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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/modules/html/Molecule.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,1016 @@ +<html> +<head> +<title>MayaChemTools:Documentation:Molecule.pm</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<tr align="left" valign="top"><td width="33%" align="left"><a href="./MolecularFormula.html" title="MolecularFormula.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./MoleculeFileIO.html" title="MoleculeFileIO.html">Next</a></td><td width="34%" align="middle"><strong>Molecule.pm</strong></td><td width="33%" align="right"><a href="././code/Molecule.html" title="View source code">Code</a> | <a href="./../pdf/Molecule.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/Molecule.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/Molecule.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/Molecule.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>Molecule - Molecule class</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>use Molecule;</p> +<p>use Molecule qw(:all);</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p><strong>Molecule</strong> class provides the following methods:</p> +<p> <a href="#new">new</a>, <a href="#addatom">AddAtom</a>, <a href="#addatoms">AddAtoms</a>, <a href="#addbond">AddBond</a>, <a href="#addbonds">AddBonds</a>, <a href="#addhydrogens">AddHydrogens</a>, <a href="#addpolarhydrogens">AddPolarHydrogens</a> +, <a href="#clearrings">ClearRings</a>, <a href="#copy">Copy</a>, <a href="#deletearomaticity">DeleteAromaticity</a>, <a href="#deleteatom">DeleteAtom</a>, <a href="#deleteatoms">DeleteAtoms</a>, <a href="#deletebond">DeleteBond</a> +, <a href="#deletebonds">DeleteBonds</a>, <a href="#deletehydrogens">DeleteHydrogens</a>, <a href="#deletepolarhydrogens">DeletePolarHydrogens</a>, <a href="#detectaromaticity">DetectAromaticity</a> +, <a href="#detectrings">DetectRings</a>, <a href="#formatelementalcompositioninformation">FormatElementalCompositionInformation</a>, <a href="#getallatompaths">GetAllAtomPaths</a> +, <a href="#getallatompathsstartingat">GetAllAtomPathsStartingAt</a>, <a href="#getallatompathsstartingatwithlength">GetAllAtomPathsStartingAtWithLength</a> +, <a href="#getallatompathsstartingatwithlengthupto">GetAllAtomPathsStartingAtWithLengthUpto</a>, <a href="#getallatompathswithlength">GetAllAtomPathsWithLength</a> +, <a href="#getallatompathswithlengthupto">GetAllAtomPathsWithLengthUpto</a>, <a href="#getaromaticrings">GetAromaticRings</a>, <a href="#getaromaticitymodel">GetAromaticityModel</a> +, <a href="#getatomneighborhoods">GetAtomNeighborhoods</a>, <a href="#getatomneighborhoodswithradiusupto">GetAtomNeighborhoodsWithRadiusUpto</a> +, <a href="#getatomneighborhoodswithsuccessoratoms">GetAtomNeighborhoodsWithSuccessorAtoms</a> +, <a href="#getatomneighborhoodswithsuccessoratomsandradiusupto">GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto</a>, <a href="#getatompathbonds">GetAtomPathBonds</a> +, <a href="#getatompaths">GetAtomPaths</a>, <a href="#getatompathsbetween">GetAtomPathsBetween</a>, <a href="#getatompathsstartingat">GetAtomPathsStartingAt</a> +, <a href="#getatompathsstartingatwithlength">GetAtomPathsStartingAtWithLength</a>, <a href="#getatompathsstartingatwithlengthupto">GetAtomPathsStartingAtWithLengthUpto</a> +, <a href="#getatompathswithlength">GetAtomPathsWithLength</a>, <a href="#getatompathswithlengthupto">GetAtomPathsWithLengthUpto</a>, <a href="#getatoms">GetAtoms</a>, <a href="#getbonds">GetBonds</a>, <a href="#getcharge">GetCharge</a> +, <a href="#getconnectedcomponents">GetConnectedComponents</a>, <a href="#getconnectedcomponentsatoms">GetConnectedComponentsAtoms</a>, <a href="#getdimensionality">GetDimensionality</a> +, <a href="#getelementalcomposition">GetElementalComposition</a>, <a href="#getelementsandnonelements">GetElementsAndNonElements</a>, <a href="#getexactmass">GetExactMass</a>, <a href="#getformalcharge">GetFormalCharge</a> +, <a href="#getfreeradicalelectrons">GetFreeRadicalElectrons</a>, <a href="#getfusedandnonfusedrings">GetFusedAndNonFusedRings</a>, <a href="#getlargestconnectedcomponent">GetLargestConnectedComponent</a> +, <a href="#getlargestconnectedcomponentatoms">GetLargestConnectedComponentAtoms</a>, <a href="#getlargestring">GetLargestRing</a>, <a href="#getmolecularformula">GetMolecularFormula</a> +, <a href="#getmolecularweight">GetMolecularWeight</a>, <a href="#getnumofaromaticrings">GetNumOfAromaticRings</a>, <a href="#getnumofatoms">GetNumOfAtoms</a>, <a href="#getnumofbonds">GetNumOfBonds</a> +, <a href="#getnumofconnectedcomponents">GetNumOfConnectedComponents</a>, <a href="#getnumofelementsandnonelements">GetNumOfElementsAndNonElements</a>, <a href="#getnumofheavyatoms">GetNumOfHeavyAtoms</a> +, <a href="#getnumofhydrogenatoms">GetNumOfHydrogenAtoms</a>, <a href="#getnumofmissinghydrogenatoms">GetNumOfMissingHydrogenAtoms</a>, <a href="#getnumofnonhydrogenatoms">GetNumOfNonHydrogenAtoms</a> +, <a href="#getnumofrings">GetNumOfRings</a>, <a href="#getnumofringswithevensize">GetNumOfRingsWithEvenSize</a>, <a href="#getnumofringswithoddsize">GetNumOfRingsWithOddSize</a> +, <a href="#getnumofringswithsize">GetNumOfRingsWithSize</a>, <a href="#getnumofringswithsizegreaterthan">GetNumOfRingsWithSizeGreaterThan</a> +, <a href="#getnumofringswithsizelessthan">GetNumOfRingsWithSizeLessThan</a>, <a href="#getringbonds">GetRingBonds</a>, <a href="#getringbondsfromrings">GetRingBondsFromRings</a>, <a href="#getrings">GetRings</a> +, <a href="#getringswithevensize">GetRingsWithEvenSize</a>, <a href="#getringswithoddsize">GetRingsWithOddSize</a>, <a href="#getringswithsize">GetRingsWithSize</a> +, <a href="#getringswithsizegreaterthan">GetRingsWithSizeGreaterThan</a>, <a href="#getringswithsizelessthan">GetRingsWithSizeLessThan</a>, <a href="#getsizeoflargestring">GetSizeOfLargestRing</a> +, <a href="#getsizeofsmallestring">GetSizeOfSmallestRing</a>, <a href="#getsmallestring">GetSmallestRing</a>, <a href="#getspinmultiplicity">GetSpinMultiplicity</a> +, <a href="#getsupportedaromaticitymodels">GetSupportedAromaticityModels</a>, <a href="#gettopologicallysortedatoms">GetTopologicallySortedAtoms</a>, <a href="#getvalencemodel">GetValenceModel</a> +, <a href="#hasaromaticatomsinrings">HasAromaticAtomsInRings</a>, <a href="#hasaromaticatomsnotinrings">HasAromaticAtomsNotInRings</a>, <a href="#hasaromaticrings">HasAromaticRings</a>, <a href="#hasatom">HasAtom</a> +, <a href="#hasbond">HasBond</a>, <a href="#hasfusedrings">HasFusedRings</a>, <a href="#hasnorings">HasNoRings</a>, <a href="#hasonlyonering">HasOnlyOneRing</a>, <a href="#hasrings">HasRings</a>, <a href="#isaromatic">IsAromatic</a> +, <a href="#ismolecule">IsMolecule</a>, <a href="#isringaromatic">IsRingAromatic</a>, <a href="#issupportedaromaticitymodel">IsSupportedAromaticityModel</a>, <a href="#isthreedimensional">IsThreeDimensional</a> +, <a href="#istwodimensional">IsTwoDimensional</a>, <a href="#keeplargestcomponent">KeepLargestComponent</a>, <a href="#kekulizearomaticatoms">KekulizeAromaticAtoms</a>, <a href="#newatom">NewAtom</a>, <a href="#newbond">NewBond</a> +, <a