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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/AtomNeighborhoodsFingerprints.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,352 @@ +<html> +<head> +<title>MayaChemTools:Documentation:Fingerprints::AtomNeighborhoodsFingerprints.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="./FileUtil.html" title="FileUtil.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::AtomNeighborhoodsFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/AtomNeighborhoodsFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/AtomNeighborhoodsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/AtomNeighborhoodsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/AtomNeighborhoodsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/AtomNeighborhoodsFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>AtomNeighborhoodsFingerprints</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>use Fingerprints::AtomNeighborhoodsFingerprints;</p> +<p>use Fingerprints::AtomNeighborhoodsFingerprints qw(:all);</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p><strong>AtomNeighborhoodsFingerprints</strong> [ Ref 53-56, Ref 73 ] class provides the following methods:</p> +<p> <a href="#new">new</a>, <a href="#generatefingerprints">GenerateFingerprints</a>, <a href="#getdescription">GetDescription</a>, <a href="#setatomidentifiertype">SetAtomIdentifierType</a> +, <a href="#setatomicinvariantstouse">SetAtomicInvariantsToUse</a>, <a href="#setfunctionalclassestouse">SetFunctionalClassesToUse</a>, <a href="#setmaxneighborhoodradius">SetMaxNeighborhoodRadius</a> +, <a href="#setminneighborhoodradius">SetMinNeighborhoodRadius</a>, <a href="#stringifyatomneighborhoodsfingerprints">StringifyAtomNeighborhoodsFingerprints</a> +</p><p><strong>AtomNeighborhoodsFingerprints</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>AtomNeighborhoodsFingerprints</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>AtomNeighborhoodsFingerprints</strong> +corresponding to following <strong>AtomIdentifierTypes</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 +sucb as <strong>AtomicInvariantsToUse</strong> and <strong>FunctionalClassesToUse</strong>, initial atom types are +assigned to all non-hydrogen atoms in a molecule. Using atom neighborhoods +around each non-hydrogen central atom corresponding to radii between specified values +<strong>MinNeighborhoodRadius</strong> and <strong>MaxNeighborhoodRadius</strong>, unique atom types at each radii +level are counted and an atom neighborhood identifier is generated.</p> +<p>The format of an atom neighborhood identifier around a central non-hydrogen atom at a +specific radius is:</p> +<div class="OptionsBox"> + NR<n>-<AtomType>-ATC<n></div> +<div class="OptionsBox"> + NR: Neighborhood radius +<br/> AtomType: Assigned atom type +<br/> ATC: Atom type count</div> +<p>The atom neighborhood identifier for non-hydrogen central atom corresponding to all specified radii +is generated by concatenating neighborhood identifiers at each radii by colon as a delimiter:</p> +<div class="OptionsBox"> + NR<n>-<AtomType>-ATC<n>:NR<n>-<AtomType>-ATC<n>:...</div> +<p>The atom neighborhood identifiers for all non-hydrogen central atoms at all specified radii are +concatenated using space as a delimiter and constitute atom neighborhood fingerprint of the molecule.</p> +<p>The current release of MayaChemTools generates the following types of atom neighborhoods +fingerprints vector strings:</p> +<div class="OptionsBox"> + FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi +<br/> us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT +<br/> C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X +<br/> 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A +<br/> TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2 +<br/> -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...</div> +<div class="OptionsBox"> + FingerprintsVector;AtomNeighborhoods:DREIDINGAtomTypes:MinRadius0:MaxR +<br/> adius2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1: +<br/> NR1-O_2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N +<br/> _3-ATC1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-AT +<br/> C1:NR2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR +<br/> 1-N_R-ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-...