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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/modules/html/TopologicalAtomTripletsFingerprints.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,372 @@ +<html> +<head> +<title>MayaChemTools:Documentation:Fingerprints::TopologicalAtomTripletsFingerprints.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="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::TopologicalAtomTripletsFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/TopologicalAtomTripletsFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/TopologicalAtomTripletsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/TopologicalAtomTripletsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/TopologicalAtomTripletsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/TopologicalAtomTripletsFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>TopologicalAtomTripletsFingerprints</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>use Fingerprints::TopologicalAtomTripletsFingerprints;</p> +<p>use Fingerprints::TopologicalAtomTripletsFingerprints qw(:all);</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p><strong>TopologicalAtomTripletsFingerprints</strong> [ Ref 57, Ref 59, Ref 72 ] class provides the following methods:</p> +<p> <a href="#new">new</a>, <a href="#generatefingerprints">GenerateFingerprints</a>, <a href="#getatomtripletids">GetAtomTripletIDs</a>, <a href="#getdescription">GetDescription</a> +, <a href="#setatomidentifiertype">SetAtomIdentifierType</a>, <a href="#setatomicinvariantstouse">SetAtomicInvariantsToUse</a>, <a href="#setfunctionalclassestouse">SetFunctionalClassesToUse</a> +, <a href="#setmaxdistance">SetMaxDistance</a>, <a href="#setmindistance">SetMinDistance</a>, <a href="#stringifytopologicalatomtripletsfingerprints">StringifyTopologicalAtomTripletsFingerprints</a> +</p><p><strong>TopologicalAtomTripletsFingerprints</strong> is derived from <strong>Fingerprints</strong> class which in turn +is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined +in <strong>TopologicalAtomTripletsFingerprints</strong>, <strong>Fingerprints</strong> or <strong>ObjectProperty</strong> classes 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>The current release of MayaChemTools supports generation of <strong>TopologicalAtomTripletsFingerprints</strong> +corresponding to following <strong>AtomtomIdentifierTypes</strong>:</p> +<div class="OptionsBox"> + AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +<br/> FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, +<br/> SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</div> +<p>Based on the values specified for <strong>AtomIdentifierType</strong> along with other specified +parameters such as <strong>AtomicInvariantsToUse</strong> and <strong>FunctionalClassesToUse</strong>, initial +atom types are assigned to all non-hydrogen atoms in a molecule. Using the distance +matrix for the molecule and initial atom types assigned to non-hydrogen atoms, all unique atom +triplets within <strong>MinDistance</strong> and <strong>MaxDistance</strong> are identified and counted. An atom triplet +identifier is generated for each unique atom triplet; the format of atom triplet identifier is:</p> +<div class="OptionsBox"> + <ATx>-Dyz-<ATy>-Dxz-<ATz>-Dxy</div> +<div class="OptionsBox"> + ATx, ATy, ATz: Atom types assigned to atom x, atom y, and atom z +<br/> Dxy: Distance between atom x and atom y +<br/> Dxz: Distance between atom x and atom z +<br/> Dyz: Distance between atom y and atom z</div> +<div class="OptionsBox"> + where <AT1>-D23 <= <AT2>-D13 <= <AT3>-D12</div> +<p>The atom triplet identifiers for all unique atom triplets corresponding to non-hydrogen atoms constitute +topological atom triplets fingerprints of the molecule.</p> +<p>The current release of MayaChemTools generates the following types of topological atom triplets +fingerprints vector strings:</p> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M +<br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1 +<br/> .BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D1 +<br/> 0-C.X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1 +<br/> -C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3....; +<br/> 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 +<br/> 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M +<br/> inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString +<br/> ;C.X1.BO1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 1 C.X1.BO1.H3-D1-C.X2.BO +<br/> 2.H2-D10-C.X3.BO4-D9 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 2 C.X +<br/> 1.BO1.H3-D1-C.X2.BO2.H2-D4-C.X2.BO2.H2-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2 +<br/> -D6-C.X3.BO3.H1-D5 2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D6-C.X3.BO3.H1-D7 2...