> definition
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deepakjadmin
parents:
diff changeset
1268 of hydrogen bond donors and acceptors.</p>
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deepakjadmin
parents:
diff changeset
1269 </dd>
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deepakjadmin
parents:
diff changeset
1270 <dt><strong><a name="ishalogen" class="item"><strong>IsHalogen</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1271 <dd>
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deepakjadmin
parents:
diff changeset
1272 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1273 $Status =$Atom-&gt;IsHalogen();</div>
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deepakjadmin
parents:
diff changeset
1274 <p>Returns 1 or 0 based on whether it's a halogen <em>Atom</em>.</p>
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deepakjadmin
parents:
diff changeset
1275 </dd>
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deepakjadmin
parents:
diff changeset
1276 <dt><strong><a name="isheteroatom" class="item"><strong>IsHeteroAtom</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1277 <dd>
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deepakjadmin
parents:
diff changeset
1278 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1279 $Status = $Atom-&gt;IsHeteroAtom();</div>
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deepakjadmin
parents:
diff changeset
1280 <p>Returns 0 or 1 based on whether it's a hetro <em>Atom</em>. Following atoms are considered hetro atoms:
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deepakjadmin
parents:
diff changeset
1281 <strong>N, O, F, P, S, Cl, Br, I</strong>.</p>
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deepakjadmin
parents:
diff changeset
1282 </dd>
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deepakjadmin
parents:
diff changeset
1283 <dt><strong><a name="ishydrogen" class="item"><strong>IsHydrogen</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1284 <dd>
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deepakjadmin
parents:
diff changeset
1285 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1286 $Status = $Atom-&gt;IsHydrogen();</div>
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deepakjadmin
parents:
diff changeset
1287 <p>Returns 1 or 0 based on whether it's a hydrogen <em>Atom</em>.</p>
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deepakjadmin
parents:
diff changeset
1288 </dd>
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deepakjadmin
parents:
diff changeset
1289 <dt><strong><a name="ishydrophobic" class="item"><strong>IsHydrophobic</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1290 <dd>
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deepakjadmin
parents:
diff changeset
1291 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1292 $Status =$Atom-&gt;IsHydrophobic();</div>
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deepakjadmin
parents:
diff changeset
1293 <p>Returns 1 or 0 based on whether it's a hydrophobic <em>Atom</em>.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1294 </dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1295 <dt><strong><a name="isinring" class="item"><strong>IsInRing</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1296 <dd>
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deepakjadmin
parents:
diff changeset
1297 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1298 $Status = $Atom-&gt;IsInRing();</div>
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deepakjadmin
parents:
diff changeset
1299 <p>Returns 1 or 0 based on whether <em>Atom</em> is present in a ring.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1300 </dd>
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deepakjadmin
parents:
diff changeset
1301 <dt><strong><a name="isinringofsize" class="item"><strong>IsInRingOfSize</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1302 <dd>
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deepakjadmin
parents:
diff changeset
1303 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1304 $Status = $Atom-&gt;IsInRingOfSize($Size);</div>
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deepakjadmin
parents:
diff changeset
1305 <p>Returns 1 or 0 based on whether <em>Atom</em> is present in a ring of specific <em>Size</em>.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1306 </dd>
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deepakjadmin
parents:
diff changeset
1307 <dt><strong><a name="isiodine" class="item"><strong>IsIodine</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1308 <dd>
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deepakjadmin
parents:
diff changeset
1309 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1310 $Status = $Atom-&gt;IsIodine();</div>
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deepakjadmin
parents:
diff changeset
1311 <p>Returns 1 or 0 based on whether it's an iodine <em>Atom</em>.</p>
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deepakjadmin
parents:
diff changeset
1312 </dd>
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deepakjadmin
parents:
diff changeset
1313 <dt><strong><a name="isisotope" class="item"><strong>IsIsotope</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1314 <dd>
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deepakjadmin
parents:
diff changeset
1315 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1316 $Status =$Atom-&gt;IsIsotope();</div>
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deepakjadmin
parents:
diff changeset
1317 <p>Returns 1 or 0 based on whether it's an isotope <em>Atom</em>.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1318 </dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1319 <dt><strong><a name="islipophilic" class="item"><strong>IsLipophilic</strong></a></strong></dt>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1320 <dd>
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deepakjadmin
parents:
diff changeset
1321 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1322 $Status =$Atom-&gt;IsLipophilic();</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1323 <p>Returns 1 or 0 based on whether it's a lipophilic <em>Atom</em>.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1324 </dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1325 <dt><strong><a name="ismetallic" class="item"><strong>IsMetallic</strong></a></strong></dt>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1326 <dd>
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deepakjadmin
parents:
