view mayachemtools/docs/modules/man3/MolecularVolumeDescriptors.3 @ 0:73ae111cf86f draft

Uploaded

.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22)
.\"
.\" Standard preamble:
.\" ========================================================================
.de Sp \" Vertical space (when we can't use .PP)
.if t .sp .5v
.if n .sp
..
.de Vb \" Begin verbatim text
.ft CW
.nf
.ne \\$1
..
.de Ve \" End verbatim text
.ft R
.fi
..
.\" Set up some character translations and predefined strings.  \*(-- will
.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left
.\" double quote, and \*(R" will give a right double quote.  \*(C+ will
.\" give a nicer C++.  Capital omega is used to do unbreakable dashes and
.\" therefore won't be available.  \*(C` and \*(C' expand to `' in nroff,
.\" nothing in troff, for use with C<>.
.tr \(*W-
.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p'
.ie n \{\
.    ds -- \(*W-
.    ds PI pi
.    if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch
.    if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\"  diablo 12 pitch
.    ds L" ""
.    ds R" ""
.    ds C` ""
.    ds C' ""
'br\}
.el\{\
.    ds -- \|\(em\|
.    ds PI \(*p
.    ds L" ``
.    ds R" ''
'br\}
.\"
.\" Escape single quotes in literal strings from groff's Unicode transform.
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.\"
.\" If the F register is turned on, we'll generate index entries on stderr for
.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index
.\" entries marked with X<> in POD.  Of course, you'll have to process the
.\" output yourself in some meaningful fashion.
.ie \nF \{\
.    de IX
.    tm Index:\\$1\t\\n%\t"\\$2"
..
.    nr % 0
.    rr F
.\}
.el \{\
.    de IX
..
.\}
.\"
.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2).
.\" Fear.  Run.  Save yourself.  No user-serviceable parts.
.    \" fudge factors for nroff and troff
.if n \{\
.    ds #H 0
.    ds #V .8m
.    ds #F .3m
.    ds #[ \f1
.    ds #] \fP
.\}
.if t \{\
.    ds #H ((1u-(\\\\n(.fu%2u))*.13m)
.    ds #V .6m
.    ds #F 0
.    ds #[ \&
.    ds #] \&
.\}
.    \" simple accents for nroff and troff
.if n \{\
.    ds ' \&
.    ds ` \&
.    ds ^ \&
.    ds , \&
.    ds ~ ~
.    ds /
.\}
.if t \{\
.    ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u"
.    ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u'
.    ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u'
.    ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u'
.    ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u'
.    ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u'
.\}
.    \" troff and (daisy-wheel) nroff accents
.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V'
.ds 8 \h'\*(#H'\(*b\h'-\*(#H'
.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#]
.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H'
.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u'
.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#]
.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#]
.ds ae a\h'-(\w'a'u*4/10)'e
.ds Ae A\h'-(\w'A'u*4/10)'E
.    \" corrections for vroff
.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u'
.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u'
.    \" for low resolution devices (crt and lpr)
.if \n(.H>23 .if \n(.V>19 \
\{\
.    ds : e
.    ds 8 ss
.    ds o a
.    ds d- d\h'-1'\(ga
.    ds D- D\h'-1'\(hy
.    ds th \o'bp'
.    ds Th \o'LP'
.    ds ae ae
.    ds Ae AE
.\}
.rm #[ #] #H #V #F C
.\" ========================================================================
.\"
.IX Title "MOLECULARVOLUMEDESCRIPTORS 1"
.TH MOLECULARVOLUMEDESCRIPTORS 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"
MolecularVolumeDescriptors
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
use MolecularDescriptors::MolecularVolumeDescriptors;
.PP
use MolecularDescriptors::MolecularVolumeDescriptors qw(:all);
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
\&\fBMolecularVolumeDescriptors\fR class provides the following methods:
.PP
new, GenerateDescriptors, GetDescriptorNames,
GetVDWAtomRadiiAndVolumesData, StringifyMolecularVolumeDescriptors
.PP
\&\fBMolecularVolumeDescriptors\fR is derived from \fBMolecularDescriptors\fR class which in turn
is  derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
in \fBMolecularVolumeDescriptors\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
van der Waals molecular volume [ Ref 93 ] (A**3/molecule) of a molecule is
calculated using atomic and bonds contributions along with adjustments for
aromatic and non-aromatic rings using the following equation:
.PP
.Vb 4
\&    vdwMolecularVolume = SumOfAtomicVDWVolumeContributions
\&                         \- 5.92 * NumOfBonds
\&                         \- 14.7 * NumOfAromaticRings
\&                         \- 3.8 * NumOfNonAromaticRings
.Ve
.PP
van der Waals atomic volume for atoms is taken from data file VDWAtomRadiiAndVolumes.csv
distributed with MayaChemTools. It contains van der Waals atom radii and atom and volumes
data for 38 elements; Table 2 [ Ref 93 ] contains data for only 15 elements. After converting
valid van der Waals atom radius data from pm (picometer) to A (Angstrom) available under column
name VanderWaalsRadius in PeriodicTableElementsData.csv data file, van der Waals atom volume
is calculated using: 4/3 * \s-1PI\s0 * (Radius ** 3). For elements specified in Table 2 [ Ref 93 ] \-
H, B, C, N, O, F, Si, P, S, Cl, As, Se, Br, Te, I \- the van der Waals atom radii and calculated
atom volumes match the values in the table.
