Mercurial > repos > deepakjadmin > mayatool3_test3
diff mayachemtools/docs/modules/man3/EStateIndiciesFingerprints.3 @ 0:73ae111cf86f draft
Uploaded
author | deepakjadmin |
---|---|
date | Wed, 20 Jan 2016 11:55:01 -0500 |
parents | |
children |
line wrap: on
line diff
--- /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 <msud@san.rr.com> +.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.