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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/modules/html/TopologicalPharmacophoreAtomPairsFingerprints.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,394 @@ +<html> +<head> +<title>MayaChemTools:Documentation:Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints.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="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html" title="TopologicalPharmacophoreAtomTripletsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/TopologicalPharmacophoreAtomPairsFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>TopologicalPharmacophoreAtomPairsFingerprints</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>use Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints;</p> +<p>use Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints qw(:all);</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p><strong>TopologicalPharmacophoreAtomPairsFingerprints</strong> [ Ref 60-62, Ref 65, Ref 68 ] class provides +the following methods:</p> +<p>new, GenerateFingerprints, GetDescription, GetAtomPairIDs, SetAtomTypesToUse, +SetAtomTypesWeight, SetFuzzFactor, SetFuzzificationMethodology, +SetFuzzificationMode, SetMaxDistance, SetMinDistance, +SetNormalizationMethodology, SetValuesPrecision, +StringifyTopologicalPharmacophoreAtomPairsFingerprints</p> +<p><strong>TopologicalPharmacophoreAtomPairsFingerprints</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>TopologicalPharmacophoreAtomPairsFingerprints</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>Based on the values specified for <strong>AtomTypesToUse</strong>, pharmacophore atom types are +assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated. +A pharmacophore atom pairs basis set is initialized for all unique possible pairs within +<strong>MinDistance</strong> and <strong>MaxDistance</strong> range.</p> +<div class="OptionsBox"> + Let:</div> +<div class="OptionsBox"> + P = Valid pharmacophore atom type</div> +<div class="OptionsBox"> + Px = Pharmacophore atom type x +<br/> Py = Pharmacophore atom type y</div> +<div class="OptionsBox"> + Dmin = Minimum distance corresponding to number of bonds between two atoms +<br/> Dmax = Maximum distance corresponding to number of bonds between two atoms +<br/> D = Distance corresponding to number of bonds between two atoms</div> +<div class="OptionsBox"> + Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at distance Dn</div> +<div class="OptionsBox"> + P = Number of pharmacophore atom types to consider +<br/> PPDn = Number of possible unique pharmacophore atom pairs at a distance Dn</div> +<div class="OptionsBox"> + PPT = Total number of possible pharmacophore atom pairs at all distances between Dmin and Dmax</div> +<div class="OptionsBox"> + Then:</div> +<div class="OptionsBox"> + PPD = (P * (P - 1))/2 + P</div> +<div class="OptionsBox"> + PPT = ((Dmax - Dmin) + 1) * ((P * (P - 1))/2 + P) +<br/> = ((Dmax - Dmin) + 1) * PPD</div> +<div class="OptionsBox"> + So for default values of Dmin = 1, Dmax = 10 and P = 5,</div> +<div class="OptionsBox"> + PPD = (5 * (5 - 1))/2 + 5 = 15 +<br/> PPT = ((10 - 1) + 1) * 15 = 150</div> +<div class="OptionsBox"> + The pharmacophore atom pairs bais set includes 150 values.</div> +<div class="OptionsBox"> + The atom pair IDs correspond to:</div> +<div class="OptionsBox"> + Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at distance Dn</div> +<div class="OptionsBox"> + For example: H-D1-H, H-D2-HBA, PI-D5-PI and so on</div> +<p>Using distance matrix and pharmacohore atom types, occurrence of unique pharmacohore atom +pairs is counted. The contribution of each atom type to atom pair interaction is optionally +weighted by specified <strong>AtomTypesWeight</strong> before assigning its count to appropriate distance +bin. Based on <strong>NormalizationMethodology</strong> option, pharmacophore atom pairs count is optionally +normalized. Additionally, pharmacohore atom pairs count is optionally fuzzified before or after +the normalization controlled by values of <strong>FuzzifyAtomPairsCount</strong>, <strong>FuzzificationMode</strong>, +<strong>FuzzificationMethodology</strong> and <strong>FuzzFactor</strong>.</p> +<p>The final pharmacophore atom pairs count along with atom pair identifiers involving all non-hydrogen +atoms, with optional normalization and fuzzification, constitute pharmacophore topological atom pairs +fingerprints of the molecule.