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:DREIDINGAtomTypes:MinDistan +<br/> ce1:MaxDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D +<br/> 9-C_3-D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_ +<br/> 3-D9 C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_ +<br/> 2-D1-C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D...; +<br/> 1 1 1 2 1 1 3 1 1 2 2 1 1 1 1 1 1 1 1 2 1 3 4 5 1 1 6 4 2 2 3 1 1 1 2 +<br/> 2 1 2 1 1 2 2 2 1 2 1 2 1 1 3 3 2 6 4 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:EStateAtomTypes:MinDistance +<br/> 1:MaxDistance10;3298;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH-D +<br/> 1-aaCH-D2 aaCH-D1-aaCH-D1-aasC-D2 aaCH-D1-aaCH-D10-aaCH-D9 aaCH-D1-aaC +<br/> H-D10-aasC-D9 aaCH-D1-aaCH-D2-aaCH-D3 aaCH-D1-aaCH-D2-aasC-D1 aaCH-D1- +<br/> aaCH-D2-aasC-D3 aaCH-D1-aaCH-D3-aasC-D2 aaCH-D1-aaCH-D4-aasC-D5 aa...; +<br/> 6 4 24 4 16 8 8 4 8 8 8 12 10 14 4 16 24 4 12 2 2 4 1 10 2 2 15 2 2 2 +<br/> 2 2 2 14 4 2 2 2 2 1 2 10 2 2 4 1 2 4 8 3 3 3 4 6 4 2 2 3 3 1 1 1 2 1 +<br/> 2 2 4 2 3 2 1 2 4 5 3 2 2 1 2 4 3 2 8 12 6 2 2 4 4 7 1 4 2 4 2 2 2 ...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:FunctionalClassAtomTypes:Mi +<br/> nDistance1:MaxDistance10;2182;NumericalValues;IDsAndValuesString;Ar-D1 +<br/> -Ar-D1-Ar-D2 Ar-D1-Ar-D1-Ar.HBA-D2 Ar-D1-Ar-D10-Ar-D9 Ar-D1-Ar-D10-Hal +<br/> -D9 Ar-D1-Ar-D2-Ar-D2 Ar-D1-Ar-D2-Ar-D3 Ar-D1-Ar-D2-Ar.HBA-D1 Ar-D1-Ar +<br/> -D2-Ar.HBA-D2 Ar-D1-Ar-D2-Ar.HBA-D3 Ar-D1-Ar-D2-HBD-D1 Ar-D1-Ar-D2...; +<br/> 27 1 32 2 2 63 3 2 1 2 1 2 3 1 1 40 3 1 2 2 2 2 4 2 2 47 4 2 2 1 2 1 5 +<br/> 2 2 51 4 3 1 3 1 9 1 1 50 3 3 4 1 9 50 2 2 3 3 5 45 1 1 1 2 1 2 2 3 3 +<br/> 4 4 3 2 1 1 3 4 5 5 3 1 2 3 2 3 5 7 2 7 3 7 1 1 2 2 2 2 3 1 4 3 1 2...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:MMFF94AtomTypes:MinDistance +<br/> 1:MaxDistance10;2966;NumericalValues;IDsAndValuesString;C5A-D1-C5A-D1- +<br/> N5-D2 C5A-D1-C5A-D2-C5B-D2 C5A-D1-C5A-D3-CB-D2 C5A-D1-C5A-D3-CR-D2 C5A +<br/> -D1-C5B-D1-C5B-D2 C5A-D1-C5B-D2-C=ON-D1 C5A-D1-C5B-D2-CB-D1 C5A-D1-C5B +<br/> -D3-C=ON-D2 C5A-D1-C5B-D3-CB-D2 C5A-D1-C=ON-D3-NC=O-D2 C5A-D1-C=ON-D3- +<br/> O=CN-D2 C5A-D1-C=ON-D4-NC=O-D3 C5A-D1-C=ON-D4-O=CN-D3 C5A-D1-CB-D1-...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:SLogPAtomTypes:MinDistance1 +<br/> :MaxDistance10;3710;NumericalValues;IDsAndValuesString;C1-D1-C1-D1-C11 +<br/> -D2 C1-D1-C1-D1-CS-D2 C1-D1-C1-D10-C5-D9 C1-D1-C1-D3-C10-D2 C1-D1-C1-D +<br/> 3-C5-D2 C1-D1-C1-D3-CS-D2 C1-D1-C1-D3-CS-D4 C1-D1-C1-D4-C10-D5 C1-D1-C +<br/> 1-D4-C11-D5 C1-D1-C1-D5-C10-D4 C1-D1-C1-D5-C5-D4 C1-D1-C1-D6-C11-D7 C1 +<br/> -D1-C1-D6-CS-D5 C1-D1-C1-D6-CS-D7 C1-D1-C1-D8-C11-D9 C1-D1-C1-D8-CS...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1 +<br/> :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2-D1-C.2-D9-C +<br/> .3-D10 C.2-D1-C.2-D9-C.ar-D10 C.2-D1-C.3-D1-C.3-D2 C.2-D1-C.3-D10-C.3- +<br/> D9 C.2-D1-C.3-D2-C.3-D3 C.2-D1-C.3-D2-C.ar-D3 C.2-D1-C.3-D3-C.3-D4 C.2 +<br/> -D1-C.3-D3-N.ar-D4 C.2-D1-C.3-D3-O.3-D2 C.2-D1-C.3-D4-C.3-D5 C.2-D1-C. +<br/> 3-D5-C.3-D6 C.2-D1-C.3-D5-O.3-D4 C.2-D1-C.3-D6-C.3-D7 C.2-D1-C.3-D7...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:TPSAAtomTypes:MinDistance1: +<br/> MaxDistance10;1007;NumericalValues;IDsAndValuesString;N21-D1-N7-D3-Non +<br/> e-D4 N21-D1-N7-D5-None-D4 N21-D1-None-D1-None-D2 N21-D1-None-D2-None-D +<br/> 2 N21-D1-None-D2-None-D3 N21-D1-None-D3-None-D4 N21-D1-None-D4-None-D5 + N21-D1-None-D4-O3-D3 N21-D1-None-D4-O4-D3 N21-D1-None-D5-None-D6 N21- +<br/> D1-None-D6-None-D7 N21-D1-None-D6-O4-D5 N21-D1-None-D7-None-D8 N21-...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTriplets:UFFAtomTypes:MinDistance1:M +<br/> axDistance10;2377;NumericalValues;IDsAndValuesString;C_2-D1-C_2-D9-C_3 +<br/> -D10 C_2-D1-C_2-D9-C_R-D10 C_2-D1-C_3-D1-C_3-D2 C_2-D1-C_3-D10-C_3-D9 +<br/> C_2-D1-C_3-D2-C_3-D3 C_2-D1-C_3-D2-C_R-D3 C_2-D1-C_3-D3-C_3-D4 C_2-D1- +<br/> C_3-D3-N_R-D4 C_2-D1-C_3-D3-O_3-D2 C_2-D1-C_3-D4-C_3-D5 C_2-D1-C_3-D5- +<br/> C_3-D6 C_2-D1-C_3-D5-O_3-D4 C_2-D1-C_3-D6-C_3-D7 C_2-D1-C_3-D7-C_3-...