</div> +<div class="OptionsBox"> + FingerprintsVector;AtomNeighborhoods:EStateAtomTypes:MinRadius0:MaxRad +<br/> ius2;41;AlphaNumericalValues;ValuesString;NR0-aaCH-ATC1:NR1-aaCH-ATC1: +<br/> NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-aaCH-ATC1:NR +<br/> 1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0- +<br/> aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 NR0- +<br/> aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 N...</div> +<div class="OptionsBox"> + FingerprintsVector;AtomNeighborhoods:FunctionalClassAtomTypes:MinRadiu +<br/> s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-Ar-ATC1:NR1-Ar- +<br/> ATC1:NR1-Ar.HBA-ATC1:NR1-None-ATC1:NR2-Ar-ATC2:NR2-None-ATC4 NR0-Ar-AT +<br/> C1:NR1-Ar-ATC2:NR1-Ar.HBA-ATC1:NR2-Ar-ATC5:NR2-None-ATC1 NR0-Ar-ATC1:N +<br/> R1-Ar-ATC2:NR1-HBD-ATC1:NR2-Ar-ATC2:NR2-None-ATC1 NR0-Ar-ATC1:NR1-Ar-A +<br/> TC2:NR1-Hal-ATC1:NR2-Ar-ATC2 NR0-Ar-ATC1:NR1-Ar-ATC2:NR1-None-ATC1:...</div> +<div class="OptionsBox"> + FingerprintsVector;AtomNeighborhoods:MMFF94AtomTypes:MinRadius0:MaxRad +<br/> ius2;41;AlphaNumericalValues;ValuesString;NR0-C5A-ATC1:NR1-C5B-ATC1:NR +<br/> 1-CB-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C5B-ATC1:NR2-CB-ATC3:NR2-CR-ATC +<br/> 1 NR0-C5A-ATC1:NR1-C5B-ATC1:NR1-CR-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C +<br/> 5B-ATC1:NR2-C=ON-ATC1:NR2-CR-ATC3 NR0-C5B-ATC1:NR1-C5A-ATC1:NR1-C5B-AT +<br/> C1:NR1-C=ON-ATC1:NR2-C5A-ATC1:NR2-CB-ATC1:NR2-CR-ATC1:NR2-N5-ATC1:N...</div> +<div class="OptionsBox"> + FingerprintsVector;AtomNeighborhoods:SLogPAtomTypes:MinRadius0:MaxRadi +<br/> us2;41;AlphaNumericalValues;ValuesString;NR0-C1-ATC1:NR1-C10-ATC1:NR1- +<br/> CS-ATC1:NR2-C1-ATC1:NR2-N11-ATC1:NR2-O2-ATC1 NR0-C1-ATC1:NR1-C11-ATC1: +<br/> NR2-C1-ATC1:NR2-C21-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:NR2-C1-ATC1:NR2-C21- +<br/> ATC1 NR0-C1-ATC1:NR1-C5-ATC1:NR1-CS-ATC1:NR2-C1-ATC1:NR2-O2-ATC2:NR2-O +<br/> 9-ATC1 NR0-C1-ATC1:NR1-CS-ATC2:NR2-C1-ATC2:NR2-O2-ATC2 NR0-C10-ATC1...</div> +<div class="OptionsBox"> + FingerprintsVector;AtomNeighborhoods:SYBYLAtomTypes:MinRadius0:MaxRadi +<br/> us2;41;AlphaNumericalValues;ValuesString;NR0-C.2-ATC1:NR1-C.3-ATC1:NR1 +<br/> -O.co2-ATC2:NR2-C.3-ATC1 NR0-C.2-ATC1:NR1-C.ar-ATC1:NR1-N.am-ATC1:NR1- +<br/> O.2-ATC1:NR2-C.ar-ATC3 NR0-C.3-ATC1:NR1-C.2-ATC1:NR1-C.3-ATC1:NR2-C.3- +<br/> ATC1:NR2-O.3-ATC1:NR2-O.co2-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR1-N.ar-AT +<br/> C1:NR2-C.3-ATC1:NR2-C.ar-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR2-C.3-ATC...</div> +<div class="OptionsBox"> + FingerprintsVector;AtomNeighborhoods:TPSAAtomTypes:MinRadius0:MaxRadiu +<br/> s2;41;AlphaNumericalValues;ValuesString;NR0-N21-ATC1:NR1-None-ATC3:NR2 +<br/> -None-ATC5 NR0-N7-ATC1:NR1-None-ATC2:NR2-None-ATC3:NR2-O3-ATC1 NR0-Non +<br/> e-ATC1:NR1-N21-ATC1:NR1-None-ATC1:NR2-None-ATC3 NR0-None-ATC1:NR1-N21- +<br/> ATC1:NR1-None-ATC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N21-ATC1:NR1-None-A +<br/> TC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N7-ATC1:NR1-None-ATC1:NR1-O3-AT...</div> +<div class="OptionsBox"> + FingerprintsVector;AtomNeighborhoods:UFFAtomTypes:MinRadius0:MaxRadius +<br/> 2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:NR1-O +<br/> _2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N_3-AT +<br/> C1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-ATC1:NR +<br/> 2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR1-N_R +<br/> -ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-C_3-A...</div> +<p> +</p> +<h2>METHODS</h2> +<dl> +<dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NewAtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints( + %NamesAndValues);</div> +<p>Using specified <em>AtomNeighborhoodsFingerprints</em> property names and values hash, <strong>new</strong> +method creates a new object and returns a reference to newly created <strong>AtomNeighborhoodsFingerprints</strong> +object. By default, the following properties are initialized:</p> +<div class="OptionsBox"> + Molecule = '' +<br/> Type = 'AtomNeighborhoods' +<br/> MinNeighborhoodRadius = 0 +<br/> MaxNeighborhoodRadius = 2 +<br/> AtomIdentifierType = '' +<br/> AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC', 'MN'] +<br/> FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']</div> +<p>Examples:</p> +<div