diff changeset
1327 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1328 $Status = $Atom-&gt;IsMetallic();</div>
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deepakjadmin
parents:
diff changeset
1329 <p>Returns 1 or 0 based on whether it's a metallic <em>Atom</em>.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1330 </dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1331 <dt><strong><a name="isnegativelyionizable" class="item"><strong>IsNegativelyIonizable</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1332 <dd>
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deepakjadmin
parents:
diff changeset
1333 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1334 $Status =$Atom-&gt;IsNegativelyIonizable();</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1335 <p>Returns 1 or 0 based on whether it's a negatively ionizable atom <em>Atom</em>.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1336 </dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1337 <dt><strong><a name="isnitrogen" class="item"><strong>IsNitrogen</strong></a></strong></dt>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1338 <dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1339 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1340 $Status = $Atom-&gt;IsNitrogen();</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1341 <p>Returns 1 or 0 based on whether it's a nitrogen <em>Atom</em>.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1342 </dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1343 <dt><strong><a name="isnoncarbonorhydrogen" class="item"><strong>IsNonCarbonOrHydrogen</strong></a></strong></dt>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1344 <dd>
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deepakjadmin
parents:
diff changeset
1345 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1346 $Status =$Atom-&gt;IsNonCarbonOrHydrogen();</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1347 <p>Returns 1 or 0 based on whether it's not a carbon or hydrogen <em>Atom</em>.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1348 </dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1349 <dt><strong><a name="isnotinring" class="item"><strong>IsNotInRing</strong></a></strong></dt>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1350 <dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1351 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1352 $Status = $Atom-&gt;IsNotInRing();</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1353 <p>Returns 1 or 0 based on whether <em>Atom</em> is not present in a ring.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1354 </dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1355 <dt><strong><a name="isonlyinonering" class="item"><strong>IsOnlyInOneRing</strong></a></strong></dt>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1356 <dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1357 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1358 $Status = $Atom-&gt;IsOnlyInOneRing();</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1359 <p>Returns 1 or 0 based on whether <em>Atom</em> is only present in one ring.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1360 </dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1361 <dt><strong><a name="isoxygen" class="item"><strong>IsOxygen</strong></a></strong></dt>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1362 <dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1363 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1364 $Status = $Atom-&gt;IsOxygen();</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1365 <p>Returns 0 or 1 based on whether it's an oxygen <em>Atom</em>.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1366 </dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1367 <dt><strong><a name="isphosphorus" class="item"><strong>IsPhosphorus</strong></a></strong></dt>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1368 <dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1369 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1370 $Status = $Atom-&gt;IsPhosphorus();</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1371 <p>Returns 0 or 1 based on whether it's a phosphorus <em>Atom</em>.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1372 </dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1373 <dt><strong><a name="isphosphateoxygen" class="item"><strong>IsPhosphateOxygen</strong></a></strong></dt>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1374 <dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1375 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1376 $Status = $Atom-&gt;IsPhosphateOxygen();</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1377 <p>Returns 1 or 0 based on whether it's a phosphate oxygen in phosphate group.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1378 <p>A phosphate group is defined as:</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1379 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1380 AO-(O=)P(-OA)-OA</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1381 <p>Where:</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1382 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1383 A - Any group of atoms including hydrogens</div>
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deepakjadmin
parents:
diff changeset
1384 </dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1385 <dt><strong><a name="isphosphatephosphorus" class="item"><strong>IsPhosphatePhosphorus</strong></a></strong></dt>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1386 <dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1387 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1388 $Status = $Atom-&gt;IsPhosphatePhosphorus();</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1389 <p>Returns 1 or 0 based on whether it's a phosphate phosphorus in phosphate group.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1390 </dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1391 <dt><strong><a name="ispolaratom" class="item"><strong>IsPolarAtom</strong></a></strong></dt>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1392 <dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1393 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1394 $Status = $Atom-&gt;IsPolarAtom();</div>
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deepakjadmin
parents:
diff changeset
1395 <p>Returns 0 or 1 based on whether it's a polar <em>Atom</em>. Following atoms are considered polar atoms:
