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+.\" ========================================================================
+.\"
+.IX Title "MOLECULARDESCRIPTORSGENERATOR 1"
+.TH MOLECULARDESCRIPTORSGENERATOR 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
+.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
+.\" way too many mistakes in technical documents.
+.if n .ad l
+.nh
+.SH "NAME"
+MolecularDescriptorsGenerator
+.SH "SYNOPSIS"
+.IX Header "SYNOPSIS"
+use MolecularDescriptors::MolecularDescriptorsGenerator;
+.PP
+use MolecularDescriptors::MolecularDescriptorsGenerator qw(:all);
+.SH "DESCRIPTION"
+.IX Header "DESCRIPTION"
+\&\fBMolecularDescriptorsGenerator\fR class provides the following methods:
+.PP
+new, GenerateDescriptors, GetAvailableClassAndDescriptorNames,
+GetAvailableClassNameForDescriptorName, GetAvailableDescriptorClassNames,
+GetAvailableDescriptorNames, GetAvailableDescriptorNamesForDescriptorClass,
+GetDescriptorClassParameters, GetDescriptorNames, GetDescriptorNamesAndValues,
+GetDescriptorValueByName, GetDescriptorValues, GetRuleOf3DescriptorNames,
+GetRuleOf5DescriptorNames, IsDescriptorClassNameAvailable,
+IsDescriptorNameAvailable, IsDescriptorsGenerationSuccessful,
+SetDescriptorClassParameters, SetDescriptorNames, SetMode, SetMolecule,
+StringifyMolecularDescriptorsGenerator
+.PP
+\&\fBMolecularDescriptorsGenerator\fR is derived from is derived from \fBObjectProperty\fR
+base class that provides methods not explicitly defined in \fBMolecularDescriptorsGenerator\fR
+or \fBObjectProperty\fR classes using Perl's \s-1AUTOLOAD\s0 functionality. These methods are
+generated on-the-fly for a specified object property:
+.PP
+.Vb 3
+\&    Set<PropertyName>(<PropertyValue>);
+\&    $PropertyValue = Get<PropertyName>();
+\&    Delete<PropertyName>();
+.Ve
+.PP
+\&\fBMolecularDescriptorsGenerator\fR is designed to provide a plug-in environment for
+molecular descriptors development. The molecular descriptor class modules available
+in \fBMolecularDescriptors\fR directory under \fBMayaChemTools/lib\fR directory are
+automatically detected and loaded into the system. The descriptor names provided
+by each descriptor class module through its \fBGetDescriptorNames\fR function are
+retrieved and are made available for calculations of their values for a specified
+molecule.
+.PP
+Any combination of available descriptor names can be specified during calculation
+of descriptor values using \fBGenerateDescriptors\fR 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.
+.PP
+RuleOf5 [ Ref 91 ] descriptor names are: MolecularWeight, HydrogenBondDonors,
+HydrogenBondAcceptors, SLogP. RuleOf5 states: MolecularWeight <= 500,
+HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, and logP <= 5.
+.PP
+RuleOf3 [ Ref 92 ] descriptor names are: MolecularWeight, RotatableBonds,
+HydrogenBondDonors, HydrogenBondAcceptors, SLogP, \s-1TPSA\s0. RuleOf3 states:
+MolecularWeight <= 300, RotatableBonds <= 3, HydrogenBondDonors <= 3,
+HydrogenBondAcceptors <= 3, logP <= 3, and \s-1TPSA\s0 <= 60.
+.PP
+Before calculation of a specified set of descriptors by \fBGenerateDescriptors\fR
+method, a set of descriptor calculation control parameters for a specific descriptor
+class name can be set using \fBSetDescriptorClassParameters\fR 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.