class="OptionsBox"> + $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + "AtomicInvariantsAtomTypes");</div> +<div class="OptionsBox"> + $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints( + 'Molecule' => $Molecule, + 'MinNeighborhoodRadius' => 0, + 'MaxNeighborhoodRadius' => 2, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes', + 'AtomicInvariantsToUse' => + ['AS', 'X', 'BO', 'H', 'FC'] );</div> +<div class="OptionsBox"> + $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'SYBYLAtomTypes');</div> +<div class="OptionsBox"> + $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'MMFF94AtomTypes');</div> +<div class="OptionsBox"> + $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes');</div> +<div class="OptionsBox"> + $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints( + 'Molecule' => $Molecule, + 'MinNeighborhoodRadius' => 0, + 'MaxNeighborhoodRadius' => 2, + 'AtomIdentifierType' => + 'FunctionalClassAtomTypes', + 'FunctionalClassesToUse' => + ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] );</div> +<div class="OptionsBox"> + $AtomNeighborhoodsFingerprints->GenerateFingerprints(); +<br/> print "$AtomNeighborhoodsFingerprints\n";</div> +</dd> +<dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomNeighborhoodsFingerprints->GenerateFingerprints();</div> +<p>Generates atom neighborhood fingerprints and returns <em>AtomNeighborhoodsFingerprints</em>.</p> +</dd> +<dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Description = $AtomNeighborhoodsFingerprints->GetDescription();</div> +<p>Returns a string containing description of atom neighborhood fingerprints.</p> +</dd> +<dt><strong><a name="setatomidentifiertype" class="item"><strong>SetAtomIdentifierType</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomNeighborhoodsFingerprints->SetAtomIdentifierType($IdentifierType);</div> +<p>Sets atom <em>IdentifierType</em> to use during atom neighborhood fingerprints generation and +returns <em>AtomNeighborhoodsFingerprints</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"> + $AtomNeighborhoodsFingerprints->SetAtomicInvariantsToUse($ValuesRef); +<br/> $AtomNeighborhoodsFingerprints->SetAtomicInvariantsToUse(@Values);</div> +<p>Sets atomic invariants to use during <em>AtomicInvariantsAtomTypes</em> value of <em>AtomIdentifierType</em> +for atom neighborhood fingerprints generation and returns <em>AtomNeighborhoodsFingerprints</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"> + $AtomNeighborhoodsFingerprints->SetFunctionalClassesToUse($ValuesRef); +<br/> $AtomNeighborhoodsFingerprints->SetFunctionalClassesToUse(@Values);</div> +<p>Sets functional classes invariants to use during <em>FunctionalClassAtomTypes</em> value of <em>AtomIdentifierType</em> +for atom neighborhoods fingerprints generation and returns <em>AtomNeighborhoodsFingerprints</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="setmaxneighborhoodradius" class="item"><strong>SetMaxNeighborhoodRadius</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomNeighborhoodsFingerprints->SetMaxNeighborhoodRadius($Radius);</div> +<p>Sets maximum neighborhood radius to use during atom neighborhood fingerprints generation and +returns <em>AtomNeighborhoodsFingerprints</em>.</p> +</dd> +<dt><strong><a name="setminneighborhoodradius" class="item"><strong>SetMinNeighborhoodRadius</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomNeighborhoodsFingerprints->SetMinNeighborhoodRadius($Radius);</div> +<p>Sets minimum neighborhood radius to use during atom neighborhood fingerprints generation and +returns <em>AtomNeighborhoodsFingerprints</em>.</p> +</dd> +<dt><strong><a name="stringifyatomneighborhoodsfingerprints" class="item"><strong>StringifyAtomNeighborhoodsFingerprints</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $String = $Fingerprints->StringifyAtomNeighborhoodsFingerprints();</div> +<p>Returns a string containing information about <em>AtomNeighborhoodsFingerprints</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="./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="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.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="./FileUtil.html" title="FileUtil.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::AtomNeighborhoodsFingerprints.pm</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>