</p> +<p>For <em>ArbitrarySize</em> value of <strong>AtomPairsSetSizeToUse</strong>, the fingerprint vector correspond to +only those topological pharmacophore atom pairs which are present and have non-zero count. However, +for <em>FixedSize</em> value of <strong>AtomPairsSetSizeToUse</strong>, the fingerprint vector contains all possible +valid topological pharmacophore atom pairs with both zero and non-zero count values.</p> +<p>The current release of MayaChemTools generates the following types of topological pharmacophore +atom pairs fingerprints vector strings:</p> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min +<br/> Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H +<br/> -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2- +<br/> HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H +<br/> BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...; +<br/> 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 +<br/> 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist +<br/> ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0 +<br/> 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1 +<br/> 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0 +<br/> 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0 +<br/> 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist +<br/> ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H-D1 +<br/> -H H-D1-HBA H-D1-HBD H-D1-NI H-D1-PI HBA-D1-HBA HBA-D1-HBD HBA-D1-NI H +<br/> BA-D1-PI HBD-D1-HBD HBD-D1-NI HBD-D1-PI NI-D1-NI NI-D1-PI PI-D1-PI H-D +<br/> 2-H H-D2-HBA H-D2-HBD H-D2-NI H-D2-PI HBA-D2-HBA HBA-D2-HBD HBA-D2...; +<br/> 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 +<br/> 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 +<br/> 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0</div> +<p> +</p> +<h2>METHODS</h2> +<dl> +<dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints( + %NamesAndValues);</div> +<p>Using specified <em>TopologicalPharmacophoreAtomPairsFingerprints</em> property names and +values hash, <strong>new</strong> method creates a new object and returns a reference to newly created +<strong>TopologicalPharmacophoreAtomPairsFingerprints</strong> object. By default, the following properties +are initialized:</p> +<div class="OptionsBox"> + Molecule = '' +<br/> Type = 'TopologicalPharmacophoreAtomPairs' +<br/> MinDistance = 1 +<br/> MaxDistance = 10 +<br/> NormalizationMethodology = 'None' +<br/> AtomTypesToUse = ['HBD', 'HBA', 'PI', 'NI', 'H']</div> +<div class="OptionsBox"> + FuzzifyAtomPairsCount = 0 +<br/> FuzzificationMode = 'AfterNormalization' +<br/> FuzzificationMethodology = 'FuzzyBinning' +<br/> FuzzFactor = 0.15</div> +<div class="OptionsBox"> + ValuesPrecision = 2</div> +<p>Examples:</p> +<div class="OptionsBox"> + $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints( + 'Molecule' => $Molecule);</div> +<div class="OptionsBox"> + $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints( + 'Molecule' => $Molecule, + 'AtomPairsSetSizeToUse' => 'ArbitrarySize', + 'MinDistance' => 1, + 'MaxDistance' => 10, + 'NormalizationMethodology' => 'None', + 'AtomTypesToUse' => ['HBD', 'HBA', 'PI', 'NI', 'H'], + 'FuzzifyAtomPairsCount' => 0);</div> +<div class="OptionsBox"> + $TPAPFP = new TopologicalPharmacophoreAtomPairsFingerprints( + 'Molecule' => $Molecule, + 'AtomPairsSetSizeToUse' => 'FizedSize', + 'MinDistance' => 1, + 'MaxDistance' => 10, + 'NormalizationMethodology' => 'None', + 'AtomTypesToUse' => ['HBD', 'HBA', 'PI', 'NI', 'H'], + 'FuzzifyAtomPairsCount' => 1, + 'FuzzificationMethodology' => 'FuzzyBinning', + 'FuzzFactor' => 0.15, + 'ValuesPrecision' => 2);</div> +<div class="OptionsBox"> + $TPAPFP->GenerateFingerprints(); +<br/> print "$TPAPFP\n";</div> +</dd> +<dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Description = $TopologicalPharmacophoreAtomPairsFP->GetDescription();</div> +<p>Returns a string containing description of topological pharmacophore atom pairs fingerprints.</p> +</dd> +<dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalPharmacophoreAtomPairsFP->GenerateFingerprints();</div> +<p>Generates topological pharmacophore atom pairs fingerprints and returns +<em>TopologicalPharmacophoreAtomPairsFP</em>.</p> +</dd> +<dt><strong><a name="getatompairids" class="item"><strong>GetAtomPairIDs</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $AtomPairIDsRef = $TopologicalPharmacophoreAtomPairsFP->GetAtomPairIDs(); +<br/> @AtomPairIDs = $TopologicalPharmacophoreAtomPairsFP->GetAtomPairIDs();</div> +<p>Returns atom pair IDs corresponding to atom pairs count values in topological pharmacophore +atom pairs fingerprints vector as an array or reference to an array.