diff mayachemtools/docs/modules/man3/MolecularDescriptors.3 @ 0:73ae111cf86f draft

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+.\" ========================================================================
+.\"
+.IX Title "MOLECULARDESCRIPTORS 1"
+.TH MOLECULARDESCRIPTORS 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"
+MolecularDescriptors \- MolecularDescriptors class
+.SH "SYNOPSIS"
+.IX Header "SYNOPSIS"
+use MolecularDescriptors::MolecularDescriptors;
+.PP
+use MolecularDescriptors::MolecularDescriptors qw(:all);
+.SH "DESCRIPTION"
+.IX Header "DESCRIPTION"
+\&\fBMolecularDescriptors\fR base class used to derive all other molecular descriptors classes provides the following methods:
+.PP
+new, AddDescriptorNames, AddDescriptorValues, GetDescriptorNames,
+GetDescriptorNamesAndValues, GetDescriptorValueByName, GetDescriptorValues,
+IsDescriptorsGenerationSuccessful, SetDescriptorNames, SetDescriptorValues,
+SetMolecule, SetType
+.PP
+\&\fBMolecularDescriptors\fR class is  derived from \fBObjectProperty\fR base class which provides methods not
+explicitly defined in \fBFingerprints\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
+.SS "\s-1METHODS\s0"
+.IX Subsection "METHODS"
+.IP "\fBnew\fR" 4
+.IX Item "new"
+.Vb 2
+\&    $NewMolecularDescriptors = new MolecularDescriptors::
+\&                               MolecularDescriptors(%NamesAndValues);
+.Ve
+.Sp
+Using specified \fIMolecularDescriptors\fR property names and values hash, \fBnew\fR method creates a new object
+and returns a reference to newly created \fBMolecularDescriptors\fR object. By default, following properties are
+initialized:
+.Sp
+.Vb 2
+\&    Molecule = \*(Aq\*(Aq;
+\&    Type = \*(Aq\*(Aq;
+.Ve
+.IP "\fBAddDescriptorNames\fR" 4
+.IX Item "AddDescriptorNames"
+.Vb 1
+\&    $MolecularDescriptors\->AddDescriptorNames(@Name);
+.Ve
+.Sp
+Adds specified descriptor \fINames\fR to the list of available descriptor names and returns
+\&\fIMolecularDescriptors\fR.
+.IP "\fBAddDescriptorValues\fR" 4
+.IX Item "AddDescriptorValues"
+.Vb 1
+\&    $MolecularDescriptors\->AddDescriptorValues(@Values);
+.Ve
+.Sp
+Adds specified descriptor \fIValues\fR to the list of calculated descriptor values and returns
+\&\fIMolecularDescriptors\fR.
+.IP "\fBGetDescriptorNames\fR" 4
+.IX Item "GetDescriptorNames"
+.Vb 1
+\&    @Names = $MolecularDescriptors\->GetDescriptorNames();
+.Ve
+.Sp
+Returns an array  containing all available descriptor names.
+.IP "\fBGetDescriptorNamesAndValues\fR" 4
+.IX Item "GetDescriptorNamesAndValues"
+.Vb 2
+\&    %NamesAndValuesReturn = $MolecularDescriptors\->
+\&                              GetDescriptorNamesAndValues();
+.Ve
+.Sp
+Returns a hash containing all available descriptor names and calculated values.
+.IP "\fBGetDescriptorValueByName\fR" 4
+.IX Item "GetDescriptorValueByName"
+.Vb 2
+\&    $Value = $MolecularDescriptors\->
+\&                              GetDescriptorValueByName($Name);
+.Ve
+.Sp
+Returns calculated value for a specified descriptor name. A string \fBNone\fR is returned for
+unknown descriptor names or for those descriptors whose values haven't been calculated.
+.IP "\fBGetDescriptorValues\fR" 4
+.IX Item "GetDescriptorValues"
+.Vb 1
+\&    @Values = $MolecularDescriptors\->GetDescriptorValues();
+.Ve
+.Sp
+Returns an array containing calculated descriptor values for all available descriptors.
+Unless \fBCalculateDescriptorsValues\fR method has been successfully invoked on a
+\&\fIMolecularDescriptors\fR object, value of each descriptor corresponds to string \fBNone\fR.
+.IP "\fBIsDescriptorsGenerationSuccessful\fR" 4
+.IX Item "IsDescriptorsGenerationSuccessful"
+.Vb 2
+\&    $Status = $MolecularDescriptors\->
+\&                              IsDescriptorsGenerationSuccessful();
+.Ve
+.Sp
+Returns 1 or 0 based on whether molecular descriptors generation was successful.
+For a successful molecular descriptors calculation, all available descriptors must have
+a values other than a string \fINone\fR which are set by \fBCalculateDescriptorsValues\fR
+method after successful completion of descriptors calculation.
+.IP "\fBSetDescriptorNames\fR" 4
+.IX Item "SetDescriptorNames"
+.Vb 1
+\&    $MolecularDescriptors\->SetDescriptorNames(@Names);
+.Ve
+.Sp
+Sets names of available descriptors to specified names and returns \fIMolecularDescriptors\fR.
+.IP "\fBSetDescriptorValues\fR" 4
+.IX Item "SetDescriptorValues"
+.Vb 1
+\&    $MolecularDescriptors\->SetDescriptorValues(@Values);
+.Ve
+.Sp
+Sets values of available descriptors to specified values and returns \fIMolecularDescriptors\fR.
+.IP "\fBSetMolecule\fR" 4
+.IX Item "SetMolecule"
+.Vb 1
+\&    $MolecularDescriptors\->SetMolecule($Molecule);
+.Ve
+.Sp
+Sets molecule to use during calculation of molecular descriptors and returns \fIMolecularDescriptors\fR.
+.IP "\fBSetType\fR" 4
+.IX Item "SetType"
+.Vb 1
+\&    $MolecularDescriptors\->SetType($Type);
+.Ve
+.Sp
+Sets \fIType\fR for \fIMolecularDescriptors\fR object and returns \fIMolecularDescriptors\fR.
+.SH "AUTHOR"
+.IX Header "AUTHOR"
+Manish Sud <[e-mail]>
+.SH "SEE ALSO"
+.IX Header "SEE ALSO"
+MolecularDescriptorsGenerator.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.