href="#setactiverings">SetActiveRings</a>, <a href="#setaromaticitymodel">SetAromaticityModel</a>, <a href="#setid">SetID</a>, <a href="#setvalencemodel">SetValenceModel</a>, <a href="#stringifymolecule">StringifyMolecule</a> +</p><p>The following methods can also be used as functions:</p> +<p>FormatElementalCompositionInformation, IsMolecule</p> +<p><strong>Molecule</strong> class is derived from <strong>ObjectProperty</strong> base class which provides methods not explicitly +defined in <strong>Molecule</strong> or <strong>ObjectProperty</strong> class using Perl's AUTOLOAD functionality. These methods +are generated on-the-fly for a specified object property:</p> +<div class="OptionsBox"> + Set<PropertyName>(<PropertyValue>); +<br/> $PropertyValue = Get<PropertyName>(); +<br/> Delete<PropertyName>();</div> +<p> +</p> +<h2>METHODS</h2> +<dl> +<dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NewMolecule = new Molecule([%PropertyNameAndValues]);</div> +<p>Using specified <em>Atom</em> property names and values hash, <strong>new</strong> method creates a new object +and returns a reference to newly created <strong>Atom</strong> object. By default, the following properties are +initialized:</p> +<div class="OptionsBox"> + ID = SequentialObjectID +<br/> Name = "Molecule <SequentialObjectID>"</div> +<p>Examples:</p> +<div class="OptionsBox"> + $Molecule = new Molecule();</div> +<div class="OptionsBox"> + $WaterMolecule = new Molecule('Name' => 'Water');</div> +<div class="OptionsBox"> + $Oxygen = new Atom('AtomSymbol' => 'O', 'XYZ' => [0, 0, 0]); +<br/> $Hydrogen1 = new Atom('AtomSymbol' => 'H', + 'XYZ' => [0.7144, 0.4125, 0]); +<br/> $Hydrogen2 = new Atom('AtomSymbol' => 'H', + 'XYZ' => [1.1208, -0.2959, 0]); +<br/> $WaterMolecule->AddAtoms($Oxygen, $Hydrogen1, $Hydrogen2);</div> +<div class="OptionsBox"> + $Bond1 = new Bond('Atoms' => [$Oxygen, $Hydrogen1], + 'BondOrder' => 1); +<br/> $Bond2 = new Bond('Atoms' => [$Oxygen, $Hydrogen2], + 'BondOrder' => 1); +<br/> $WaterMolecule->AddBonds($Bond1, $Bond2);</div> +</dd> +<dt><strong><a name="addatom" class="item"><strong>AddAtom</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Molecule->AddAtom($Atom);</div> +<p>Adds an <em>Atom</em> to a <em>Molecule</em> and returns <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="addatoms" class="item"><strong>AddAtoms</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Molecule->AddAtoms(@Atoms);</div> +<p>Adds <em>Atoms</em> to a <em>Molecule</em> and returns <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="addbond" class="item"><strong>AddBond</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Molecule->AddBond($Bond);</div> +<p>Adds a <em>Bond</em> to a <em>Molecule</em> and returns <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="addbonds" class="item"><strong>AddBonds</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Molecule->AddBonds(@Bonds);</div> +<p>Adds <em>Bonds</em> to a <em>Molecule</em> and returns <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="addhydrogens" class="item"><strong>AddHydrogens</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NumOfHydrogensAdded = $Molecule->AddHydrogens();</div> +<p>Adds hydrogens to each atom in a <em>Molecule</em> and returns total number of hydrogens +added. The current release of MayaChemTools doesn't assign hydrogen positions.</p> +</dd> +<dt><strong><a name="addpolarhydrogens" class="item"><strong>AddPolarHydrogens</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NumOfHydrogensAdded = $Molecule->AddPolarHydrogens();</div> +<p>Adds hydrogens to each polar atom - N, O, P or S - in a <em>Molecule</em> and returns total +number of polar hydrogens added. The current release of MayaChemTools doesn't +assign hydrogen positions.</p> +</dd> +<dt><strong><a name="clearrings" class="item"><strong>ClearRings</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Molecule->ClearRings();</div> +<p>Deletes all rings associated with <em>Molecule</em> and returns <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="copy" class="item"><strong>Copy</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $MoleculeCopy = $Molecule->Copy();</div> +<p>Copies <em>Molecule</em> and its associated data using <strong>Storable::dclone</strong> and returns a new +<strong>Molecule</strong> object.</p> +</dd> +<dt><strong><a name="deletearomaticity" class="item"><strong>DeleteAromaticity</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Molecule->DeleteAromaticity();</div> +<p>Deletes aromatic property associated with all atoms and bonds in a <em>Molecule</em> and returns +<em>Molecule</em>.</p> +</dd> +<dt><strong><a name="deleteatom" class="item"><strong>DeleteAtom</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Molecule->DeleteAtom($Atom);</div> +<p>Deletes <em>Atom</em> from a <em>Molecule</em> and returns <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="deleteatoms" class="item"><strong>DeleteAtoms</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Molecule->DeleteAtoms(@Atoms);</div> +<p>Deletes <em>Atoms</em> from a <em>Molecule</em> and returns <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="deletebond" class="item"><strong>DeleteBond</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Molecule->DeleteBond($Bond);</div> +<p>Deletes <em>Bond</em> from a <em>Molecule</em> and returns <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="deletebonds" class="item"><strong>DeleteBonds</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Molecule->DeleteBonds(@Bonds);</div> +<p>Deletes <em>Bonds</em> from a <em>Molecule</em> and returns <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="deletehydrogens" class="item"><strong>DeleteHydrogens</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NumOfHydrogensDeleted = $Molecule->DeleteHydrogens();</div> +<p>Removes hydrogens from each atom in a <em>Molecule</em> and returns total number of hydrogens +deleted.</p> +</dd> +<dt><strong><a name="deletepolarhydrogens" class="item"><strong>DeletePolarHydrogens</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NumOfHydrogensDeleted = $Molecule->DeletePolarHydrogens();</div> +<p>Removes hydrogens to each polar atom - N, O, P or S - in a <em>Molecule</em> and returns total +number of polar hydrogens deleted.</p> +</dd> +<dt><strong><a name="detectaromaticity" class="item"><strong>DetectAromaticity</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Molecule->DetectAromaticity();</div> +<p>Associates <em>Aromatic</em> property to atoms and bonds involved in aromatic rings or ring +systems in a <em>Molecule</em> and returns <em>Molecule</em>.</p> +<p>This method assumes the ring detection has already been perfomed using <strong>DetectRings</strong>. +And any existing <em>Aromatic</em> property associated with atoms and bonds is deleted before +performing aromaticity detection.