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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mayachemtools/docs/modules/man3/EStateIndiciesFingerprints.3	Wed Jan 20 11:55:01 2016 -0500
@@ -0,0 +1,308 @@
+.\" 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 "ESTATEINDICIESFINGERPRINTS 1"
+.TH ESTATEINDICIESFINGERPRINTS 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"
+EStateIndiciesFingerprints
+.SH "SYNOPSIS"
+.IX Header "SYNOPSIS"
+use Fingerprints::EStateIndiciesFingerprints;
+.PP
+use Fingerprints::EStateIndiciesFingerprints qw(:all);
+.SH "DESCRIPTION"
+.IX Header "DESCRIPTION"
+\&\fBEStateIndiciesFingerprints\fR [ Ref 75\-78 ] class provides the following methods:
+.PP
+new, GenerateFingerprints, GetDescription, SetEStateAtomTypesSetToUse,
+SetValuesPrecision, StringifyEStateIndiciesFingerprints
+.PP
+\&\fBEStateIndiciesFingerprints\fR is derived from \fBFingerprints\fR class which in turn
+is  derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
+in \fBAtomNeighborhoodsFingerprints\fR, \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
+.PP
+E\-state atom types are assigned to all non-hydrogen atoms in a molecule using module
+AtomTypes::EStateAtomTypes.pm and E\-state values are calculated using module
+AtomicDescriptors::EStateValues.pm. Using E\-state atom types and E\-state values,
+\&\fBEStateIndiciesFingerprints\fR constituting sum of E\-state values for E\-sate atom types
+are generated.
+.PP
+Two types of E\-state atom types set size are allowed:
+.PP
+.Vb 4
+\&    ArbitrarySize \- Corresponds to only E\-state atom types detected
+\&                    in molecule
+\&    FixedSize \- Corresponds to fixed number of E\-state atom types previously
+\&                defined
+.Ve
+.PP
+Module AtomTypes::EStateAtomTypes.pm, used to assign E\-state atom types to
+non-hydrogen atoms in the molecule, is able to assign atom types to any valid
+atom group. However, for \fIFixedSize\fR value of \fBEStateAtomTypesSetToUse\fR, only a
+fixed set of E\-state atom types corresponding to specific atom groups [ Appendix \s-1III\s0 in
+Ref 77 ] are used for fingerprints.
+.PP
+The fixed size E\-state atom type set size used during generation of fingerprints contains
+87 E\-state non-hydrogen atom types in EStateAtomTypes.csv data file distributed with
+MayaChemTools.
+.PP
+Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of
+E\-state indicies fingerprints:
+.PP
+.Vb 1
+\&    Type                        EStateAtomTypesSetToUse
+\&
+\&    EStateIndicies              ArbitrarySize      [ default fingerprints ]
+\&    EStateIndicies              FixedSize
+.Ve
+.PP
+The current release of MayaChemTools generates the following types of E\-state
+fingerprints vector strings:
+.PP
+.Vb 4
+\&    FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
+\&    AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
+\&    H SsssCH;24.778 4.387 1.993 25.023 \-1.435 3.975 14.006 29.759 \-0.073 3
+\&    .024 \-2.270
+\&
+\&    FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
+\&    ValuesString;0 0 0 0 0 0 0 3.975 0 \-0.073 0 0 24.778 \-2.270 0 0 \-1.435
+\&    4.387 0 0 0 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 1
+\&    4.006 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
+\&    0 0 0 0 0 0 0 0 0 0 0 0 0 0
+\&
+\&    FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
+\&    IDsAndValuesString;SsLi SssBe SssssBem SsBH2 SssBH SsssB SssssBm SsCH3
+\&    SdCH2 SssCH2 StCH SdsCH SaaCH SsssCH SddC StsC SdssC SaasC SaaaC Sssss
+\&    C SsNH3p SsNH2 SssNH2p SdNH SssNH SaaNH StN SsssNHp SdsN SaaN SsssN Sd
+\&    0 0 0 0 0 0 0 3.975 0 \-0.073 0 0 24.778 \-2.270 0 0 \-1.435 4.387 0 0 0
+\&    0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 14.006 0 0 0 0
+\&    0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...
