Mercurial > repos > deepakjadmin > mayatool3_test3
diff mayachemtools/docs/modules/man3/AtomNeighborhoodsFingerprints.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/AtomNeighborhoodsFingerprints.3 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,499 @@ +.\" 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 "ATOMNEIGHBORHOODSFINGERPRINTS 1" +.TH ATOMNEIGHBORHOODSFINGERPRINTS 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" +AtomNeighborhoodsFingerprints +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +use Fingerprints::AtomNeighborhoodsFingerprints; +.PP +use Fingerprints::AtomNeighborhoodsFingerprints qw(:all); +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +\&\fBAtomNeighborhoodsFingerprints\fR [ Ref 53\-56, Ref 73 ] class provides the following methods: +.PP +new, GenerateFingerprints, GetDescription, SetAtomIdentifierType, +SetAtomicInvariantsToUse, SetFunctionalClassesToUse, SetMaxNeighborhoodRadius, +SetMinNeighborhoodRadius, StringifyAtomNeighborhoodsFingerprints +.PP +\&\fBAtomNeighborhoodsFingerprints\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 +The current release of MayaChemTools supports generation of \fBAtomNeighborhoodsFingerprints\fR +corresponding to following \fBAtomIdentifierTypes\fR: +.PP +.Vb 3 +\& AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +\& FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, +\& SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes +.Ve +.PP +Based on the values specified for \fBAtomIdentifierType\fR along with other specified +sucb as \fBAtomicInvariantsToUse\fR and \fBFunctionalClassesToUse\fR, initial atom types are +assigned to all non-hydrogen atoms in a molecule. Using atom neighborhoods +around each non-hydrogen central atom corresponding to radii between specified values +\&\fBMinNeighborhoodRadius\fR and \fBMaxNeighborhoodRadius\fR, unique atom types at each radii +level are counted and an atom neighborhood identifier is generated. +.PP +The format of an atom neighborhood identifier around a central non-hydrogen atom at a +specific radius is: +.PP +.Vb 1 +\& NR<n>\-<AtomType>\-ATC<n> +\& +\& NR: Neighborhood radius +\& AtomType: Assigned atom type +\& ATC: Atom type count +.Ve +.PP +The atom neighborhood identifier for non-hydrogen central atom corresponding to all specified radii +is generated by concatenating neighborhood identifiers at each radii by colon as a delimiter: +.PP +.Vb 1 +\& NR<n>\-<AtomType>\-ATC<n>:NR<n>\-<AtomType>\-ATC<n>:... +.Ve +.PP +The atom neighborhood identifiers for all non-hydrogen central atoms at all specified radii are +concatenated using space as a delimiter and constitute atom neighborhood fingerprint of the molecule. +.PP +The current release of MayaChemTools generates the following types of atom neighborhoods +fingerprints vector strings: +.PP +.Vb 6 +\& FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi +\& us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-C.X1.BO1.H3\-AT +\& C1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-ATC1 NR0\-C.X +\& 1.BO1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-A +\& TC1 NR0\-C.X2.BO2.H2\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2 +\& \-C.X2.BO2.H2\-ATC1:NR2\-N.X3.BO3\-ATC1:NR2\-O.X1.BO1.H1\-ATC1 NR0\-C.X2.B... +\& +\& FingerprintsVector;AtomNeighborhoods:DREIDINGAtomTypes:MinRadius0:MaxR +\& adius2;41;AlphaNumericalValues;ValuesString;NR0\-C_2\-ATC1:NR1\-C_3\-ATC1: +\& NR1\-O_2\-ATC1:NR1\-O_3\-ATC1:NR2\-C_3\-ATC1 