</p> +<p>What is aromaticity? [ Ref 124 ] It's in the code of the implementer, did you +say? Agree. The implementation of aromaticity varies widely across different +packages [ Ref 125 ]; additionally, the implementation details are not always +completely available, and it's not possible to figure out the exact implementation +of aromaticity across various packages. Using the publicly available information, +however, one can try to reproduce the available results to the extent possible, +along with parameterizing all the control parameters used to implement different +aromaticity models, and that's exactly what the current release of MayaChemTools +does.</p> +<p>The implementation of aromaticity corresponding to various aromaticity models in +MayaChemTools package is driven by an external CSV file AromaticityModelsData.csv, +which is distributed with the package and is available in lib/data directory. The CSV +files contains names of supported aromaticity models, along with various control +parameters and their values. This file is loaded and processed during instantiation +of Molecule class and data corresponding to specific aromaticity model are used +to detect aromaticity for that model. Any new aromaticity model added to the +aromaticity data file, using different combinations of values for existing control +parameters, would work without any changes to the code; the addition of any new +control parameters, however, requires its implementation in the code used to +calculate number of pi electrons available towards delocalization in a ring or ring +systems.</p> +<p>The current release of MayaChemTools package supports these aromaticity +models: MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel, +ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, +DaylightAromaticityModel, MayaChemToolsAromaticityModel.</p> +<p>The current list of control parameters available to detect aromaticity corresponding +to different aromaticity models are: AllowHeteroRingAtoms, HeteroRingAtomsList, +AllowExocyclicDoubleBonds, AllowHomoNuclearExocyclicDoubleBonds, +AllowElectronegativeRingAtomExocyclicDoubleBonds, AllowRingAtomFormalCharge, +AllowHeteroRingAtomFormalCharge, MinimumRingSize. The values for these control +parameters are specified in AromaticityModelsData.csv file.</p> +<p>Although definition of aromaticity differs across various aromaticity models, a ring +or a ring system containing 4n + 2 pi electrons (Huckel's rule) corresponding to +alternate single and double bonds, in general, is considered aromatic.</p> +<p>The available valence free electrons on heterocyclic ring atoms, involved in two single +ring bonds, are also allowed to participate in pi electron delocalizaiton for most of +the supported aromaticity models.</p> +<p>The presence of exocyclic terminal double bond on ring atoms involved in pi electron +delocalization is only allowed for some of the aromaticity models. Additionally, the type +atoms involved in exocyclic terminal double bonds may result in making a ring or ring +system non-aromatic.</p> +<p>For molecules containing fused rings, each fused ring set is considered as one aromatic +system for counting pi electrons to satisfy Huckel's rule; In case of a failure, rings in +fused set are treated individually for aromaticity detection. Additionally, non-fused +rings are handled on their own during aromaticity detection.</p> +</dd> +<dt><strong><a name="detectrings" class="item"><strong>DetectRings</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Molecule->DetectRings();</div> +<p>Detects rings in a <em>Molecule</em> and returns <em>Molecule</em>. Ring detection is performed using +<strong>DetectCycles</strong> method avaible in <strong>Graph</strong> class which in turn uses methods available +<strong>Graph::CyclesDetection</strong> class. <strong>Graph::CyclesDetection</strong> class implements collapsing path graph +[Ref 31] methodology to detect all cycles in a graph.</p> +</dd> +<dt><strong><a name="formatelementalcompositioninformation" class="item"><strong>FormatElementalCompositionInformation</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $FormattedInfo = $Molecule->FormatElementalCompositionInformation( + $ElementsRef, $ElementCompositionRef, + [$Precision]); +<br/> $FormattedInfo = Molecule::FormatElementalCompositionInformation( + $ElementsRef, $ElementCompositionRef, + [$Precision]);</div> +<p>Using <em>ElementsRef</em> and <em>ElementCompositionRef</em> arrays referneces containg informatio +about elements and their composition, formats elemental composition information and returns +a <em>FormattedInfo</em> string. Defaule <em>Precision</em> value: <em>2</em>.</p> +</dd> +<dt><strong><a name="getaromaticitymodel" class="item"><strong>GetAromaticityModel</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AromaticityModel = $Molecule->GetAromaticityModel();</div> +<p>Returns name of <strong>AromaticityModel</strong> set for <em>Molecule</em> corresponding to <strong>AromaticityModel</strong> +property or default model name of <strong>MayaChemToolsAromaticityModel</strong>.</p> +</dd> +<dt><strong><a name="getallatompaths" class="item"><strong>GetAllAtomPaths</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomPathsRef = $Molecule->GetAllAtomPaths([$AllowCycles]);</div> +<p>Returns all paths as a reference to an array containing reference to arrays with path +<strong>Atom</strong> objects.</p> +<p>Path atoms correspond to to all possible paths for each atom in molecule with all +possible lengths and sharing of bonds in paths traversed. By default, rings are +included in paths. A path containing a ring is terminated at an atom completing the ring.</p> +<p>For molecule without any rings, this method returns the same set of atom paths as +<strong>GetAtomPaths</strong> method.</p> +</dd> +<dt><strong><a name="getallatompathsstartingat" class="item"><strong>GetAllAtomPathsStartingAt</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomPathsRef = $Molecule->GetAllAtomPathsStartingAt($StartAtom, + [$AllowCycles]);</div> +<p>Returns all atom paths starting from <em>StartAtom</em> as a reference to an array containing +reference to arrays with path <strong>Atom</strong> objects.</p> +<p>Path atoms atoms correspond to to all possible paths for specified atom in molecule with all +possible lengths and sharing of bonds in paths traversed. By default, rings are +included in paths. A path containing a ring is terminated at an atom completing the ring.</p> +<p>For molecule without any rings, this method returns the same set of atom paths as +<strong>GetAtomPathsStartingAt</strong> method.</p> +</dd> +<dt><strong><a name="getallatompathsstartingatwithlength" class="item"><strong>GetAllAtomPathsStartingAtWithLength</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomPathsRef = $Molecule->GetAllAtomPathsStartingAtWithLength( + $StartAtom, $Length, [$AllowCycles]);</div> +<p>Returns all atom paths starting from <em>StartAtom</em> with specified <em>Length</em>as a reference +to an array containing reference to arrays with path <strong>Atom</strong> objects.</p> +<p>Path atoms atoms correspond to to all possible paths for specified atom in molecule with all +possible lengths and sharing of bonds in paths traversed. By default, rings are +included in paths. A path containing a ring is terminated at an atom completing the ring.</p> +<p>For molecule without any rings, this method returns the same set of atom paths as +<strong>GetAtomPathsStartingAtWithLength</strong> method.