+.SS "\s-1METHODS\s0"
+.IX Subsection "METHODS"
+.IP "\fBnew\fR" 4
+.IX Item "new"
+.Vb 3
+\&    $NewMolecularDescriptorsGenerator = new MolecularDescriptors::
+\&                                        MolecularDescriptorsGenerator(
+\&                                        %NamesAndValues);
+.Ve
+.Sp
+Using specified \fIMolecularDescriptorsGenerator\fR property names and values hash, \fBnew\fR
+method creates a new object and returns a reference to newly created \fBMolecularDescriptorsGenerator\fR
+object. By default, the following properties are initialized:
+.Sp
+.Vb 6
+\&    Mode = \*(AqAll\*(Aq
+\&    @{$This\->{DescriptorNames}} = ()
+\&    %{$This\->{DescriptorClassParameters}} = ()
+\&    @{$This\->{DescriptorClassNames}} = ()
+\&    %{$This\->{DescriptorClassObjects}} = ()
+\&    @{$This\->{DescriptorValues}} = ()
+.Ve
+.Sp
+Examples:
+.Sp
+.Vb 3
+\&    $MolecularDescriptorsGenerator = new MolecularDescriptors::
+\&                                     MolecularDescriptorsGenerator(
+\&                              \*(AqMolecule\*(Aq => $Molecule);
+\&
+\&    @DescriptorNames = qw(MolecularWeight HydrogenBondDonors Fsp3Carbons)
+\&    $MolecularDescriptorsGenerator = new MolecularDescriptors::
+\&                                     MolecularDescriptorsGenerator(
+\&                              \*(AqMode\*(Aq => \*(AqSpecify\*(Aq,
+\&                              \*(AqDescriptorNames\*(Aq => \e@DescriptorNames);
+\&
+\&    $MolecularDescriptorsGenerator\->SetDescriptorClassParameters(
+\&                              \*(AqDescriptorClassName\*(Aq => \*(AqWeightAndMassDescriptors\*(Aq,
+\&                              \*(AqWeightPrecision\*(Aq => 2,
+\&                              \*(AqMassPrecision\*(Aq => 2);
+\&
+\&    $MolecularDescriptorsGenerator\->SetDescriptorClassParameters(
+\&                              \*(AqDescriptorClassName\*(Aq => \*(AqHydrogenBondsDescriptors\*(Aq,
+\&                              \*(AqHydrogenBondsType\*(Aq => \*(AqHBondsType1\*(Aq);
+\&
+\&    $MolecularDescriptorsGenerator\->SetMolecule($Molecule);
+\&    $MolecularDescriptorsGenerator\->GenerateDescriptors();
+\&    print "MolecularDescriptorsGenerator: $MolecularDescriptorsGenerator\en";
+.Ve
+.IP "\fBGenerateDescriptors\fR" 4
+.IX Item "GenerateDescriptors"
+.Vb 1
+\&    $MolecularDescriptorsGenerator\->GenerateDescriptors();
+.Ve
+.Sp
+Calculates descriptor values for specified descriptors and returns \fIMolecularDescriptorsGenerator\fR.
+.Sp
+Descriptor class objects are instantiated only once at first invocation. During
+subsequent calls to \fBGenerateDescriptors\fR method, descriptor values are
+initialized and \fBGenerateDescriptors\fR method provided by descriptor class is
+used to calculate descriptor values for specified descriptors.
+.IP "\fBGetAvailableClassAndDescriptorNames\fR" 4
+.IX Item "GetAvailableClassAndDescriptorNames"
+.Vb 5
+\&    %ClassAndDescriptorNames = $MolecularDescriptorsGenerator\->
+\&                              GetAvailableClassAndDescriptorNames();
+\&    %ClassAndDescriptorNames = MolecularDescriptors::
+\&                               MolecularDescriptorsGenerator::
+\&                               GetAvailableClassAndDescriptorNames();
+.Ve
+.Sp
+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.
+.IP "\fBGetAvailableClassNameForDescriptorName\fR" 4
+.IX Item "GetAvailableClassNameForDescriptorName"
+.Vb 2
+\&    $DescriptorClassName = $MolecularDescriptorsGenerator\->
+\&                      GetAvailableClassNameForDescriptorName($DescriptorName);
+\&
+\&    $DescriptorClassName = MolecularDescriptors::MolecularDescriptorsGenerator::
+\&                      GetAvailableClassNameForDescriptorName($DescriptorName);
+.Ve
+.Sp
+Returns available descriptor class name for a descriptor name.
+.IP "\fBGetAvailableDescriptorClassNames\fR" 4
+.IX Item "GetAvailableDescriptorClassNames"
+.Vb 1
+\&    $Return = $MolecularDescriptorsGenerator\->GetAvailableDescriptorClassNames();
+\&
+\&    @DescriptorClassNames = $MolecularDescriptorsGenerator\->
+\&                              GetAvailableDescriptorClassNames();
+\&    @DescriptorClassNames = MolecularDescriptors::
+\&                              MolecularDescriptorsGenerator::
+\&                              GetAvailableDescriptorClassNames();
+.Ve
+.Sp
+Returns available descriptor class names as an array or number of available descriptor
+class names in scalar context.