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1396 <strong>N, O, P, S</strong>.</p>
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deepakjadmin
parents:
diff changeset
1397 </dd>
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deepakjadmin
parents:
diff changeset
1398 <dt><strong><a name="ispolarhydrogen" class="item"><strong>IsPolarHydrogen</strong></a></strong></dt>
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parents:
diff changeset
1399 <dd>
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deepakjadmin
parents:
diff changeset
1400 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1401 $Status = $Atom-&gt;IsPolarHydrogen();</div>
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deepakjadmin
parents:
diff changeset
1402 <p>Returns 0 or 1 based on whether it's a hydrogen <em>Atom</em> bonded to a polar atom.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1403 </dd>
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parents:
diff changeset
1404 <dt><strong><a name="ispositivelyionizable" class="item"><strong>IsPositivelyIonizable</strong></a></strong></dt>
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parents:
diff changeset
1405 <dd>
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deepakjadmin
parents:
diff changeset
1406 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1407 $Status =$Atom-&gt;IsPositivelyIonizable();</div>
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deepakjadmin
parents:
diff changeset
1408 <p>Returns 1 or 0 based on whether it's a positively ionizable <em>Atom</em>.</p>
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deepakjadmin
parents:
diff changeset
1409 </dd>
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parents:
diff changeset
1410 <dt><strong><a name="issaturated" class="item"><strong>IsSaturated</strong></a></strong></dt>
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parents:
diff changeset
1411 <dd>
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parents:
diff changeset
1412 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1413 $Status = $Atom-&gt;IsSaturated();</div>
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deepakjadmin
parents:
diff changeset
1414 <p>Returns 1 or 0 based on whether it's a saturated <em>Atom</em>. An atom attached
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parents:
diff changeset
1415 to other atoms with only single bonds is considered a saturated atom.</p>
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deepakjadmin
parents:
diff changeset
1416 </dd>
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deepakjadmin
parents:
diff changeset
1417 <dt><strong><a name="isselenium" class="item"><strong>IsSelenium</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1418 <dd>
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deepakjadmin
parents:
diff changeset
1419 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1420 $Status = $Atom-&gt;IsSelenium();</div>
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deepakjadmin
parents:
diff changeset
1421 <p>Returns 0 or 1 based on whether it's a selenium <em>Atom</em>.</p>
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deepakjadmin
parents:
diff changeset
1422 </dd>
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parents:
diff changeset
1423 <dt><strong><a name="isstereocenter" class="item"><strong>IsStereoCenter</strong></a></strong></dt>
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parents:
diff changeset
1424 <dd>
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deepakjadmin
parents:
diff changeset
1425 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1426 $Status = $Atom-&gt;IsStereoCenter();</div>
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deepakjadmin
parents:
diff changeset
1427 <p>Returns 0 or 1 based on whether it's marked as a stero center <em>Atom</em> by explicit setting
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1428 of <em>StereoCenter</em> atom propert to value of <em>1</em>.</p>
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deepakjadmin
parents:
diff changeset
1429 </dd>
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parents:
diff changeset
1430 <dt><strong><a name="issilicon" class="item"><strong>IsSilicon</strong></a></strong></dt>
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parents:
diff changeset
1431 <dd>
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parents:
diff changeset
1432 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1433 $Status = $Atom-&gt;IsSilicon();</div>
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deepakjadmin
parents:
diff changeset
1434 <p>Returns 0 or 1 based on whether it's a silicon <em>Atom</em>.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1435 </dd>
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deepakjadmin
parents:
diff changeset
1436 <dt><strong><a name="issulfur" class="item"><strong>IsSulfur</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1437 <dd>
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deepakjadmin
parents:
diff changeset
1438 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1439 $Status = $Atom-&gt;IsSulfur();</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1440 <p>Returns 0 or 1 based on whether it's a sulfur <em>Atom</em>.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1441 </dd>
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deepakjadmin
parents:
diff changeset
1442 <dt><strong><a name="issulphur" class="item"><strong>IsSulphur</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1443 <dd>
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deepakjadmin
parents:
diff changeset
1444 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1445 $Status = $Atom-&gt;IsSulphur();</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1446 <p>Returns 0 or 1 based on whether it's a sulfur <em>Atom</em>.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1447 </dd>
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deepakjadmin
parents:
diff changeset
1448 <dt><strong><a name="istellurium" class="item"><strong>IsTellurium</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1449 <dd>
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deepakjadmin
parents:
diff changeset
1450 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1451 $Status = $Atom-&gt;IsTellurium();</div>
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deepakjadmin
parents:
diff changeset
1452 <p>Returns 0 or 1 based on whether it's a tellurium <em>Atom</em>.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1453 </dd>