</p> +</dd> +<dt><strong><a name="setatompairssetsizetouse" class="item"><strong>SetAtomPairsSetSizeToUse</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalPharmacophoreAtomPairsFP->SetAtomPairsSetSizeToUse($Values);</div> +<p>Sets pharmacophore atom pairs set size to use for topological pharmacophore fingerprints +generation and returns <em>TopologicalPharmacophoreAtomPairsFingerprints</em>.</p> +<p>Possible values for pharmacophore atom pairs set size are: <em>ArbitrarySize, FizedSize</em>. +Default value: <em>ArbitrarySize</em>.</p> +<p>For <em>ArbitrarySize</em> value of <strong>AtomPairsSetSizeToUse</strong>, the fingerprint vector correspond to +only those topological pharmacophore atom pairs which are present and have non-zero count. However, +for <em>FixedSize</em> value of <strong>AtomPairsSetSizeToUse</strong>, the fingerprint vector contains all possible +valid topological pharmacophore atom pairs with both zero and non-zero count values.</p> +</dd> +<dt><strong><a name="setatomtypestouse" class="item"><strong>SetAtomTypesToUse</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalPharmacophoreAtomPairsFP->SetAtomTypesToUse($ValuesRef); +<br/> $TopologicalPharmacophoreAtomPairsFP->SetAtomTypesToUse(@Values);</div> +<p>Sets pharmacophore atom types to use for topological pharmacophore fingerprints +generation and returns <em>TopologicalPharmacophoreAtomPairsFingerprints</em>.</p> +<p>Possible values for pharmacophore atom types are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>. +Default value [ Ref 60-62 ] : <em>HBD,HBA,PI,NI,H</em>.</p> +<p>The pharmacophore atom types 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> +<p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign pharmacophore 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="setatomtypesweight" class="item"><strong>SetAtomTypesWeight</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalPharmacophoreAtomPairsFP->SetAtomTypesWeight( +<br/> %AtomTypesToWeight);</div> +<p>Sets weights of specified pharmacophore atom types to use during calculation of their contribution +to atom pair count and returns <em>TopologicalPharmacophoreAtomPairsFP</em>. Default values: <em>1 for +each atom type</em>.</p> +<p>The weight values allow to increase the importance of specific pharmacophore atom type +in the generated fingerprints. A weight value of 0 for an atom type eliminates its contribution to +atom pair count where as weight value of 2 doubles its contribution.</p> +</dd> +<dt><strong><a name="setfuzzfactor" class="item"><strong>SetFuzzFactor</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalPharmacophoreAtomPairsFP->SetFuzzFactor($Value);</div> +<p>Sets fuzz factor value to use during fuzzification of atom pairs count and returns +<em>TopologicalPharmacophoreAtomPairsFP</em>. Default value: <em>0.15</em>.</p> +<p>Valid values: For <em>FuzzyBinning</em> value of <strong>FuzzificationMethodology</strong>: <em>between 0 and 1.0</em>; For +<em>FuzzyBinSmoothing</em> value of <strong>FuzzificationMethodology</strong>: <em>between 0 and 0.5</em>.</p> +</dd> +<dt><strong><a name="setfuzzificationmethodology" class="item"><strong>SetFuzzificationMethodology</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalPharmacophoreAtomPairsFP->SetFuzzificationMethodology($Value);</div> +<p>Sets fuzzification methodology to use for fuzzification of atom pairs count and returns +<em>TopologicalPharmacophoreAtomPairsFP</em>. Default value: <em>FuzzyBinning</em>. Possible values: +<em>FuzzyBinning | FuzzyBinSmoothing</em>.</p> +<p>In conjunction with values for options <strong>FuzzifyAtomPairsCount</strong>, <strong>FuzzificationMode</strong> and +<strong>FuzzFactor</strong>, <strong>FuzzificationMethodology</strong> option is used to fuzzify pharmacophore atom +pairs count.