</p> +</dd> +<dt><strong><a name="getallatompathsstartingatwithlengthupto" class="item"><strong>GetAllAtomPathsStartingAtWithLengthUpto</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomPathsRef = $Molecule->GetAllAtomPathsStartingAtWithLengthUpto( + $StartAtom, $Length, [$AllowCycles]);</div> +<p>Returns atom paths starting from <em>StartAtom</em> with length up to <em>Length</em> as a reference +to an array containing reference to arrays with path <strong>Atom</strong> objects.</p> +<p>Path atoms atoms correspond to all possible paths for specified atom in molecule with length +up to a specified length and sharing of bonds in paths traversed. By default, rings are +included in paths. A path containing a ring is terminated at an atom completing the ring.</p> +<p>For molecule without any rings, this method returns the same set of atom paths as +<em>GetAtomPathsStartingAtWithLengthUpto</em> method.</p> +</dd> +<dt><strong><a name="getallatompathswithlength" class="item"><strong>GetAllAtomPathsWithLength</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomPathsRef = $Molecule->GetAllAtomPathsWithLength($Length, + [$AllowCycles]);</div> +<p>Returns all atom paths with specified <em>Length</em> as a reference to an array containing +reference to arrays with path <strong>Atom</strong> objects.</p> +<p>Path atoms correspond to to all possible paths for each atom in molecule with length +up to a specified length and sharing of bonds in paths traversed. By default, rings are +included in paths. A path containing a ring is terminated at an atom completing the ring.</p> +<p>For molecule without any rings, this method returns the same set of atom paths as +as <em>GetAtomPathsWithLength</em> method.</p> +</dd> +<dt><strong><a name="getallatompathswithlengthupto" class="item"><strong>GetAllAtomPathsWithLengthUpto</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomPathsRef = $Molecule->GetAllAtomPathsWithLengthUpto($Length, + [$AllowCycles]);</div> +<p>Returns all atom paths with length up to <em>Length</em> as a reference to an array containing +reference to arrays with path <strong>Atom</strong> objects.</p> +<p>Path atoms correspond to to all possible paths for each atom in molecule with length +up to a specified length and sharing of bonds in paths traversed. By default, rings are +included in paths. A path containing a ring is terminated at an atom completing the ring.</p> +<p>For molecule without any rings, this method returns the same set of atom paths as +as <em>GetAtomPathsWithLengthUpto</em> method.</p> +</dd> +<dt><strong><a name="getaromaticrings" class="item"><strong>GetAromaticRings</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @AtomaticRings = $Molecule->GetAromaticRings();</div> +<p>Returns aromatic rings as an array containing references to arrays of ring <em>Atom</em> objects +in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getatomneighborhoods" class="item"><strong>GetAtomNeighborhoods</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @Neighborhoods = $Molecule->GetAtomNeighborhoods($StartAtom);</div> +<p>Returns atom neighborhoods around a <em>StartAtom</em> as an array containing references +to arrays with neighborhood <em>Atom</em> objects at possible radii.</p> +</dd> +<dt><strong><a name="getatomneighborhoodswithradiusupto" class="item"><strong>GetAtomNeighborhoodsWithRadiusUpto</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @Neighborhoods = $Molecule->GetAtomNeighborhoodsWithRadiusUpto($StartAtom, + $Radius);</div> +<p>Returns atom neighborhoods around a <em>StartAtom</em> as an array containing references +to arrays with neighborhood <em>Atom</em> objects up to <em>Radius</em>.</p> +</dd> +<dt><strong><a name="getatomneighborhoodswithsuccessoratoms" class="item"><strong>GetAtomNeighborhoodsWithSuccessorAtoms</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @Neighborhoods = $Molecule->GetAtomNeighborhoodsWithSuccessorAtoms( + $StartAtom);</div> +<p>Returns atom neighborhood around a specified <em>StartAtom</em>, along with their successor +connected atoms, collected at all radii as an array containing references to arrays with first +value corresponding to neighborhood atom at a specific radius and second value as reference +to an array containing its successor connected atoms.</p> +<p>For a neighborhood atom at each radius level, the successor connected atoms correspond to the +neighborhood atoms at the next radius level. Consequently, the neighborhood atoms at the last +radius level don't contain any successor atoms which fall outside the range of specified radius.</p> +</dd> +<dt><strong><a name="getatomneighborhoodswithsuccessoratomsandradiusupto" class="item"><strong>GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @Neighborhoods = $Molecule->GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto( + $StartAtom, $Radius);</div> +<p>Returns atom neighborhood around a specified <em>StartAtom</em>, along with their successor +connected atoms, collected upto specified <em>Radiud</em> as an array containing references to arrays +with first value corresponding to neighborhood atom at a specific radius and second value as +reference to an array containing its successor connected atoms.</p> +<p>For a neighborhood atom at each radius level, the successor connected atoms correspond to the +neighborhood atoms at the next radius level. Consequently, the neighborhood atoms at the last +radius level don't contain any successor atoms which fall outside the range of specified radius.</p> +</dd> +<dt><strong><a name="getatompathbonds" class="item"><strong>GetAtomPathBonds</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Return = $Molecule->GetAtomPathBonds(@PathAtoms);</div> +<p>Returns an array containing <strong>Bond</strong> objects corresponding to successive pair of +atoms in <em>PathAtoms</em></p> +</dd> +<dt><strong><a name="getatompaths" class="item"><strong>GetAtomPaths</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomPathsRef = $Molecule->GetAtomPaths([$AllowCycles]);</div> +<p>Returns all paths as a reference to an array containing reference to arrays with path +<strong>Atom</strong> objects.</p> +<p>Path atoms correspond to to all possible paths for each atom in molecule with all +possible lengths and no sharing of bonds in paths traversed. By default, rings are +included in paths. A path containing a ring is terminated at an atom completing the ring.</p> +</dd> +<dt><strong><a name="getatompathsbetween" class="item"><strong>GetAtomPathsBetween</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomPathsRef = $Molecule->GetAtomPathsBetween($StartAtom, $EndAtom);</div> +<p>Returns all paths as between <em>StartAtom</em> and <em>EndAtom</em> as a reference to an array +containing reference to arrays with path <strong>Atom</strong> objects.</p> +<p>For molecules with rings, atom paths array contains may contain two paths.</p> +</dd> +<dt><strong><a name="getatompathsstartingat" class="item"><strong>GetAtomPathsStartingAt</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomPathsRef = $Molecule->GetAtomPathsStartingAt($StartAtom, [$AllowCycles]);</div> +<p>Returns paths starting at <em>StartAtom</em> as a reference to an array containing reference to +arrays with path <strong>Atom</strong> objects.