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deepakjadmin
parents:
diff changeset
1454 <dt><strong><a name="isterminal" class="item"><strong>IsTerminal</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1455 <dd>
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deepakjadmin
parents:
diff changeset
1456 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1457 $Status = $Atom-&gt;IsTerminal();</div>
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deepakjadmin
parents:
diff changeset
1458 <p>Returns 0 or 1 based on whether it's a terminal <em>Atom</em> attached to no
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1459 more than one non-hydrogen atom.</p>
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deepakjadmin
parents:
diff changeset
1460 </dd>
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deepakjadmin
parents:
diff changeset
1461 <dt><strong><a name="isunsaturated" class="item"><strong>IsUnsaturated</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1462 <dd>
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deepakjadmin
parents:
diff changeset
1463 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1464 $Status = $Atom-&gt;IsUnsaturated();</div>
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deepakjadmin
parents:
diff changeset
1465 <p>Returns 1 or 0 based on whether it's as unsaturated <em>Atom</em>. An atom attached
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1466 to other atoms with at least one non-single bond is considered an unsaturated atom.</p>
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deepakjadmin
parents:
diff changeset
1467 </dd>
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deepakjadmin
parents:
diff changeset
1468 <dt><strong><a name="istopologicalpharmacophoretype" class="item"><strong>IsTopologicalPharmacophoreType</strong></a></strong></dt>
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parents:
diff changeset
1469 <dd>
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deepakjadmin
parents:
diff changeset
1470 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1471 $Status =$Atom-&gt;IsTopologicalPharmacophoreType();</div>
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deepakjadmin
parents:
diff changeset
1472 <p>Returns 1 or 0 based on whether it's any of the supportyed topological pharmacophore
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deepakjadmin
parents:
diff changeset
1473 <em>Atom</em> type. See <em>IsFunctionalClassType</em> for a list of supported types.</p>
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deepakjadmin
parents:
diff changeset
1474 </dd>
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deepakjadmin
parents:
diff changeset
1475 <dt><strong><a name="setatomsymbol" class="item"><strong>SetAtomSymbol</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1476 <dd>
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deepakjadmin
parents:
diff changeset
1477 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1478 $Atom-&gt;SetAtomSymbol($AtomicSymbol);</div>
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deepakjadmin
parents:
diff changeset
1479 <p>Sets atom symbol for <em>Atom</em> and returns <em>Atom</em> object. The appropriate atomic number is also
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1480 set automatically.</p>
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deepakjadmin
parents:
diff changeset
1481 </dd>
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deepakjadmin
parents:
diff changeset
1482 <dt><strong><a name="setatomicnumber" class="item"><strong>SetAtomicNumber</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1483 <dd>
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parents:
diff changeset
1484 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1485 $Atom-&gt;SetAtomicNumber($AtomicNumber);</div>
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deepakjadmin
parents:
diff changeset
1486 <p>Sets atomic number for <em>Atom</em> and returns <em>Atom</em> object. The appropriate atom symbol is also
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1487 set automatically.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1488 </dd>
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deepakjadmin
parents:
diff changeset
1489 <dt><strong><a name="setmassnumber" class="item"><strong>SetMassNumber</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1490 <dd>
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deepakjadmin
parents:
diff changeset
1491 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1492 $Atom-&gt;SetMassNumber($MassNumber);</div>
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deepakjadmin
parents:
diff changeset
1493 <p>Sets mass number for <em>Atom</em> and returns <em>Atom</em> object.</p>
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deepakjadmin
parents:
diff changeset
1494 </dd>
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deepakjadmin
parents:
diff changeset
1495 <dt><strong><a name="setstereocenter" class="item"><strong>SetStereoCenter</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1496 <dd>
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deepakjadmin
parents:
diff changeset
1497 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1498 $Atom-&gt;SetStereoCenter($StereoCenter);</div>
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deepakjadmin
parents:
diff changeset
1499 <p>Sets stereo center for <em>Atom</em> and returns <em>Atom</em> object.</p>
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deepakjadmin
parents:
diff changeset
1500 </dd>
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deepakjadmin
parents:
diff changeset
1501 <dt><strong><a name="setstereochemistry" class="item"><strong>SetStereochemistry</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1502 <dd>
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deepakjadmin
parents:
diff changeset
1503 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1504 $Atom-&gt;SetStereochemistry($Stereochemistry);</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1505 <p>Sets stereo chemistry for <em>Atom</em> and returns <em>Atom</em> object.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1506 </dd>
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deepakjadmin
parents:
diff changeset
1507 <dt><strong><a name="setx" class="item"><strong>SetX</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1508 <dd>
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deepakjadmin
parents:
diff changeset
1509 <div class="OptionsBox">
