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.\" ========================================================================
.\"
.IX Title "HYDROGENBONDSDESCRIPTORS 1"
.TH HYDROGENBONDSDESCRIPTORS 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"
HydrogenBondsDescriptors
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
use MolecularDescriptors::HydrogenBondsDescriptors;
.PP
use MolecularDescriptors::HydrogenBondsDescriptors qw(:all);
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\fBHydrogenBondsDescriptors\fR class provides the following methods:
.PP
new, GenerateDescriptors, GetDescriptorNames, SetHydrogenBondsType,
StringifyHydrogenBondsDescriptors
.PP
\&\fBHydrogenBondsDescriptors\fR is derived from \fBMolecularDescriptors\fR class which in turn
is  derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
in \fBHydrogenBondsDescriptors\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
The current release of MayaChemTools supports identification of two types of hydrogen bond
donor and acceptor atoms with these names:
.PP
.Vb 2
\&    HBondsType1 or HydrogenBondsType1
\&    HBondsType2 or HydrogenBondsType2
.Ve
.PP
The names of these hydrogen bond types are rather arbitrary. However, their definitions have
specific meaning and are as follows:
.PP
.Vb 1
\&    HydrogenBondsType1 [ Ref 60\-61, Ref 65\-66 ]:
\&
\&        Donor: NH, NH2, OH \- Any N and O with available H
\&        Acceptor: N[!H], O \- Any N without available H and any O
\&
\&    HydrogenBondsType2 [ Ref 91 ]:
\&
\&        Donor: NH, NH2, OH \- N and O with available H
\&        Acceptor: N, O \- And N and O
.Ve
.PP
By default, \fIHydrogenBondsType2\fR is used to calculate number hydrogen bond donor
and acceptor atoms. This corresponds to \fBRuleOf5\fR definition of hydrogen bond donors
and acceptors.
.SS "\s-1METHODS\s0"
.IX Subsection "METHODS"
.IP "\fBnew\fR" 4
.IX Item "new"
.Vb 2
\&    $HydrogenBondsDescriptors = new MolecularDescriptors::
\&                                HydrogenBondsDescriptors(%NamesAndValues);
.Ve
.Sp
Using specified \fIHydrogenBondsDescriptors\fR property names and values hash, \fBnew\fR
method creates a new object and returns a reference to newly created \fBHydrogenBondsDescriptors\fR
object. By default, the following properties are initialized:
.Sp
.Vb 5
\&    Molecule = \*(Aq\*(Aq
\&    Type = \*(AqHydrogenBonds\*(Aq
\&    HydrogenBondsType = \*(AqHBondsType2\*(Aq
\&    @DescriptorNames = (\*(AqHydrogenBondDonors\*(Aq, \*(AqHydrogenBondAcceptors\*(Aq)
\&    @DescriptorValues = (\*(AqNone\*(Aq, \*(AqNone\*(Aq)
.Ve
.Sp
Examples:
.Sp
.Vb 2
\&    $HydrogenBondsDescriptors = new MolecularDescriptors::
\&                                HydrogenBondsDescriptors();
\&
\&    $HydrogenBondsDescriptors = new MolecularDescriptors::
\&                                HydrogenBondsDescriptors(
\&                                \*(AqHydrogenBondsType\*(Aq => \*(AqHBondsType2\*(Aq);
\&
\&    $HydrogenBondsDescriptors\->SetMolecule($Molecule);
\&    $HydrogenBondsDescriptors\->GenerateDescriptors();
\&    print "HydrogenBondsDescriptors: $HydrogenBondsDescriptors\en";
.Ve
.IP "\fBGenerateDescriptors\fR" 4
.IX Item "GenerateDescriptors"
.Vb 1
\&    $HydrogenBondsDescriptors\->GenerateDescriptors();
.Ve
.Sp
Calculates number of hydrogen bond donors and acceptors a molecule and returns
\&\fIHydrogenBondsDescriptors\fR.
.IP "\fBGetDescriptorNames\fR" 4
.IX Item "GetDescriptorNames"
.Vb 3
\&    @DescriptorNames = $HydrogenBondsDescriptors\->GetDescriptorNames();
\&    @DescriptorNames = MolecularDescriptors::HydrogenBondsDescriptors::
\&                       GetDescriptorNames();
.Ve
.Sp
Returns all available descriptor names as an array.
.IP "\fBSetHydrogenBondsType\fR" 4
.IX Item "SetHydrogenBondsType"
.Vb 1
\&    $HydrogenBondsDescriptors\->SetHydrogenBondsType($HBondsType);
.Ve
.Sp
Sets value of hydrogen bonds type to use during calculation of descriptors and returns
\&\fIHydrogenBondsDescriptors\fR. Possible values: \fIHBondsType1, HydrogenBondsType1,
HBondsType2, HydrogenBondsType2\fR.
.IP "\fBStringifyHydrogenBondsDescriptors\fR" 4
.IX Item "StringifyHydrogenBondsDescriptors"
.Vb 2
\&    $String = $HydrogenBondsDescriptors\->
\&                              StringifyHydrogenBondsDescriptors();
.Ve
.Sp
Returns a string containing information about \fIHydrogenBondsDescriptors\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.