</p> +<p>Let:</p> +<div class="OptionsBox"> + Px = Pharmacophore atom type x +<br/> Py = Pharmacophore atom type y +<br/> PPxy = Pharmacophore atom pair between atom type Px and Py</div> +<div class="OptionsBox"> + PPxyDn = Pharmacophore atom pairs count between atom type Px and Py + at distance Dn +<br/> PPxyDn-1 = Pharmacophore atom pairs count between atom type Px and Py + at distance Dn - 1 +<br/> PPxyDn+1 = Pharmacophore atom pairs count between atom type Px and Py + at distance Dn + 1</div> +<div class="OptionsBox"> + FF = FuzzFactor for FuzzyBinning and FuzzyBinSmoothing</div> +<p>Then:</p> +<p>For <em>FuzzyBinning</em>:</p> +<div class="OptionsBox"> + PPxyDn = PPxyDn (Unchanged)</div> +<div class="OptionsBox"> + PPxyDn-1 = PPxyDn-1 + PPxyDn * FF +<br/> PPxyDn+1 = PPxyDn+1 + PPxyDn * FF</div> +<p>For <em>FuzzyBinSmoothing</em>:</p> +<div class="OptionsBox"> + PPxyDn = PPxyDn - PPxyDn * 2FF for Dmin < Dn < Dmax +<br/> PPxyDn = PPxyDn - PPxyDn * FF for Dn = Dmin or Dmax</div> +<div class="OptionsBox"> + PPxyDn-1 = PPxyDn-1 + PPxyDn * FF +<br/> PPxyDn+1 = PPxyDn+1 + PPxyDn * FF</div> +<p>In both fuzzification schemes, a value of 0 for FF implies no fuzzification of occurrence counts. +A value of 1 during <em>FuzzyBinning</em> corresponds to maximum fuzzification of occurrence counts; +however, a value of 1 during <em>FuzzyBinSmoothing</em> ends up completely distributing the value over +the previous and next distance bins.</p> +<p>So for default value of <strong>FuzzFactor</strong> (FF) 0.15, the occurrence count of pharmacohore atom pairs +at distance Dn during FuzzyBinning is left unchanged and the counts at distances Dn -1 and Dn + 1 +are incremented by PPxyDn * 0.15.</p> +<p>And during <em>FuzzyBinSmoothing</em> the occurrence counts at Distance Dn is scaled back using multiplicative +factor of (1 - 2*0.15) and the occurrence counts at distances Dn -1 and Dn + 1 are incremented by +PPxyDn * 0.15. In other words, occurrence bin count is smoothed out by distributing it over the +previous and next distance value.</p> +</dd> +<dt><strong><a name="setfuzzificationmode" class="item"><strong>SetFuzzificationMode</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalPharmacophoreAtomPairsFP->SetFuzzificationMode($Value);</div> +<p>Sets fuzzification mode to use for fuzzification of atom pairs count and returns +<em>TopologicalPharmacophoreAtomPairsFP</em>. Default value: <em>AfterNormalization</em>. Possible values: +<em>BeforeNormalization | AfterNormalization</em>.</p> +</dd> +<dt><strong><a name="setmaxdistance" class="item"><strong>SetMaxDistance</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalPharmacophoreAtomPairsFP->SetMaxDistance($Value);</div> +<p>Sets maximum bond distance between atom pairs for generating topological pharmacophore atom +pairs fingerprints and returns <em>TopologicalPharmacophoreAtomPairsFP</em>.</p> +</dd> +<dt><strong><a name="setmindistance" class="item"><strong>SetMinDistance</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalPharmacophoreAtomPairsFP->SetMinDistance($Value);</div> +<p>Sets minimum bond distance between atom pairs for generating topological pharmacophore atom +pairs fingerprints and returns <em>TopologicalPharmacophoreAtomPairsFP</em>.</p> +</dd> +<dt><strong><a name="setnormalizationmethodology" class="item"><strong>SetNormalizationMethodology</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalPharmacophoreAtomPairsFP->SetNormalizationMethodology($Value);</div> +<p>Sets normalization methodology to use for scaling the occurrence count of pharmacophore atom +pairs within specified distance range and returns <em>TopologicalPharmacophoreAtomPairsFP</em>. +Default value: <em>None</em>. Possible values: <em>None, ByHeavyAtomsCount or ByAtomTypesCount</em>.</p> +</dd> +<dt><strong><a name="setvaluesprecision" class="item"><strong>SetValuesPrecision</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $TopologicalPharmacophoreAtomPairsFP->SetValuesPrecision($Value);</div> +<p>Sets precision of atom pairs count real values which might be generated after normalization +or fuzzification and returns <em>TopologicalPharmacophoreAtomPairsFP</em>. Default: up to <em>2</em> decimal +places.</p> +</dd> +<dt><strong><a name="stringifytopologicalpharmacophoreatompairsfingerprints" class="item"><strong>StringifyTopologicalPharmacophoreAtomPairsFingerprints</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $String = $TopologicalPharmacophoreAtomPairsFP-> + StringifyTopologicalPharmacophoreAtomPairsFingerprints();</div> +<p>Returns a string containing information about <em>TopologicalPharmacophoreAtomPairsFingerprints</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="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.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="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html" title="TopologicalPharmacophoreAtomTripletsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::TopologicalPharmacophoreAtomPairsFingerprints.pm</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>