</p> +<p>Path atoms correspond to all possible paths for specified atom in molecule with all +possible lengths and no sharing of bonds in paths traversed. By default, rings are +included in paths. A path containing a ring is terminated at an atom completing the ring.</p> +</dd> +<dt><strong><a name="getatompathsstartingatwithlength" class="item"><strong>GetAtomPathsStartingAtWithLength</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomPathsRef = $Molecule->GetAtomPathsStartingAtWithLength($StartAtom, + $Length, [$AllowCycles]);</div> +<p>Returns paths starting at <em>StartAtom</em> with length <em>Length</em> as a reference to an array +containing reference to arrays with path <strong>Atom</strong> objects.</p> +<p>Path atoms correspond to all possible paths for specified atom in molecule with length +upto a specified length and no sharing of bonds in paths traversed. By default, rings are +included in paths. A path containing a ring is terminated at an atom completing the ring.</p> +</dd> +<dt><strong><a name="getatompathsstartingatwithlengthupto" class="item"><strong>GetAtomPathsStartingAtWithLengthUpto</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomPathsRef = $Molecule->GetAtomPathsStartingAtWithLengthUpto($StartAtom, + $Length, [$AllowCycles]);</div> +<p>Returns paths starting at <em>StartAtom</em> with length up to <em>Length</em> as a reference to an array +containing reference to arrays with path <strong>Atom</strong> objects.</p> +<p>Path atoms correspond to all possible paths for specified atom in molecule with length +upto a specified length and no sharing of bonds in paths traversed. By default, rings are +included in paths. A path containing a ring is terminated at an atom completing the ring.</p> +</dd> +<dt><strong><a name="getatompathswithlength" class="item"><strong>GetAtomPathsWithLength</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomPathsRef = $Molecule->GetAtomPathsWithLength($Length, [$AllowCycles]);</div> +<p>Returns all paths with specified <em>Length</em> as a reference to an array containing reference +to arrays with path <strong>Atom</strong> objects.</p> +<p>Path atoms correspond to all possible paths for each atom in molecule with length +upto a specified length and no sharing of bonds in paths traversed. By default, rings are +included in paths. A path containing a ring is terminated at an atom completing the ring.</p> +</dd> +<dt><strong><a name="getatompathswithlengthupto" class="item"><strong>GetAtomPathsWithLengthUpto</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomPathsRef = $Molecule->GetAtomPathsWithLengthUpto($Length, [$AllowCycles]);</div> +<p>Returns all paths with length up to <em>Length</em> as a reference to an array containing reference +to arrays with path <strong>Atom</strong> objects.</p> +<p>Path atoms correspond to all possible paths for each atom in molecule with length +upto a specified length and no sharing of bonds in paths traversed. By default, rings are +included in paths. A path containing a ring is terminated at an atom completing the ring.</p> +</dd> +<dt><strong><a name="getatoms" class="item"><strong>GetAtoms</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @AllAtoms = $Molecule->GetAtoms(); +<br/> @PolarAtoms = $Molecule->GetAtoms('IsPolarAtom');</div> +<div class="OptionsBox"> + $NegateMethodResult = 1; +<br/> @NonHydrogenAtoms = $Molecule->GetAtoms('IsHydrogenAtom', + $NegateMethodResult);</div> +<div class="OptionsBox"> + $AtomsCount = $Molecule->GetAtoms();</div> +<p>Returns an array of <em>Atoms</em> in a <em>Molecule</em>. In scalar context, it returns number of atoms. +Additionally, <strong>Atoms</strong> array can be filtered by any user specifiable valid <strong>Atom</strong> class method +and the result of the <strong>Atom</strong> class method used to filter the atoms can also be negated by +an optional negate results flag as third parameter.</p> +</dd> +<dt><strong><a name="getbonds" class="item"><strong>GetBonds</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @Bonds = $Molecule->GetBonds(); +<br/> $BondsCount = $Molecule->GetBonds();</div> +<p>Returns an array of <em>Bonds</em> in a <em>Molecule</em>. In scalar context, it returns number of bonds.</p> +</dd> +<dt><strong><a name="getcharge" class="item"><strong>GetCharge</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Charge = $Molecule->GetCharge();</div> +<p>Returns net charge on a <em>Molecule</em> using one of the following two methods: explicitly +set <strong>Charge</strong> property or sum of partial atomic charges on each atom.</p> +</dd> +<dt><strong><a name="getconnectedcomponents" class="item"><strong>GetConnectedComponents</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @ConnectedComponents = $Molecule->GetConnectedComponents();</div> +<p>Returns a reference to an array containing <em>Molecule</em> objects corresponding +to connected components sorted in decreasing order of component size in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getconnectedcomponentsatoms" class="item"><strong>GetConnectedComponentsAtoms</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @ConnectedComponentsAtoms = + $Molecule->GetConnectedComponentsAtoms();</div> +<p>Returns an array containing references to arrays with <em>Atom</em> objects corresponding to +atoms of connected components sorted in order of component decreasing size in a +<em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getdimensionality" class="item"><strong>GetDimensionality</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Dimensionality = $Molecule->GetDimensionality();</div> +<p>Returns <em>Dimensionality</em> of a <em>Molecule</em> corresponding to explicitly set +<em>Dimensionality</em> property value or by processing atomic.</p> +<p>The <em>Dimensionality</em> value from atomic coordinates is calculated as follows:</p> +<div class="OptionsBox"> + 3D - Three dimensional: One of X, Y or Z coordinate is non-zero +<br/> 2D - Two dimensional: One of X or Y coordinate is non-zero; All Z + coordinates are zero +<br/> 0D - Zero dimensional: All atomic coordinates are zero</div> +</dd> +<dt><strong><a name="getelementalcomposition" class="item"><strong>GetElementalComposition</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + ($ElementsRef, $CompositionRef) = + $Molecule->GetElementalComposition([$IncludeMissingHydrogens]);</div> +<p>Calculates elemental composition and returns references to arrays containing elements +and their percent composition in a <em>Molecule</em>. By default, missing hydrogens are included +during the calculation.</p> +</dd> +<dt><strong><a name="getelementsandnonelements" class="item"><strong>GetElementsAndNonElements</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + ($ElementsRef, $NonElementsRef) = + $Molecule->GetElementsAndNonElements([$IncludeMissingHydrogens]);</div> +<p>Counts elements and non-elements in a <em>Molecule</em> and returns references to hashes +containing element and non-element as hash keys with values corresponding to their +count. By default, missing hydrogens are not added to the element hash.