.SS "\s-1METHODS\s0"
.IX Subsection "METHODS"
.IP "\fBnew\fR" 4
.IX Item "new"
.Vb 3
\&    $NewMolecularVolumeDescriptors = new MolecularDescriptors::
\&                                     MolecularVolumeDescriptors(
\&                                     %NamesAndValues);
.Ve
.Sp
Using specified \fIMolecularVolumeDescriptors\fR property names and values hash, \fBnew\fR
method creates a new object and returns a reference to newly created \fBMolecularVolumeDescriptors\fR
object. By default, the following properties are initialized:
.Sp
.Vb 4
\&    Molecule = \*(Aq\*(Aq
\&    Type = \*(AqMolecularVolume\*(Aq
\&    @DescriptorNames = (\*(AqMolecularVolume\*(Aq)
\&    @DescriptorValues = (\*(AqNone\*(Aq)
.Ve
.Sp
Examples:
.Sp
.Vb 2
\&    $MolecularVolumeDescriptors = new MolecularDescriptors::
\&                                  MolecularVolumeDescriptors();
\&
\&    $MolecularVolumeDescriptors\->SetMolecule($Molecule);
\&    $MolecularVolumeDescriptors\->GenerateDescriptors();
\&    print "MolecularVolumeDescriptors: $MolecularVolumeDescriptors\en";
.Ve
.IP "\fBGenerateDescriptors\fR" 4
.IX Item "GenerateDescriptors"
.Vb 1
\&    $MolecularVolumeDescriptors\->GenerateDescriptors();
.Ve
.Sp
Calculate van der Waals molecular volume descriptor for a molecule and returns
\&\fIMolecularVolumeDescriptors\fR.
.IP "\fBGetDescriptorNames\fR" 4
.IX Item "GetDescriptorNames"
.Vb 3
\&    @DescriptorNames = $MolecularVolumeDescriptors\->GetDescriptorNames();
\&    @DescriptorNames = MolecularDescriptors::MolecularVolumeDescriptors::
\&                          GetDescriptorNames();
.Ve
.Sp
Returns all available descriptor names as an array.
.IP "\fBGetVDWAtomRadiiAndVolumesData\fR" 4
.IX Item "GetVDWAtomRadiiAndVolumesData"
.Vb 4
\&    $VDWVolumeDataMapRef = $MolecularVolumeDescriptors\->
\&                              GetVDWAtomRadiiAndVolumesData();
\&    $VDWVolumeDataMapRef = MolecularDescriptors::MolecularVolumeDescriptors::
\&                              GetVDWAtomRadiiAndVolumesData();
.Ve
.Sp
Returns a hash reference to van der Waals atom symbols corresponding to atom types
and associated data loaded from VDWAtomRadiiAndVolumes.csv data file as a reference
to hash with the following hash data format:
.Sp
.Vb 5
\&    @{$VDWVolumeDataMap{AtomTypes}} \- Array of all possible atom
\&                types for all atom symbols
\&    @{$VDWVolumeDataMap\->{ColLabels}} \- Array of column labels
\&    %{$VDWVolumeDataMap\->{DataCol<Num>}} \- Hash keys pair:
\&                                                   DataCol<Num>, AtomType
.Ve
.IP "\fBStringifyMolecularVolumeDescriptors\fR" 4
.IX Item "StringifyMolecularVolumeDescriptors"
.Vb 2
\&    $String = $MolecularVolumeDescriptors\->
\&                              StringifyMolecularVolumeDescriptors();
.Ve
.Sp
Returns a string containing information about \fIMolecularVolumeDescriptors\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.