</div> +<p> +</p> +<h2>METHODS</h2> +<dl> +<dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NewTopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + %NamesAndValues);</div> +<p>Using specified <em>TopologicalAtomTripletsFingerprints</em> property names and values hash, <strong>new</strong> +method creates a new object and returns a reference to newly created <strong>TopologicalAtomTripletsFingerprints</strong> +object. By default, the following properties are initialized:</p> +<div class="OptionsBox"> + Molecule = '' +<br/> Type = 'TopologicalAtomTriplets' +<br/> MinDistance = 1 +<br/> MaxDistance = 10 +<br/> UseTriangleInequality = 1 +<br/> AtomIdentifierType = '' +<br/> AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC'] +<br/> FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']</div> +<p>Examples:</p> +<div class="OptionsBox"> + $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes');</div> +<div class="OptionsBox"> + $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'MinDistance' => 1, + 'MaxDistance' => 10, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes', + 'AtomicInvariantsToUse' => + ['AS', 'X', 'BO', 'H', 'FC'] );</div> +<div class="OptionsBox"> + $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'DREIDINGAtomTypes');</div> +<div class="OptionsBox"> + $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'MMFF94AtomTypes');</div> +<div class="OptionsBox"> + $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'TPSAAtomTypes');</div> +<div class="OptionsBox"> + $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( + 'Molecule' => $Molecule, + 'MinDistance' => 1, + 'MaxDistance' => 10, + 'AtomIdentifierType' => + 'FunctionalClassAtomTypes', + 'FunctionalClassesToUse' => + ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']);</div> +<div class="OptionsBox"> + $TopologicalAtomTripletsFingerprints->GenerateFingerprints(); +<br/> print "$TopologicalAtomTripletsFingerprints\n";</div> +</dd> +<dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Return = $TopologicalAtomTripletsFingerprints->GetDescription();</div> +<p>Returns a string containing description of topological atom triplets fingerprints.</p> +</dd> +<dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalAtomTripletsFingerprints->GenerateFingerprints();</div> +<p>Generates topological atom triplets fingerprints and returns <em>TopologicalAtomTripletsFingerprints</em>.</p> +</dd> +<dt><strong><a name="getatomtripletids" class="item"><strong>GetAtomTripletIDs</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomTripletIDsRef = $TopologicalAtomTripletsFingerprints->GetAtomTripletIDs(); +<br/> @AtomTripletIDs = $TopologicalAtomTripletsFingerprints->GetAtomTripletIDs();</div> +<p>Returns atom triplet IDs corresponding to atom triplets count values in topological atom triplets +fingerprints vector as an array or reference to an array.</p> +</dd> +<dt><strong><a name="setatomidentifiertype" class="item"><strong>SetAtomIdentifierType</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalAtomTripletsFingerprints->SetAtomIdentifierType($IdentifierType);</div> +<p>Sets atom <em>IdentifierType</em> to use during atom triplets fingerprints generation and +returns <em>TopologicalAtomTripletsFingerprints</em>.</p> +<p>Possible values: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, +TPSAAtomTypes, UFFAtomTypes</em>.</p> +</dd> +<dt><strong><a name="setatomicinvariantstouse" class="item"><strong>SetAtomicInvariantsToUse</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalAtomTripletsFingerprints->SetAtomicInvariantsToUse($ValuesRef); +<br/> $TopologicalAtomTripletsFingerprints->SetAtomicInvariantsToUse(@Values);</div> +<p>Sets atomic invariants to use during <em>AtomicInvariantsAtomTypes</em> value of <em>AtomIdentifierType</em> +for topological atom triplets fingerprints generation and returns <em>TopologicalAtomTripletsFingerprints</em>.</p> +<p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB, +H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS,X,BO,H,FC</em>.</p> +<p>The atomic invariants abbreviations correspond to:</p> +<div class="OptionsBox"> + AS = Atom symbol corresponding to element symbol</div> +<div class="OptionsBox"> + X<n> = Number of non-hydrogen atom neighbors or heavy atoms +<br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms +<br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms +<br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms +<br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms +<br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms +<br/> H<n> = Number of implicit and explicit hydrogens for atom +<br/> Ar = Aromatic annotation indicating whether atom is aromatic +<br/> RA = Ring atom annotation indicating whether atom is a ring +<br/> FC<+n/-n> = Formal charge assigned to atom +<br/> MN<n> = Mass number indicating isotope other than most abundant isotope +<br/> SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or + 3 (triplet)</div> +<p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p> +<div class="OptionsBox"> + AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></div> +<p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are +optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p> +<p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words +are also allowed:</p> +<div class="OptionsBox"> + X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors +<br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms +<br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms +<br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms +<br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms +<br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms +<br/> H : NumOfImplicitAndExplicitHydrogens +<br/> Ar : Aromatic +<br/> RA : RingAtom +<br/> FC : FormalCharge +<br/> MN : MassNumber +<br/> SM : SpinMultiplicity</div> +<p><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant +atom types.</p> +</dd> +<dt><strong><a name="setfunctionalclassestouse" class="item"><strong>SetFunctionalClassesToUse</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalTripletsFingerprints->SetFunctionalClassesToUse($ValuesRef); +<br/> $TopologicalTripletsFingerprints->SetFunctionalClassesToUse(@Values);</div> +<p>Sets functional classes invariants to use during <em>FunctionalClassAtomTypes</em> value of <em>AtomIdentifierType</em> +for topological atom triplets fingerprints generation and returns <em>TopologicalAtomTripletsFingerprints</em>.</p> +<p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>. +Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p> +<p>The functional class abbreviations correspond to:</p> +<div class="OptionsBox"> + HBD: HydrogenBondDonor +<br/> HBA: HydrogenBondAcceptor +<br/> PI : PositivelyIonizable +<br/> NI : NegativelyIonizable +<br/> Ar : Aromatic +<br/> Hal : Halogen +<br/> H : Hydrophobic +<br/> RA : RingAtom +<br/> CA : ChainAtom</div> +<div class="OptionsBox"> + Functional class atom type specification for an atom corresponds to:</div> +<div class="OptionsBox"> + Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None</div> +<p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom +types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p> +<div class="OptionsBox"> + HydrogenBondDonor: NH, NH2, OH +<br/> HydrogenBondAcceptor: N[!H], O +<br/> PositivelyIonizable: +, NH2 +<br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div> +</dd> +<dt><strong><a name="setmaxdistance" class="item"><strong>SetMaxDistance</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalAtomTripletsFingerprints->SetMaxDistance($Distance);</div> +<p>Sets maximum distance to use during topological atom triplets fingerprints generation and +returns <em>TopologicalAtomTripletsFingerprints</em>.</p> +</dd> +<dt><strong><a name="setmindistance" class="item"><strong>SetMinDistance</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalAtomTripletsFingerprints->SetMinDistance($Distance);</div> +<p>Sets minimum distance to use during topological atom triplets fingerprints generation and +returns <em>TopologicalAtomTripletsFingerprints</em>.</p> +</dd> +<dt><strong><a name="stringifytopologicalatomtripletsfingerprints" class="item"><strong>StringifyTopologicalAtomTripletsFingerprints</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $String = $TopologicalAtomTripletsFingerprints-> + StringifyTopologicalAtomTripletsFingerprints();</div> +<p>Returns a string containing information about <em>TopologicalAtomTripletsFingerprints</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="./Fingerprints.html">Fingerprints.pm</a>, <a href="./FingerprintsStringUtil.html">FingerprintsStringUtil.pm</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pm</a>,  +<a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>, <a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>, <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>,  +<a href="./MACCSKeys.html">MACCSKeys.pm</a>, <a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>, <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>,  +<a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>, <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>,  +<a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.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="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html" title="TopologicalPharmacophoreAtomPairsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::TopologicalAtomTripletsFingerprints.pm</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>