</p> +</dd> +<dt><strong><a name="getexactmass" class="item"><strong>GetExactMass</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $ExactMass = $Molecule->GetExactMass();</div> +<p>Returns exact mass of a <em>Molecule</em> corresponding to sum of exact masses of all +the atoms.</p> +</dd> +<dt><strong><a name="getformalcharge" class="item"><strong>GetFormalCharge</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $FormalCharge = $Molecule->GetFormalCharge();</div> +<p>Returns net formal charge on a <em>Molecule</em> using one of the following two methods: explicitly +set <strong>FormalCharge</strong> property or sum of formal charges on each atom.</p> +<p><strong>FormalCharge</strong> is different from <strong>Charge</strong> property of the molecule which corresponds to +sum of partial atomic charges explicitly set for each atom using a specific methodology.</p> +</dd> +<dt><strong><a name="getfreeradicalelectrons" class="item"><strong>GetFreeRadicalElectrons</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $FreeRadicalElectrons = $Molecule->GetFreeRadicalElectrons();</div> +<p>Returns total number of free radical electrons available in a <em>Molecule</em> using one of the +following two methods: explicitly set <strong>FreeRadicalElectrons</strong> property or sum of available +free radical electrons on each atom.</p> +</dd> +<dt><strong><a name="getfusedandnonfusedrings" class="item"><strong>GetFusedAndNonFusedRings</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + ($FusedRingSetRef, $NonFusedRingsRef) = + $Molecule->GetFusedAndNonFusedRings();</div> +<p>Returns references to array of fused ring sets and non-fused rings in a <em>Molecule</em>. Fused ring sets +array reference contains refernces to arrays of rings corresponding to ring <em>Atom</em> objects; +Non-fused rings array reference contains references to arrays of ring <em>Atom</em> objects.</p> +</dd> +<dt><strong><a name="getlargestconnectedcomponent" class="item"><strong>GetLargestConnectedComponent</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $ComponentMolecule = $Molecule->GetLargestConnectedComponent();</div> +<p>Returns a reference to <strong>Molecule</strong> object corresponding to a largest connected component +in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getlargestconnectedcomponentatoms" class="item"><strong>GetLargestConnectedComponentAtoms</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @ComponentAtoms = $Molecule->GetLargestConnectedComponentAtoms();</div> +<p>Returns a reference to an array of <strong>Atom</strong> objects corresponding to a largest connected +component in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getlargestring" class="item"><strong>GetLargestRing</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @RingAtoms = $Molecule->GetLargestRing();</div> +<p>Returns an array of <em>Atoms</em> objects corresponding to a largest ring in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getmolecularformula" class="item"><strong>GetMolecularFormula</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $FormulaString = $Molecule->GetMolecularFormula( + [$IncludeMissingHydrogens, + $IncludeNonElements]);</div> +<p>Returns molecular formula of a <em>Molecule</em> by collecting information about all atoms in +the molecule and composing the formula using Hills ordering system:</p> +<div class="OptionsBox"> + o C shows up first and H follows assuming C is present. +<br/> o All other standard elements are sorted alphanumerically. +<br/> o All other non-stanard atom symbols are also sorted + alphanumerically and follow standard elements.</div> +<p>Notes:</p> +<div class="OptionsBox"> + o By default, missing hydrogens and nonelements are also included. +<br/> o Elements for disconnected fragments are combined into the same + formula. +<br/> o Formal charge is also used during compoisiton of molecular formula.</div> +</dd> +<dt><strong><a name="getmolecularweight" class="item"><strong>GetMolecularWeight</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $MolWeight = $Molecule->GetMolecularWeight();</div> +<p>Returns molecular weight of a <em>Molecule</em> corresponding to sum of atomic weights of all +the atoms.</p> +</dd> +<dt><strong><a name="getnumofaromaticrings" class="item"><strong>GetNumOfAromaticRings</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NumOfAromaticRings = $Molecule->GetNumOfAromaticRings();</div> +<p>Returns number of aromatic rings in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getnumofatoms" class="item"><strong>GetNumOfAtoms</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NumOfAtoms = $Molecule->GetNumOfAtoms();</div> +<p>Returns number of atoms in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getnumofbonds" class="item"><strong>GetNumOfBonds</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NumOfBonds = $Molecule->GetNumOfBonds();</div> +<p>Returns number of bonds in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getnumofconnectedcomponents" class="item"><strong>GetNumOfConnectedComponents</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NumOfComponents = $Molecule->GetNumOfConnectedComponents();</div> +<p>Returns number of connected components in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getnumofelementsandnonelements" class="item"><strong>GetNumOfElementsAndNonElements</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + ($NumOfElements, $NumOfNonElements) = $Molecule-> + GetNumOfElementsAndNonElements(); +<br/> ($NumOfElements, $NumOfNonElements) = $Molecule-> + GetNumOfElementsAndNonElements($IncludeMissingHydrogens);</div> +<p>Returns number of elements and non-elements in a <em>Molecule</em>. By default, missing +hydrogens are not added to element count.</p> +</dd> +<dt><strong><a name="getnumofheavyatoms" class="item"><strong>GetNumOfHeavyAtoms</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NumOfHeavyAtoms = $Molecule->GetNumOfHeavyAtoms();</div> +<p>Returns number of heavy atoms, non-hydrogen atoms, in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getnumofhydrogenatoms" class="item"><strong>GetNumOfHydrogenAtoms</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NumOfHydrogenAtoms = $Molecule->GetNumOfHydrogenAtoms();</div> +<p>Returns number of hydrogen atoms in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getnumofmissinghydrogenatoms" class="item"><strong>GetNumOfMissingHydrogenAtoms</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NumOfMissingHydrogenAtoms = $Molecule->GetNumOfMissingHydrogenAtoms();</div> +<p>Returns number of hydrogen atoms in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getnumofnonhydrogenatoms" class="item"><strong>GetNumOfNonHydrogenAtoms</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NumOfNonHydrogenAtoms = $Molecule->GetNumOfNonHydrogenAtoms();</div> +<p>Returns number of non-hydrogen atoms in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getnumofrings" class="item"><strong>GetNumOfRings</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $RingCount = $Molecule->GetNumOfRings();</div> +<p>Returns