comparison mayachemtools/docs/modules/txt/MolecularVolumeDescriptors.txt @ 0:73ae111cf86f draft

Uploaded

0:73ae111cf86f

NAME
    MolecularVolumeDescriptors

SYNOPSIS
    use MolecularDescriptors::MolecularVolumeDescriptors;

    use MolecularDescriptors::MolecularVolumeDescriptors qw(:all);

DESCRIPTION
    MolecularVolumeDescriptors class provides the following methods:

    new, GenerateDescriptors, GetDescriptorNames,
    GetVDWAtomRadiiAndVolumesData, StringifyMolecularVolumeDescriptors

    MolecularVolumeDescriptors is derived from MolecularDescriptors class
    which in turn is derived from ObjectProperty base class that provides
    methods not explicitly defined in MolecularVolumeDescriptors,
    MolecularDescriptors or ObjectProperty classes using Perl's AUTOLOAD
    functionality. These methods are generated on-the-fly for a specified
    object property:

        Set<PropertyName>(<PropertyValue>);
        $PropertyValue = Get<PropertyName>();
        Delete<PropertyName>();

    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:

        vdwMolecularVolume = SumOfAtomicVDWVolumeContributions
                             - 5.92 * NumOfBonds
                             - 14.7 * NumOfAromaticRings
                             - 3.8 * NumOfNonAromaticRings

    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 * PI * (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.

  METHODS
    new
            $NewMolecularVolumeDescriptors = new MolecularDescriptors::
                                             MolecularVolumeDescriptors(
                                             %NamesAndValues);

        Using specified *MolecularVolumeDescriptors* property names and
        values hash, new method creates a new object and returns a reference
        to newly created MolecularVolumeDescriptors object. By default, the
        following properties are initialized:

            Molecule = ''
            Type = 'MolecularVolume'
            @DescriptorNames = ('MolecularVolume')
            @DescriptorValues = ('None')

        Examples:

            $MolecularVolumeDescriptors = new MolecularDescriptors::
                                          MolecularVolumeDescriptors();

            $MolecularVolumeDescriptors->SetMolecule($Molecule);
            $MolecularVolumeDescriptors->GenerateDescriptors();
            print "MolecularVolumeDescriptors: $MolecularVolumeDescriptors\n";

    GenerateDescriptors
            $MolecularVolumeDescriptors->GenerateDescriptors();

        Calculate van der Waals molecular volume descriptor for a molecule
        and returns *MolecularVolumeDescriptors*.

    GetDescriptorNames
            @DescriptorNames = $MolecularVolumeDescriptors->GetDescriptorNames();
            @DescriptorNames = MolecularDescriptors::MolecularVolumeDescriptors::
                                  GetDescriptorNames();

        Returns all available descriptor names as an array.

    GetVDWAtomRadiiAndVolumesData
            $VDWVolumeDataMapRef = $MolecularVolumeDescriptors->
                                      GetVDWAtomRadiiAndVolumesData();
            $VDWVolumeDataMapRef = MolecularDescriptors::MolecularVolumeDescriptors::
                                      GetVDWAtomRadiiAndVolumesData();

        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:

            @{$VDWVolumeDataMap{AtomTypes}} - Array of all possible atom
                        types for all atom symbols
            @{$VDWVolumeDataMap->{ColLabels}} - Array of column labels
            %{$VDWVolumeDataMap->{DataCol<Num>}} - Hash keys pair:
                                                           DataCol<Num>, AtomType

    StringifyMolecularVolumeDescriptors
            $String = $MolecularVolumeDescriptors->
                                      StringifyMolecularVolumeDescriptors();

        Returns a string containing information about
        *MolecularVolumeDescriptors* object.

AUTHOR
    Manish Sud <[e-mail]>

SEE ALSO
    MolecularDescriptors.pm, MolecularDescriptorsGenerator.pm

COPYRIGHT
    Copyright (C) 2015 Manish Sud. All rights reserved.

    This file is part of MayaChemTools.

    MayaChemTools is free software; you can redistribute it and/or modify it
    under the terms of the GNU Lesser General Public License as published by
    the Free Software Foundation; either version 3 of the License, or (at
    your option) any later version.