+.Ve
+.SS "\s-1METHODS\s0"
+.IX Subsection "METHODS"
+.IP "\fBnew\fR" 4
+.IX Item "new"
+.Vb 1
+\&    $EStateIndiciesFingerprints = new EStateIndiciesFingerprints(%NamesAndValues);
+.Ve
+.Sp
+Using specified \fIEStateIndiciesFingerprints\fR property names and values hash, \fBnew\fR method creates a new object
+and returns a reference to newly created \fBPathLengthFingerprints\fR object. By default, the
+following properties are initialized:
+.Sp
+.Vb 4
+\&    Molecule = \*(Aq\*(Aq;
+\&    Type = \*(AqEStateIndicies\*(Aq
+\&    EStateAtomTypesSetToUse = \*(AqArbitrarySize\*(Aq
+\&    ValuesPrecision = 3
+.Ve
+.Sp
+Examples:
+.Sp
+.Vb 4
+\&    $EStateIndiciesFingerprints = new AtomTypesFingerprints(
+\&                              \*(AqMolecule\*(Aq => $Molecule,
+\&                              \*(AqEStateAtomTypesSetToUse\*(Aq =>
+\&                                              \*(AqArbitrarySize\*(Aq);
+\&
+\&    $EStateIndiciesFingerprints = new AtomTypesFingerprints(
+\&                              \*(AqMolecule\*(Aq => $Molecule,
+\&                              \*(AqEStateAtomTypesSetToUse\*(Aq =>
+\&                                              \*(AqFixedSize\*(Aq);
+\&
+\&    $EStateIndiciesFingerprints\->GenerateFingerprints();
+\&    print "$EStateIndiciesFingerprints\en";
+.Ve
+.IP "\fBGenerateFingerprints\fR" 4
+.IX Item "GenerateFingerprints"
+.Vb 2
+\&    $EStateIndiciesFingerprints = $EStateIndiciesFingerprints\->
+\&                                  GenerateEStateIndiciesFingerprints();
+.Ve
+.Sp
+Generates EState keys fingerprints and returns \fIEStateIndiciesFingerprints\fR.
+.IP "\fBGetDescription\fR" 4
+.IX Item "GetDescription"
+.Vb 1
+\&    $Description = $EStateIndiciesFingerprints\->GetDescription();
+.Ve
+.Sp
+Returns a string containing description of EState keys fingerprints.
+.IP "\fBSetEStateAtomTypesSetToUse\fR" 4
+.IX Item "SetEStateAtomTypesSetToUse"
+.Vb 1
+\&    $EStateIndiciesFingerprints\->SetEStateAtomTypesSetToUse($Value);
+.Ve
+.Sp
+Sets \fIValue\fR of \fIEStateAtomTypesSetToUse\fR and returns \fIEStateIndiciesFingerprints\fR.
+Possible values: \fIArbitrarySize or FixedSize\fR. Default value: \fIArbitrarySize\fR.
+.IP "\fBSetValuesPrecision\fR" 4
+.IX Item "SetValuesPrecision"
+.Vb 1
+\&    $EStateIndiciesFingerprints\->SetValuesPrecision($Precision);
+.Ve
+.Sp
+Sets precesion of E\-state values to use during generation of E\-state indices fingerprints
+and returns \fIEStateIndiciesFingerprints\fR. Possible values: \fIPositive integers\fR.
+Default value: \fI3\fR.
+.IP "\fBStringifyEStateIndiciesFingerprints\fR" 4
+.IX Item "StringifyEStateIndiciesFingerprints"
+.Vb 1
+\&    $String = $EStateIndiciesFingerprints\->StringifyEStateIndiciesFingerprints();
+.Ve
+.Sp
+Returns a string containing information about \fIEStateIndiciesFingerprints\fR object.
+.SH "AUTHOR"
+.IX Header "AUTHOR"
+Manish Sud <[e-mail]>
+.SH "SEE ALSO"
+.IX Header "SEE ALSO"
+Fingerprints.pm, FingerprintsStringUtil.pm, AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm,
+ExtendedConnectivityFingerprints.pm, MACCSKeys.pm, PathLengthFingerprints.pm,
+TopologicalAtomPairsFingerprints.pm, TopologicalAtomTripletsFingerprints.pm,
+TopologicalAtomTorsionsFingerprints.pm, TopologicalPharmacophoreAtomPairsFingerprints.pm,
+TopologicalPharmacophoreAtomTripletsFingerprints.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.