number of rings in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getnumofringswithevensize" class="item"><strong>GetNumOfRingsWithEvenSize</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $RingCount = $Molecule->GetNumOfRingsWithEvenSize();</div> +<p>Returns number of rings with even size in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getnumofringswithoddsize" class="item"><strong>GetNumOfRingsWithOddSize</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $RingCount = $Molecule->GetNumOfRingsWithOddSize();</div> +<p>Returns number of rings with odd size in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getnumofringswithsize" class="item"><strong>GetNumOfRingsWithSize</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $RingCount = $Molecule->GetNumOfRingsWithSize($Size);</div> +<p>Returns number of rings with <em>Size</em> in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getnumofringswithsizegreaterthan" class="item"><strong>GetNumOfRingsWithSizeGreaterThan</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $RingCount = $Molecule->GetNumOfRingsWithSizeGreaterThan($Size);</div> +<p>Returns number of rings with size greater than <em>Size</em> in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getnumofringswithsizelessthan" class="item"><strong>GetNumOfRingsWithSizeLessThan</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $RingCount = $Molecule->GetNumOfRingsWithSizeLessThan($Size);</div> +<p>Returns number of rings with size less than <em>Size</em> in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getringbonds" class="item"><strong>GetRingBonds</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @RingBonds = $Molecule->GetRingBonds(@RingAtoms);</div> +<p>Returns an array of ring <strong>Bond</strong> objects correponding to an array of ring <em>Atoms</em> in a +<em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getringbondsfromrings" class="item"><strong>GetRingBondsFromRings</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @RingBondsSets = $Molecule->GetRingBondsFromRings(@RingAtomsSets);</div> +<p>Returns an array containing references to arrays of ring <strong>Bond</strong> objects for rings specified +in an array of references to ring <em>Atom</em> objects.</p> +</dd> +<dt><strong><a name="getrings" class="item"><strong>GetRings</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @Rings = $Molecule->GetRings();</div> +<p>Returns rings as an array containing references to arrays of ring <em>Atom</em> objects in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getringswithevensize" class="item"><strong>GetRingsWithEvenSize</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @Rings = $Molecule->GetRingsWithEvenSize();</div> +<p>Returns even size rings as an array containing references to arrays of ring <em>Atom</em> objects in +a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getringswithoddsize" class="item"><strong>GetRingsWithOddSize</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @Rings = $Molecule->GetRingsWithOddSize();</div> +<p>Returns odd size rings as an array containing references to arrays of ring <em>Atom</em> objects in +a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getringswithsize" class="item"><strong>GetRingsWithSize</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @Rings = $Molecule->GetRingsWithSize($Size);</div> +<p>Returns rings with <em>Size</em> as an array containing references to arrays of ring <em>Atom</em> objects in +a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getringswithsizegreaterthan" class="item"><strong>GetRingsWithSizeGreaterThan</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @Rings = $Molecule->GetRingsWithSizeGreaterThan($Size);</div> +<p>Returns rings with size greater than <em>Size</em> as an array containing references to arrays of +ring <em>Atom</em> objects in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getringswithsizelessthan" class="item"><strong>GetRingsWithSizeLessThan</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @Rings = $Molecule->GetRingsWithSizeLessThan($Size);</div> +<p>Returns rings with size less than <em>Size</em> as an array containing references to arrays of +ring <em>Atom</em> objects in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getsizeoflargestring" class="item"><strong>GetSizeOfLargestRing</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Size = $Molecule->GetSizeOfLargestRing();</div> +<p>Returns size of the largest ring in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getsizeofsmallestring" class="item"><strong>GetSizeOfSmallestRing</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Size = $Molecule->GetSizeOfSmallestRing();</div> +<p>Returns size of the smalles ring in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getsmallestring" class="item"><strong>GetSmallestRing</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @RingAtoms = $Molecule->GetSmallestRing();</div> +<p>Returns an array containing <em>Atom</em> objects corresponding to the smallest ring in +a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="getspinmultiplicity" class="item"><strong>GetSpinMultiplicity</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $SpinMultiplicity = $Molecule->GetSpinMultiplicity();</div> +<p>Returns net spin multiplicity of a <em>Molecule</em> using one of the following two methods: explicitly +set <strong>SpinMultiplicity</strong> property or sum of spin multiplicity on each atom.</p> +</dd> +<dt><strong><a name="getsupportedaromaticitymodels" class="item"><strong>GetSupportedAromaticityModels</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @SupportedModels = $Molecule->GetSupportedAromaticityModels();</div> +<p>Returns an array containing a list of supported aromaticity models.</p> +</dd> +<dt><strong><a name="getvalencemodel" class="item"><strong>GetValenceModel</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $ValenceModel = $Molecule->GetValenceModel();</div> +<p>Returns valence model for <em>Molecule</em> using one of the following two methods: explicitly +set <strong>ValenceModel</strong> property or defaul value of <em>InternalValenceModel</em>.