+.IP "\fBGetAvailableDescriptorNames\fR" 4
+.IX Item "GetAvailableDescriptorNames"
+.Vb 5
+\&    @DescriptorNames = $MolecularDescriptorsGenerator\->
+\&                              GetAvailableDescriptorNames();
+\&    @DescriptorNames = MolecularDescriptors::
+\&                              MolecularDescriptorsGenerator::
+\&                              GetAvailableDescriptorNames();
+.Ve
+.Sp
+Returns available descriptor names as an array or number of available descriptor
+names in scalar context.
+.IP "\fBGetAvailableDescriptorNamesForDescriptorClass\fR" 4
+.IX Item "GetAvailableDescriptorNamesForDescriptorClass"
+.Vb 5
+\&    @DescriptorNames = $MolecularDescriptorsGenerator\->
+\&          GetAvailableDescriptorNamesForDescriptorClass($DescriptorClassName);
+\&    @DescriptorNames = MolecularDescriptors::
+\&                       MolecularDescriptorsGenerator::
+\&          GetAvailableDescriptorNamesForDescriptorClass($DescriptorClassName);
+.Ve
+.Sp
+Returns available descriptors names for a descriptor class as an array or number
+of available descriptor names in scalar context.
+.IP "\fBGetDescriptorClassParameters\fR" 4
+.IX Item "GetDescriptorClassParameters"
+.Vb 5
+\&    $DescriptorClassParametersRef = $MolecularDescriptorsGenerator\->
+\&                              GetDescriptorClassParameters();
+\&    $DescriptorClassParametersRef = MolecularDescriptors::
+\&                                    MolecularDescriptorsGenerator::
+\&                                    GetDescriptorClassParameters();
+.Ve
+.Sp
+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.
+.IP "\fBGetDescriptorNames\fR" 4
+.IX Item "GetDescriptorNames"
+.Vb 3
+\&    @DescriptorNames = $MolecularDescriptorsGenerator\->GetDescriptorNames();
+\&    @DescriptorNames = MolecularDescriptors::MolecularDescriptorsGenerator::
+\&                       GetDescriptorNames();
+.Ve
+.Sp
+Returns all available descriptor names as an array or number of available descriptors
+in scalar context.
+.IP "\fBGetDescriptorNamesAndValues\fR" 4
+.IX Item "GetDescriptorNamesAndValues"
+.Vb 2
+\&    %NamesAndValues = $MolecularDescriptorsGenerator\->
+\&                              GetDescriptorNamesAndValues();
+.Ve
+.Sp
+Returns calculated molecular descriptor names and values as a hash with descriptor
+names and values as hash key and value pairs.
+.IP "\fBGetDescriptorValueByName\fR" 4
+.IX Item "GetDescriptorValueByName"
+.Vb 2
+\&    $Value = $MolecularDescriptorsGenerator\->
+\&                              GetDescriptorValueByName($Name);
+.Ve
+.Sp
+Returns calculated descriptor values for a specified descriptor name.
+.IP "\fBGetDescriptorValues\fR" 4
+.IX Item "GetDescriptorValues"
+.Vb 1
+\&    @DescriptorValues = $MolecularDescriptorsGenerator\->GetDescriptorValues();
+.Ve
+.Sp
+Returns all calculated descriptor values as an array corresponding to specified
+descriptor names.
+.IP "\fBGetRuleOf3DescriptorNames\fR" 4
+.IX Item "GetRuleOf3DescriptorNames"
+.Vb 5
+\&    @DescriptorNames = $MolecularDescriptorsGenerator\->
+\&                       GetRuleOf3DescriptorNames();
+\&    @DescriptorNames = MolecularDescriptors::
+\&                       MolecularDescriptorsGenerator::
+\&                       GetRuleOf3DescriptorNames();
+.Ve
+.Sp
+Returns rule of 3  descriptor names as an array or number of rule of 3 descriptors in scalar
+context.
+.Sp
+RuleOf3 [ Ref 92 ] descriptor names are: MolecularWeight, RotatableBonds,
+HydrogenBondDonors, HydrogenBondAcceptors, SLogP, \s-1TPSA\s0. RuleOf3 states:
+MolecularWeight <= 300, RotatableBonds <= 3, HydrogenBondDonors <= 3,
+HydrogenBondAcceptors <= 3, logP <= 3, and \s-1TPSA\s0 <= 60.
+.IP "\fBGetRuleOf5DescriptorNames\fR" 4
+.IX Item "GetRuleOf5DescriptorNames"
+.Vb 4
+\&    @DescriptorNames = $MolecularDescriptorsGenerator\->
+\&                              GetRuleOf5DescriptorNames();
+\&    @DescriptorNames = $MolecularDescriptorsGenerator::
+\&                             GetRuleOf5DescriptorNames();
+.Ve
+.Sp
+Returns rule of 5  descriptor names as an array or number of rule of 4 descriptors in scalar
+context.
