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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/MolecularDescriptorsGenerator.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,357 @@ +<html> +<head> +<title>MayaChemTools:Documentation:MolecularDescriptors::MolecularDescriptorsGenerator.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="./MolecularDescriptors.html" title="MolecularDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./MolecularVolumeDescriptors.html" title="MolecularVolumeDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>MolecularDescriptors::MolecularDescriptorsGenerator.pm</strong></td><td width="33%" align="right"><a href="././code/MolecularDescriptorsGenerator.html" title="View source code">Code</a> | <a href="./../pdf/MolecularDescriptorsGenerator.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/MolecularDescriptorsGenerator.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/MolecularDescriptorsGenerator.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/MolecularDescriptorsGenerator.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>MolecularDescriptorsGenerator</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>use MolecularDescriptors::MolecularDescriptorsGenerator;</p> +<p>use MolecularDescriptors::MolecularDescriptorsGenerator qw(:all);</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p><strong>MolecularDescriptorsGenerator</strong> class provides the following methods:</p> +<p> <a href="#new">new</a>, <a href="#generatedescriptors">GenerateDescriptors</a>, <a href="#getavailableclassanddescriptornames">GetAvailableClassAndDescriptorNames</a> +, <a href="#getavailableclassnamefordescriptorname">GetAvailableClassNameForDescriptorName</a>, <a href="#getavailabledescriptorclassnames">GetAvailableDescriptorClassNames</a> +, <a href="#getavailabledescriptornames">GetAvailableDescriptorNames</a>, <a href="#getavailabledescriptornamesfordescriptorclass">GetAvailableDescriptorNamesForDescriptorClass</a> +, <a href="#getdescriptorclassparameters">GetDescriptorClassParameters</a>, <a href="#getdescriptornames">GetDescriptorNames</a>, <a href="#getdescriptornamesandvalues">GetDescriptorNamesAndValues</a> +, <a href="#getdescriptorvaluebyname">GetDescriptorValueByName</a>, <a href="#getdescriptorvalues">GetDescriptorValues</a>, <a href="#getruleof3descriptornames">GetRuleOf3DescriptorNames</a> +, <a href="#getruleof5descriptornames">GetRuleOf5DescriptorNames</a>, <a href="#isdescriptorclassnameavailable">IsDescriptorClassNameAvailable</a> +, <a href="#isdescriptornameavailable">IsDescriptorNameAvailable</a>, <a href="#isdescriptorsgenerationsuccessful">IsDescriptorsGenerationSuccessful</a> +, <a href="#setdescriptorclassparameters">SetDescriptorClassParameters</a>, <a href="#setdescriptornames">SetDescriptorNames</a>, <a href="#setmode">SetMode</a>, <a href="#setmolecule">SetMolecule</a> +, <a href="#stringifymoleculardescriptorsgenerator">StringifyMolecularDescriptorsGenerator</a> +</p><p><strong>MolecularDescriptorsGenerator</strong> is derived from is derived from <strong>ObjectProperty</strong> +base class that provides methods not explicitly defined in <strong>MolecularDescriptorsGenerator</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><strong>MolecularDescriptorsGenerator</strong> is designed to provide a plug-in environment for +molecular descriptors development. The molecular descriptor class modules available +in <strong>MolecularDescriptors</strong> directory under <strong>MayaChemTools/lib</strong> directory are +automatically detected and loaded into the system. The descriptor names provided +by each descriptor class module through its <strong>GetDescriptorNames</strong> function are +retrieved and are made available for calculations of their values for a specified +molecule.</p> +<p>Any combination of available descriptor names can be specified during calculation +of descriptor values using <strong>GenerateDescriptors</strong> method. The current release of +MayaChemTools supports generation of four sets of descriptors: All available +descriptors, rule of 5 or 3 descriptors, or a specified set of descriptor names.</p> +<p>RuleOf5 [ Ref 91 ] descriptor names are: MolecularWeight, HydrogenBondDonors, +HydrogenBondAcceptors, SLogP. RuleOf5 states: MolecularWeight <= 500, +HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, and logP <= 5.</p> +<p>RuleOf3 [ Ref 92 ] descriptor names are: MolecularWeight, RotatableBonds, +HydrogenBondDonors, HydrogenBondAcceptors, SLogP, TPSA. RuleOf3 states: +MolecularWeight <= 300, RotatableBonds <= 3, HydrogenBondDonors <= 3, +HydrogenBondAcceptors <= 3, logP <= 3, and TPSA <= 60.