</p> +</dd> +<dt><strong><a name="gettopologicallysortedatoms" class="item"><strong>GetTopologicallySortedAtoms</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @SortedAtoms = $Molecule->GetTopologicallySortedAtoms([$StartAtom]);</div> +<p>Returns an array of topologically sorted <em>Atom</em> objects starting from <em>StartAtom</em> or +an arbitrary atom in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="hasaromaticrings" class="item"><strong>HasAromaticRings</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Molecule->HasAromaticRings();</div> +<p>Returns 1 or 0 based on whether any aromatic ring is present in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="hasaromaticatomsinrings" class="item"><strong>HasAromaticAtomsInRings</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Molecule->HasAromaticAtomsInRings();</div> +<p>Returns 1 or 0 based on whether any aromatic ring atom is present in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="hasaromaticatomsnotinrings" class="item"><strong>HasAromaticAtomsNotInRings</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Molecule->HasAromaticAtomsNotInRings();</div> +<p>Returns 1 or 0 based on whether any non-ring atom is marked aromatic in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="hasatom" class="item"><strong>HasAtom</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Molecule->HasAtom($Atom);</div> +<p>Returns 1 or 0 based on whether <em>Atom</em> is present in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="hasbond" class="item"><strong>HasBond</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Molecule->HasBond($Bond);</div> +<p>Returns 1 or 0 based on whether <em>Bond</em> is present in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="hasfusedrings" class="item"><strong>HasFusedRings</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Molecule->HasFusedRings();</div> +<p>Returns 1 or 0 based on whether any fused rings set is present in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="hasnorings" class="item"><strong>HasNoRings</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Molecule->HasNoRings();</div> +<p>Returns 0 or 1 based on whether any ring is present in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="hasonlyonering" class="item"><strong>HasOnlyOneRing</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Molecule->HasOnlyOneRing();</div> +<p>Returns 1 or 0 based on whether only one ring is present in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="hasrings" class="item"><strong>HasRings</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Molecule->HasRings();</div> +<p>Returns 1 or 0 based on whether rings are present in a <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="isaromatic" class="item"><strong>IsAromatic</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Molecule->IsAromatic();</div> +<p>Returns 1 or 0 based on whether <em>Molecule</em> is aromatic.</p> +</dd> +<dt><strong><a name="ismolecule" class="item"><strong>IsMolecule</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = Molecule::IsMolecule();</div> +<p>Returns 1 or 0 based on whether <em>Object</em> is a <strong>Molecule</strong> object.</p> +</dd> +<dt><strong><a name="isringaromatic" class="item"><strong>IsRingAromatic</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Molecule->IsRingAromatic(@RingAtoms);</div> +<p>Returns 1 or 0 based on whether all <em>RingAtoms</em> are aromatic.</p> +</dd> +<dt><strong><a name="issupportedaromaticitymodel" class="item"><strong>IsSupportedAromaticityModel</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Molecule->IsSupportedAromaticityModel($AromaticityModel); +<br/> $Status = Molecule::IsSupportedAromaticityModel($AromaticityModel);</div> +<p>Returns 1 or 0 based on whether specified <em>AromaticityModel</em> is supported.</p> +</dd> +<dt><strong><a name="istwodimensional" class="item"><strong>IsTwoDimensional</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Molecule->IsTwoDimensional();</div> +<p>Returns 1 or 0 based on whether any atom in <em>Molecule</em> has a non-zero value +for X or Y coordinate and all atoms have zero value for Z coordinates.</p> +</dd> +<dt><strong><a name="isthreedimensional" class="item"><strong>IsThreeDimensional</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Molecule->IsThreeDimensional();</div> +<p>Returns 1 or 0 based on whether any atom in <em>Molecule</em> has a non-zero value +for Z coordinate.</p> +</dd> +<dt><strong><a name="keeplargestcomponent" class="item"><strong>KeepLargestComponent</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Molecule->KeepLargestComponent();</div> +<p>Deletes atoms corresponding to all other connected components Except for the largest +connected component in a <em>Molecule</em> and returns <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="kekulizearomaticatoms" class="item"><strong>KekulizeAromaticAtoms</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $Molecule->KekulizeAromaticAtoms();</div> +<p>Kekulize marked ring and non-ring aromatic atoms in a molecule and return 1 or 1 based +on whether the kekulization succeeded.</p> +</dd> +<dt><strong><a name="newatom" class="item"><strong>NewAtom</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NewAtom = $Molecule->NewAtom(%AtomPropertyNamesAndValues);</div> +<p>Creates a new atom using <em>AtomPropertyNamesAndValues</em>, add its to <em>Molecule</em>, and returns +new <strong>Atom</strong> object.</p> +</dd> +<dt><strong><a name="newbond" class="item"><strong>NewBond</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NewBond = $Molecule->NewBond(%BondPropertyNamesAndValues);</div> +<p>Creates a new bond using <em>AtomPropertyNamesAndValues</em>, add its to <em>Molecule</em>, and returns +new <strong>Bond</strong> object.</p> +</dd> +<dt><strong><a name="setactiverings" class="item"><strong>SetActiveRings</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Molecule->SetActiveRings($RingsType);</div> +<p>Sets up type of detected ring sets to use during all ring related methods and returns <em>Molecule</em>. +Possible <em>RingType</em> values: <em>Independent or All</em>. By default, <em>Independent</em> ring set is used +during all ring methods.</p> +</dd> +<dt><strong><a name="setaromaticitymodel" class="item"><strong>SetAromaticityModel</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Molecule = $Molecule->SetAromaticityModel($AromaticityModel);</div> +<p>Sets up <em>AromaticityModel</em> property value for <em>Molecule</em> and retrurns <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="setvalencemodel" class="item"><strong>SetValenceModel</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Molecule = $Molecule->SetValenceModel(ValenceModel);</div> +<p>Sets up <em>ValenceModel</em> property value for <em>Molecule</em> and retrurns <em>Molecule</em>.</p> +</dd> +<dt><strong><a name="stringifymolecule" class="item"><strong>StringifyMolecule</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $MoleculeString = $Molecule->StringifyMolecule();</div> +<p>Returns a string containing information about <em>Molecule</em> object</p> +</dd> +</dl> +<p> +</p> +<h2>AUTHOR</h2> +<p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> +<p> +</p> +<h2>SEE ALSO</h2> +<p><a href="./Atom.html">Atom.pm</a>, <a href="./Bond.html">Bond.pm</a>, <a href="./MoleculeFileIO.html">MoleculeFileIO.pm</a>, <a href="./MolecularFormula.html">MolecularFormula.pm</a> +</p> +<p> +</p> +<h2>COPYRIGHT</h2> +<p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> +<p>This file is part of MayaChemTools.</p> +<p>MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the GNU Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.</p> +<p> </p><p> </p><div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<tr align="left" valign="top"><td width="33%" align="left"><a href="./MolecularFormula.html" title="MolecularFormula.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./MoleculeFileIO.html" title="MoleculeFileIO.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Molecule.pm</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>