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

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+.\" ========================================================================
+.\"
+.IX Title "ROTATABLEBONDSDESCRIPTORS 1"
+.TH ROTATABLEBONDSDESCRIPTORS 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"
+RotatableBondsDescriptors
+.SH "SYNOPSIS"
+.IX Header "SYNOPSIS"
+use MolecularDescriptors::RotatableBondsDescriptors;
+.PP
+use MolecularDescriptors::RotatableBondsDescriptors qw(:all);
+.SH "DESCRIPTION"
+.IX Header "DESCRIPTION"
+\&\fBRotatableBondsDescriptors\fR class provides the following methods:
+.PP
+new, GenerateDescriptors, GetDescriptorNames,
+StringifyRotatableBondsDescriptors
+.PP
+\&\fBRotatableBondsDescriptors\fR is derived from \fBMolecularDescriptors\fR class which in turn
+is  derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
+in \fBRotatableBondsDescriptors\fR, \fBMolecularDescriptors\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
+A rotatable bond [ Ref 92 ] is defined as any single bond which is not in a ring and involves only non-hydrogen
+atoms. By default, the following types of single bonds are not considered rotatable bonds:
+.PP
+.Vb 5
+\&    o Terminal bonds
+\&    o Bonds attached to triple bonds
+\&    o Amide C\-N bonds
+\&    o Thioamide C\-N bond bonds
+\&    o Sulfonamide S\-N bonds
+.Ve
+.SS "\s-1METHODS\s0"
+.IX Subsection "METHODS"
+.IP "\fBnew\fR" 4
+.IX Item "new"
+.Vb 3
+\&    $RotatableBondsDescriptors = new MolecularDescriptors::
+\&                                 RotatableBondsDescriptors(
+\&                                 %NamesAndValues);
+.Ve
+.Sp
+Using specified \fIRotatableBondsDescriptors\fR property names and values hash, \fBnew\fR
+method creates a new object and returns a reference to newly created \fBRotatableBondsDescriptors\fR
+object. By default, the following properties are initialized:
+.Sp
+.Vb 9
+\&    Molecule = \*(Aq\*(Aq
+\&    Type = \*(AqRotatableBonds\*(Aq
+\&    IgnoreTerminalBonds = 1
+\&    IgnoreBondsToTripleBonds = 1
+\&    IgnoreAmideBonds = 1
+\&    IgnoreThioamideBonds = 1
+\&    IgnoreSulfonamideBonds = 1
+\&    @DescriptorNames = (\*(AqRotatableBonds\*(Aq)
+\&    @DescriptorValues = (\*(AqNone\*(Aq)
+.Ve
+.Sp
+Examples:
+.Sp
+.Vb 2
+\&    $RotatableBondsDescriptors = new MolecularDescriptors::
+\&                                 RotatableBondsDescriptors();
+\&
+\&    $RotatableBondsDescriptors = new MolecularDescriptors::
+\&                                 RotatableBondsDescriptors(
+\&                                 \*(AqIgnoreAmideBonds\*(Aq => 0,
+\&                                 \*(AqIgnoreThioamideBonds\*(Aq => 0,
+\&                                 \*(AqIgnoreSulfonamideBonds\*(Aq => 0);
+\&
+\&    $RotatableBondsDescriptors\->SetMolecule($Molecule);
+\&    $RotatableBondsDescriptors\->GenerateDescriptors();
+\&    print "RotatableBondsDescriptors: $RotatableBondsDescriptors\en";
+.Ve
+.IP "\fBGenerateDescriptors\fR" 4
+.IX Item "GenerateDescriptors"
+.Vb 1
+\&    $RotatableBondsDescriptors\->GenerateDescriptors();
+.Ve
+.Sp
+Calculates number of rotatable bonds descriptors in a molecule and returns
+\&\fIRotatableBondsDescriptors\fR.
+.IP "\fBGetDescriptorNames\fR" 4
+.IX Item "GetDescriptorNames"
+.Vb 3
+\&    @DescriptorNames = $RotatableBondsDescriptors\->GetDescriptorNames();
+\&    @DescriptorNames = MolecularDescriptors::RotatableBondsDescriptors::
+\&                       GetDescriptorNames();
+.Ve
+.Sp
+Returns all available descriptor names as an array.
+.IP "\fBStringifyRotatableBondsDescriptors\fR" 4
+.IX Item "StringifyRotatableBondsDescriptors"
+.Vb 1
+\&    $String = $RotatableBondsDescriptors\->StringifyRotatableBondsDescriptors();
+.Ve
+.Sp
+Returns a string containing information about \fIRotatableBondsDescriptors\fR object.
+.SH "AUTHOR"
+.IX Header "AUTHOR"
+Manish Sud <[e-mail]>
+.SH "SEE ALSO"
+.IX Header "SEE ALSO"
+MolecularDescriptors.pm, 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.