</p> +<p>Before calculation of a specified set of descriptors by <strong>GenerateDescriptors</strong> +method, a set of descriptor calculation control parameters for a specific descriptor +class name can be set using <strong>SetDescriptorClassParameters</strong> method. The specified +control parameter names and values are simply passed on to specified descriptor +class during instantiation of descriptor class object without performing any validation +of parameter names and associated values. It's up to the appropriate descriptor class methods +to validate these parameters and values. In addition to specified parameter names and +values, the parameter hash must also contain descriptor class name as key and +value pair with DescriptorClassName as key with class name as value.</p> +<p> +</p> +<h2>METHODS</h2> +<dl> +<dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NewMolecularDescriptorsGenerator = new MolecularDescriptors:: + MolecularDescriptorsGenerator( + %NamesAndValues);</div> +<p>Using specified <em>MolecularDescriptorsGenerator</em> property names and values hash, <strong>new</strong> +method creates a new object and returns a reference to newly created <strong>MolecularDescriptorsGenerator</strong> +object. By default, the following properties are initialized:</p> +<div class="OptionsBox"> + Mode = 'All' +<br/> @{$This->{DescriptorNames}} = () +<br/> %{$This->{DescriptorClassParameters}} = () +<br/> @{$This->{DescriptorClassNames}} = () +<br/> %{$This->{DescriptorClassObjects}} = () +<br/> @{$This->{DescriptorValues}} = ()</div> +<p>Examples:</p> +<div class="OptionsBox"> + $MolecularDescriptorsGenerator = new MolecularDescriptors:: + MolecularDescriptorsGenerator( + 'Molecule' => $Molecule);</div> +<div class="OptionsBox"> + @DescriptorNames = qw(MolecularWeight HydrogenBondDonors Fsp3Carbons) +<br/> $MolecularDescriptorsGenerator = new MolecularDescriptors:: + MolecularDescriptorsGenerator( + 'Mode' => 'Specify', + 'DescriptorNames' => \@DescriptorNames);</div> +<div class="OptionsBox"> + $MolecularDescriptorsGenerator->SetDescriptorClassParameters( + 'DescriptorClassName' => 'WeightAndMassDescriptors', + 'WeightPrecision' => 2, + 'MassPrecision' => 2);</div> +<div class="OptionsBox"> + $MolecularDescriptorsGenerator->SetDescriptorClassParameters( + 'DescriptorClassName' => 'HydrogenBondsDescriptors', + 'HydrogenBondsType' => 'HBondsType1');</div> +<div class="OptionsBox"> + $MolecularDescriptorsGenerator->SetMolecule($Molecule); +<br/> $MolecularDescriptorsGenerator->GenerateDescriptors(); +<br/> print "MolecularDescriptorsGenerator: $MolecularDescriptorsGenerator\n";</div> +</dd> +<dt><strong><a name="generatedescriptors" class="item"><strong>GenerateDescriptors</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $MolecularDescriptorsGenerator->GenerateDescriptors();</div> +<p>Calculates descriptor values for specified descriptors and returns <em>MolecularDescriptorsGenerator</em>.</p> +<p>Descriptor class objects are instantiated only once at first invocation. During +subsequent calls to <strong>GenerateDescriptors</strong> method, descriptor values are +initialized and <strong>GenerateDescriptors</strong> method provided by descriptor class is +used to calculate descriptor values for specified descriptors.</p> +</dd> +<dt><strong><a name="getavailableclassanddescriptornames" class="item"><strong>GetAvailableClassAndDescriptorNames</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + %ClassAndDescriptorNames = $MolecularDescriptorsGenerator-> + GetAvailableClassAndDescriptorNames(); +<br/> %ClassAndDescriptorNames = MolecularDescriptors:: + MolecularDescriptorsGenerator:: + GetAvailableClassAndDescriptorNames();</div> +<p>Returns available descriptors class and descriptors names as a hash containing key +and value pairs corresponding to class name and an array of descriptor names +available for the class.</p> +</dd> +<dt><strong><a name="getavailableclassnamefordescriptorname" class="item"><strong>GetAvailableClassNameForDescriptorName</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $DescriptorClassName = $MolecularDescriptorsGenerator-> + GetAvailableClassNameForDescriptorName($DescriptorName);</div> +<div class="OptionsBox"> + $DescriptorClassName = MolecularDescriptors::MolecularDescriptorsGenerator:: + GetAvailableClassNameForDescriptorName($DescriptorName);</div> +<p>Returns available descriptor class name for a descriptor name.