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deepakjadmin
parents:
diff changeset
1510 $Atom-&gt;SetX($Value);</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1511 <p>Sets X-coordinate value for <em>Atom</em> and returns <em>Atom</em> object.</p>
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deepakjadmin
parents:
diff changeset
1512 </dd>
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deepakjadmin
parents:
diff changeset
1513 <dt><strong><a name="setxyz" class="item"><strong>SetXYZ</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1514 <dd>
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deepakjadmin
parents:
diff changeset
1515 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1516 $Atom-&gt;SetXYZ(@XYZValues);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1517 <br/> $Atom-&gt;SetXYZ($XYZValuesRef);
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1518 <br/> $Atom-&gt;SetXYZ($XYZVector);</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1519 <p>Sets <em>Atom</em> coordinates using an array, reference to an array or a <em>Vector</em> object and
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1520 returns <em>Atom</em> object.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1521 </dd>
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deepakjadmin
parents:
diff changeset
1522 <dt><strong><a name="sety" class="item"><strong>SetY</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1523 <dd>
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deepakjadmin
parents:
diff changeset
1524 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1525 $Atom-&gt;SetY($Value);</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1526 <p>Sets Y-coordinate value for <em>Atom</em> and returns <em>Atom</em> object.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1527 </dd>
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deepakjadmin
parents:
diff changeset
1528 <dt><strong><a name="setz" class="item"><strong>SetZ</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1529 <dd>
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deepakjadmin
parents:
diff changeset
1530 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1531 $Atom-&gt;SetZ($Value);</div>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1532 <p>Sets Z-coordinate value for <em>Atom</em> and returns <em>Atom</em> object.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1533 </dd>
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deepakjadmin
parents:
diff changeset
1534 <dt><strong><a name="stringifyatom" class="item"><strong>StringifyAtom</strong></a></strong></dt>
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deepakjadmin
parents:
diff changeset
1535 <dd>
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deepakjadmin
parents:
diff changeset
1536 <div class="OptionsBox">
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1537 $AtomString = $Atom-&gt;StringifyAtom();</div>
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deepakjadmin
parents:
diff changeset
1538 <p>Returns a string containing information about <em>Atom</em> object.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1539 </dd>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1540 </dl>
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deepakjadmin
parents:
diff changeset
1541 <p>
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deepakjadmin
parents:
diff changeset
1542 </p>
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deepakjadmin
parents:
diff changeset
1543 <h2>AUTHOR</h2>
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deepakjadmin
parents:
diff changeset
1544 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1545 <p>
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deepakjadmin
parents:
diff changeset
1546 </p>
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deepakjadmin
parents:
diff changeset
1547 <h2>SEE ALSO</h2>
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deepakjadmin
parents:
diff changeset
1548 <p><a href="./Bond.html">Bond.pm</a>,&nbsp<a href="./Molecule.html">Molecule.pm</a>,&nbsp<a href="./MoleculeFileIO.html">MoleculeFileIO.pm</a>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1549 </p>
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deepakjadmin
parents:
diff changeset
1550 <p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1551 </p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1552 <h2>COPYRIGHT</h2>
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deepakjadmin
parents:
diff changeset
1553 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1554 <p>This file is part of MayaChemTools.</p>
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deepakjadmin
parents:
diff changeset
1555 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1556 the terms of the GNU Lesser General Public License as published by the Free
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1557 Software Foundation; either version 3 of the License, or (at your option)
73ae111cf86f Uploaded
deepakjadmin
parents:
diff changeset
1558 any later version.</p>
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deepakjadmin
parents:
diff changeset
1559 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
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deepakjadmin
parents:
diff changeset
1560 <table width="100%" border=0 cellpadding=0 cellspacing=2>
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deepakjadmin
parents:
diff changeset
1561 <tr align="left" valign="top"><td width="33%" align="left"><a href="./AminoAcids.html" title="AminoAcids.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<a href="./AtomicDescriptors.html" title="AtomicDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Atom.pm</strong></td></tr>
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parents:
diff changeset
1562 </table>
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deepakjadmin
parents:
diff changeset
1563 </div>
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deepakjadmin
parents:
diff changeset
1564 <br />
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deepakjadmin
parents:
diff changeset
1565 <center>
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deepakjadmin
parents:
diff changeset
1566 <img src="../../images/h2o2.png">
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deepakjadmin
parents:
diff changeset
1567 </center>
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parents:
diff changeset
1568 </body>
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deepakjadmin
parents:
diff changeset
1569 </html>