+.Sp
+RuleOf5 [ Ref 91 ] descriptor names are: MolecularWeight, HydrogenBondDonors,
+HydrogenBondAcceptors, SLogP. RuleOf5 states: MolecularWeight <= 500,
+HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, and logP <= 5.
+.IP "\fBIsDescriptorClassNameAvailable\fR" 4
+.IX Item "IsDescriptorClassNameAvailable"
+.Vb 5
+\&    $Status = $MolecularDescriptorsGenerator\->
+\&                              IsDescriptorClassNameAvailable($ClassName);
+\&    $Status = MolecularDescriptors::
+\&                              MolecularDescriptorsGenerator::
+\&                              IsDescriptorClassNameAvailable($ClassName);
+.Ve
+.Sp
+Returns 1 or 0 based on whether specified descriptor class name is available.
+.IP "\fBIsDescriptorNameAvailable\fR" 4
+.IX Item "IsDescriptorNameAvailable"
+.Vb 5
+\&    $Status = $MolecularDescriptorsGenerator\->
+\&                              IsDescriptorNameAvailable($DescriptorName);
+\&    $Status = MolecularDescriptors::
+\&                              MolecularDescriptorsGenerator::
+\&                              IsDescriptorNameAvailable($DescriptorName);
+.Ve
+.Sp
+Returns 1 or 0 based on whether specified descriptor name is available.
+.IP "\fBIsDescriptorsGenerationSuccessful\fR" 4
+.IX Item "IsDescriptorsGenerationSuccessful"
+.Vb 2
+\&    $Status = $MolecularDescriptorsGenerator\->
+\&                              IsDescriptorsGenerationSuccessful();
+.Ve
+.Sp
+Returns 1 or 0 based on whether descriptors generation is successful.
+.IP "\fBSetDescriptorClassParameters\fR" 4
+.IX Item "SetDescriptorClassParameters"
+.Vb 2
+\&    $MolecularDescriptorsGenerator\->SetDescriptorClassParameters(
+\&                              %NamesAndValues);
+.Ve
+.Sp
+Sets descriptor calculation control parameters for a specified descriptor class name
+and returns \fIMolecularDescriptorsGenerator\fR.
+.Sp
+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.
+.Sp
+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.
+.IP "\fBSetDescriptorNames\fR" 4
+.IX Item "SetDescriptorNames"
+.Vb 2
+\&    $MolecularDescriptorsGenerator\->SetDescriptorNames(@Names);
+\&    $MolecularDescriptorsGenerator\->SetDescriptorNames(\e@Names);
+.Ve
+.Sp
+Sets descriptor names to use for generating descriptor values using an array
+or reference to an array and returns \fIMolecularDescriptorsGenerator\fR.
+.IP "\fBSetMode\fR" 4
+.IX Item "SetMode"
+.Vb 1
+\&    $MolecularDescriptorsGenerator\->SetMode($Mode);
+.Ve
+.Sp
+Sets descriptors generation mode and returns \fIMolecularDescriptorsGenerator\fR.
+Possible \fIMode\fR values: \fIAll, RuleOf5, RuleOf3, Specify\fR.
+.IP "\fBSetMolecule\fR" 4
+.IX Item "SetMolecule"
+.Vb 1
+\&    $MolecularDescriptorsGenerator\->SetMolecule($Molecule);
+.Ve
+.Sp
+Sets molecule to use during calculation of molecular descriptors and returns
+\&\fIMolecularDescriptorsGenerator\fR.
+.IP "\fBStringifyMolecularDescriptorsGenerator\fR" 4
+.IX Item "StringifyMolecularDescriptorsGenerator"
+.Vb 1
+\&    $String = $MolecularDescriptorsGenerator\->StringifyMolecularDescriptorsGenerator();
+.Ve
+.Sp
+Returns a string containing information about \fIMolecularDescriptorsGenerator\fR object.
+.SH "AUTHOR"
+.IX Header "AUTHOR"
+Manish Sud <[e-mail]>
+.SH "SEE ALSO"
+.IX Header "SEE ALSO"
+MolecularDescriptors.pm
+.SH "COPYRIGHT"
+.IX Header "COPYRIGHT"
+Copyright (C) 2015 Manish Sud. All rights reserved.
+.PP
+This file is part of MayaChemTools.
+.PP
+MayaChemTools is free software; you can redistribute it and/or modify it under
+the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
+Software Foundation; either version 3 of the License, or (at your option)
+any later version.