</p> +</dd> +<dt><strong><a name="getavailabledescriptorclassnames" class="item"><strong>GetAvailableDescriptorClassNames</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Return = $MolecularDescriptorsGenerator->GetAvailableDescriptorClassNames();</div> +<div class="OptionsBox"> + @DescriptorClassNames = $MolecularDescriptorsGenerator-> + GetAvailableDescriptorClassNames(); +<br/> @DescriptorClassNames = MolecularDescriptors:: + MolecularDescriptorsGenerator:: + GetAvailableDescriptorClassNames();</div> +<p>Returns available descriptor class names as an array or number of available descriptor +class names in scalar context.</p> +</dd> +<dt><strong><a name="getavailabledescriptornames" class="item"><strong>GetAvailableDescriptorNames</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @DescriptorNames = $MolecularDescriptorsGenerator-> + GetAvailableDescriptorNames(); +<br/> @DescriptorNames = MolecularDescriptors:: + MolecularDescriptorsGenerator:: + GetAvailableDescriptorNames();</div> +<p>Returns available descriptor names as an array or number of available descriptor +names in scalar context.</p> +</dd> +<dt><strong><a name="getavailabledescriptornamesfordescriptorclass" class="item"><strong>GetAvailableDescriptorNamesForDescriptorClass</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @DescriptorNames = $MolecularDescriptorsGenerator-> + GetAvailableDescriptorNamesForDescriptorClass($DescriptorClassName); +<br/> @DescriptorNames = MolecularDescriptors:: + MolecularDescriptorsGenerator:: + GetAvailableDescriptorNamesForDescriptorClass($DescriptorClassName);</div> +<p>Returns available descriptors names for a descriptor class as an array or number +of available descriptor names in scalar context.</p> +</dd> +<dt><strong><a name="getdescriptorclassparameters" class="item"><strong>GetDescriptorClassParameters</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $DescriptorClassParametersRef = $MolecularDescriptorsGenerator-> + GetDescriptorClassParameters(); +<br/> $DescriptorClassParametersRef = MolecularDescriptors:: + MolecularDescriptorsGenerator:: + GetDescriptorClassParameters();</div> +<p>Returns descriptor name parameters as a reference to hash of hashes with hash +keys corresponding to class name and class parameter name with hash value +as class parameter value.</p> +</dd> +<dt><strong><a name="getdescriptornames" class="item"><strong>GetDescriptorNames</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @DescriptorNames = $MolecularDescriptorsGenerator->GetDescriptorNames(); +<br/> @DescriptorNames = MolecularDescriptors::MolecularDescriptorsGenerator:: + GetDescriptorNames();</div> +<p>Returns all available descriptor names as an array or number of available descriptors +in scalar context.</p> +</dd> +<dt><strong><a name="getdescriptornamesandvalues" class="item"><strong>GetDescriptorNamesAndValues</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + %NamesAndValues = $MolecularDescriptorsGenerator-> + GetDescriptorNamesAndValues();</div> +<p>Returns calculated molecular descriptor names and values as a hash with descriptor +names and values as hash key and value pairs.</p> +</dd> +<dt><strong><a name="getdescriptorvaluebyname" class="item"><strong>GetDescriptorValueByName</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Value = $MolecularDescriptorsGenerator-> + GetDescriptorValueByName($Name);</div> +<p>Returns calculated descriptor values for a specified descriptor name.</p> +</dd> +<dt><strong><a name="getdescriptorvalues" class="item"><strong>GetDescriptorValues</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @DescriptorValues = $MolecularDescriptorsGenerator->GetDescriptorValues();</div> +<p>Returns all calculated descriptor values as an array corresponding to specified +descriptor names.</p> +</dd> +<dt><strong><a name="getruleof3descriptornames" class="item"><strong>GetRuleOf3DescriptorNames</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @DescriptorNames = $MolecularDescriptorsGenerator-> + GetRuleOf3DescriptorNames(); +<br/> @DescriptorNames = MolecularDescriptors:: + MolecularDescriptorsGenerator:: + GetRuleOf3DescriptorNames();</div> +<p>Returns rule of 3 descriptor names as an array or number of rule of 3 descriptors in scalar +context.</p> +<p>RuleOf3 [ Ref 92 ] descriptor names are: MolecularWeight, RotatableBonds, +HydrogenBondDonors, HydrogenBondAcceptors, SLogP, TPSA. RuleOf3 states: +MolecularWeight <= 300, RotatableBonds <= 3, HydrogenBondDonors <= 3, +HydrogenBondAcceptors <= 3, logP <= 3, and TPSA <= 60.</p> +</dd> +<dt><strong><a name="getruleof5descriptornames" class="item"><strong>GetRuleOf5DescriptorNames</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + @DescriptorNames = $MolecularDescriptorsGenerator-> + GetRuleOf5DescriptorNames(); +<br/> @DescriptorNames = $MolecularDescriptorsGenerator:: + GetRuleOf5DescriptorNames();</div> +<p>Returns rule of 5 descriptor names as an array or number of rule of 4 descriptors in scalar +context.</p> +<p>RuleOf5 [ Ref 91 ] descriptor names are: MolecularWeight, HydrogenBondDonors, +HydrogenBondAcceptors, SLogP. RuleOf5 states: MolecularWeight <= 500, +HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, and logP <= 5.</p> +</dd> +<dt><strong><a name="isdescriptorclassnameavailable" class="item"><strong>IsDescriptorClassNameAvailable</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $MolecularDescriptorsGenerator-> + IsDescriptorClassNameAvailable($ClassName); +<br/> $Status = MolecularDescriptors:: + MolecularDescriptorsGenerator:: + IsDescriptorClassNameAvailable($ClassName);</div> +<p>Returns 1 or 0 based on whether specified descriptor class name is available.</p> +</dd> +<dt><strong><a name="isdescriptornameavailable" class="item"><strong>IsDescriptorNameAvailable</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $MolecularDescriptorsGenerator-> + IsDescriptorNameAvailable($DescriptorName); +<br/> $Status = MolecularDescriptors:: + MolecularDescriptorsGenerator:: + IsDescriptorNameAvailable($DescriptorName);</div> +<p>Returns 1 or 0 based on whether specified descriptor name is available.</p> +</dd> +<dt><strong><a name="isdescriptorsgenerationsuccessful" class="item"><strong>IsDescriptorsGenerationSuccessful</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Status = $MolecularDescriptorsGenerator-> + IsDescriptorsGenerationSuccessful();</div> +<p>Returns 1 or 0 based on whether descriptors generation is successful.</p> +</dd> +<dt><strong><a name="setdescriptorclassparameters" class="item"><strong>SetDescriptorClassParameters</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $MolecularDescriptorsGenerator->SetDescriptorClassParameters( + %NamesAndValues);</div> +<p>Sets descriptor calculation control parameters for a specified descriptor class name +and returns <em>MolecularDescriptorsGenerator</em>.</p> +<p>The specified parameter names and values are simply passed on to specified descriptor +class during instantiation of descriptor class object without any performing any validation +of parameter names and associated values. It's up to the appropriate descriptor class methods +to validate these parameters and values.</p> +<p>In addition to specified parameter names and values, the parameter hash must also contain +descriptor class name as key and value pair with DescriptorClassName as key with class +name as value.</p> +</dd> +<dt><strong><a name="setdescriptornames" class="item"><strong>SetDescriptorNames</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $MolecularDescriptorsGenerator->SetDescriptorNames(@Names); +<br/> $MolecularDescriptorsGenerator->SetDescriptorNames(\@Names);</div> +<p>Sets descriptor names to use for generating descriptor values using an array +or reference to an array and returns <em>MolecularDescriptorsGenerator</em>.</p> +</dd> +<dt><strong><a name="setmode" class="item"><strong>SetMode</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $MolecularDescriptorsGenerator->SetMode($Mode);</div> +<p>Sets descriptors generation mode and returns <em>MolecularDescriptorsGenerator</em>. +Possible <em>Mode</em> values: <em>All, RuleOf5, RuleOf3, Specify</em>.</p> +</dd> +<dt><strong><a name="setmolecule" class="item"><strong>SetMolecule</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $MolecularDescriptorsGenerator->SetMolecule($Molecule);</div> +<p>Sets molecule to use during calculation of molecular descriptors and returns +<em>MolecularDescriptorsGenerator</em>.</p> +</dd> +<dt><strong><a name="stringifymoleculardescriptorsgenerator" class="item"><strong>StringifyMolecularDescriptorsGenerator</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $String = $MolecularDescriptorsGenerator->StringifyMolecularDescriptorsGenerator();</div> +<p>Returns a string containing information about <em>MolecularDescriptorsGenerator</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="./MolecularDescriptors.html">MolecularDescriptors.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="./MolecularDescriptors.html" title="MolecularDescriptors.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./MolecularVolumeDescriptors.html" title="MolecularVolumeDescriptors.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MolecularDescriptors::MolecularDescriptorsGenerator.pm</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>