NR0\-C_2\-ATC1:NR1\-C_R\-ATC1:NR1\-N +\& _3\-ATC1:NR1\-O_2\-ATC1:NR2\-C_R\-ATC3 NR0\-C_3\-ATC1:NR1\-C_2\-ATC1:NR1\-C_3\-AT +\& C1:NR2\-C_3\-ATC1:NR2\-O_2\-ATC1:NR2\-O_3\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR +\& 1\-N_R\-ATC1:NR2\-C_3\-ATC1:NR2\-C_R\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR2\-... +\& +\& FingerprintsVector;AtomNeighborhoods:EStateAtomTypes:MinRadius0:MaxRad +\& ius2;41;AlphaNumericalValues;ValuesString;NR0\-aaCH\-ATC1:NR1\-aaCH\-ATC1: +\& NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC1:NR2\-sF\-ATC1 NR0\-aaCH\-ATC1:NR +\& 1\-aaCH\-ATC1:NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC1:NR2\-sF\-ATC1 NR0\- +\& aaCH\-ATC1:NR1\-aaCH\-ATC1:NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC2 NR0\- +\& aaCH\-ATC1:NR1\-aaCH\-ATC1:NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC2 N... +\& +\& FingerprintsVector;AtomNeighborhoods:FunctionalClassAtomTypes:MinRadiu +\& s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-Ar\-ATC1:NR1\-Ar\- +\& ATC1:NR1\-Ar.HBA\-ATC1:NR1\-None\-ATC1:NR2\-Ar\-ATC2:NR2\-None\-ATC4 NR0\-Ar\-AT +\& C1:NR1\-Ar\-ATC2:NR1\-Ar.HBA\-ATC1:NR2\-Ar\-ATC5:NR2\-None\-ATC1 NR0\-Ar\-ATC1:N +\& R1\-Ar\-ATC2:NR1\-HBD\-ATC1:NR2\-Ar\-ATC2:NR2\-None\-ATC1 NR0\-Ar\-ATC1:NR1\-Ar\-A +\& TC2:NR1\-Hal\-ATC1:NR2\-Ar\-ATC2 NR0\-Ar\-ATC1:NR1\-Ar\-ATC2:NR1\-None\-ATC1:... +\& +\& FingerprintsVector;AtomNeighborhoods:MMFF94AtomTypes:MinRadius0:MaxRad +\& ius2;41;AlphaNumericalValues;ValuesString;NR0\-C5A\-ATC1:NR1\-C5B\-ATC1:NR +\& 1\-CB\-ATC1:NR1\-N5\-ATC1:NR2\-C5A\-ATC1:NR2\-C5B\-ATC1:NR2\-CB\-ATC3:NR2\-CR\-ATC +\& 1 NR0\-C5A\-ATC1:NR1\-C5B\-ATC1:NR1\-CR\-ATC1:NR1\-N5\-ATC1:NR2\-C5A\-ATC1:NR2\-C +\& 5B\-ATC1:NR2\-C=ON\-ATC1:NR2\-CR\-ATC3 NR0\-C5B\-ATC1:NR1\-C5A\-ATC1:NR1\-C5B\-AT +\& C1:NR1\-C=ON\-ATC1:NR2\-C5A\-ATC1:NR2\-CB\-ATC1:NR2\-CR\-ATC1:NR2\-N5\-ATC1:N... +\& +\& FingerprintsVector;AtomNeighborhoods:SLogPAtomTypes:MinRadius0:MaxRadi +\& us2;41;AlphaNumericalValues;ValuesString;NR0\-C1\-ATC1:NR1\-C10\-ATC1:NR1\- +\& CS\-ATC1:NR2\-C1\-ATC1:NR2\-N11\-ATC1:NR2\-O2\-ATC1 NR0\-C1\-ATC1:NR1\-C11\-ATC1: +\& NR2\-C1\-ATC1:NR2\-C21\-ATC1 NR0\-C1\-ATC1:NR1\-C11\-ATC1:NR2\-C1\-ATC1:NR2\-C21\- +\& ATC1 NR0\-C1\-ATC1:NR1\-C5\-ATC1:NR1\-CS\-ATC1:NR2\-C1\-ATC1:NR2\-O2\-ATC2:NR2\-O +\& 9\-ATC1 NR0\-C1\-ATC1:NR1\-CS\-ATC2:NR2\-C1\-ATC2:NR2\-O2\-ATC2 NR0\-C10\-ATC1... +\& +\& FingerprintsVector;AtomNeighborhoods:SYBYLAtomTypes:MinRadius0:MaxRadi +\& us2;41;AlphaNumericalValues;ValuesString;NR0\-C.2\-ATC1:NR1\-C.3\-ATC1:NR1 +\& \-O.co2\-ATC2:NR2\-C.3\-ATC1 NR0\-C.2\-ATC1:NR1\-C.ar\-ATC1:NR1\-N.am\-ATC1:NR1\- +\& O.2\-ATC1:NR2\-C.ar\-ATC3 NR0\-C.3\-ATC1:NR1\-C.2\-ATC1:NR1\-C.3\-ATC1:NR2\-C.3\- +\& ATC1:NR2\-O.3\-ATC1:NR2\-O.co2\-ATC2 NR0\-C.3\-ATC1:NR1\-C.3\-ATC1:NR1\-N.ar\-AT +\& C1:NR2\-C.3\-ATC1:NR2\-C.ar\-ATC2 NR0\-C.3\-ATC1:NR1\-C.3\-ATC1:NR2\-C.3\-ATC... +\& +\& FingerprintsVector;AtomNeighborhoods:TPSAAtomTypes:MinRadius0:MaxRadiu +\& s2;41;AlphaNumericalValues;ValuesString;NR0\-N21\-ATC1:NR1\-None\-ATC3:NR2 +\& \-None\-ATC5 NR0\-N7\-ATC1:NR1\-None\-ATC2:NR2\-None\-ATC3:NR2\-O3\-ATC1 NR0\-Non +\& e\-ATC1:NR1\-N21\-ATC1:NR1\-None\-ATC1:NR2\-None\-ATC3 NR0\-None\-ATC1:NR1\-N21\- +\& ATC1:NR1\-None\-ATC2:NR2\-None\-ATC6 NR0\-None\-ATC1:NR1\-N21\-ATC1:NR1\-None\-A +\& TC2:NR2\-None\-ATC6 NR0\-None\-ATC1:NR1\-N7\-ATC1:NR1\-None\-ATC1:NR1\-O3\-AT... +\& +\& FingerprintsVector;AtomNeighborhoods:UFFAtomTypes:MinRadius0:MaxRadius +\& 2;41;AlphaNumericalValues;ValuesString;NR0\-C_2\-ATC1:NR1\-C_3\-ATC1:NR1\-O +\& _2\-ATC1:NR1\-O_3\-ATC1:NR2\-C_3\-ATC1 NR0\-C_2\-ATC1:NR1\-C_R\-ATC1:NR1\-N_3\-AT +\& C1:NR1\-O_2\-ATC1:NR2\-C_R\-ATC3 NR0\-C_3\-ATC1:NR1\-C_2\-ATC1:NR1\-C_3\-ATC1:NR +\& 2\-C_3\-ATC1:NR2\-O_2\-ATC1:NR2\-O_3\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR1\-N_R +\& \-ATC1:NR2\-C_3\-ATC1:NR2\-C_R\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR2\-C_3\-A... +.Ve +.SS "\s-1METHODS\s0" +.IX Subsection "METHODS" +.IP "\fBnew\fR" 4 +.IX Item "new" +.Vb 2 +\& $NewAtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints( +\& %NamesAndValues); +.Ve +.Sp +Using specified \fIAtomNeighborhoodsFingerprints\fR property names and values hash, \fBnew\fR +method creates a new object and returns a reference to newly created \fBAtomNeighborhoodsFingerprints\fR +object. By default, the following properties are initialized: +.Sp +.Vb 7 +\& Molecule = \*(Aq\*(Aq +\& Type = \*(AqAtomNeighborhoods\*(Aq +\& MinNeighborhoodRadius = 0 +\& MaxNeighborhoodRadius = 2 +\& AtomIdentifierType = \*(Aq\*(Aq +\& AtomicInvariantsToUse = [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq, \*(AqMN\*(Aq] +\& FunctionalClassesToUse = [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq] +.Ve +.Sp +Examples: +.Sp +.Vb 4 +\& $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqAtomIdentifierType\*(Aq => +\& "AtomicInvariantsAtomTypes"); +\& +\& $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqMinNeighborhoodRadius\*(Aq => 0, +\& \*(AqMaxNeighborhoodRadius\*(Aq => 2, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqAtomicInvariantsAtomTypes\*(Aq, +\& \*(AqAtomicInvariantsToUse\*(Aq => +\& [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq] ); +\& +\& $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqSYBYLAtomTypes\*(Aq); +\& +\& $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqMMFF94AtomTypes\*(Aq); +\& +\& $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqAtomicInvariantsAtomTypes\*(Aq); +\& +\& $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqMinNeighborhoodRadius\*(Aq => 0, +\& \*(AqMaxNeighborhoodRadius\*(Aq => 2, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqFunctionalClassAtomTypes\*(Aq, +\& \*(AqFunctionalClassesToUse\*(Aq => +\& [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq] ); +\& +\& $AtomNeighborhoodsFingerprints\->GenerateFingerprints(); +\& print "$AtomNeighborhoodsFingerprints\en"; +.Ve +.IP "\fBGenerateFingerprints\fR" 4 +.IX Item "GenerateFingerprints" +.Vb 1 +\& $AtomNeighborhoodsFingerprints\->GenerateFingerprints(); +.Ve +.Sp +Generates atom neighborhood fingerprints and returns \fIAtomNeighborhoodsFingerprints\fR. +.IP "\fBGetDescription\fR" 4 +.IX Item "GetDescription" +.Vb 1 +\& $Description = $AtomNeighborhoodsFingerprints\->GetDescription(); +.Ve +.Sp +Returns a string containing description of atom neighborhood fingerprints. +.IP "\fBSetAtomIdentifierType\fR" 4 +.IX Item "SetAtomIdentifierType" +.Vb 1 +\& $AtomNeighborhoodsFingerprints\->SetAtomIdentifierType($IdentifierType); +.Ve +.Sp +Sets atom \fIIdentifierType\fR to use during atom neighborhood fingerprints generation and +returns \fIAtomNeighborhoodsFingerprints\fR. +.Sp +Possible values: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, +TPSAAtomTypes, UFFAtomTypes\fR. +.IP "\fBSetAtomicInvariantsToUse\fR" 4 +.IX Item "SetAtomicInvariantsToUse" +.Vb 2 +\& $AtomNeighborhoodsFingerprints\->SetAtomicInvariantsToUse($ValuesRef); +\& $AtomNeighborhoodsFingerprints\->SetAtomicInvariantsToUse(@Values); +.Ve +.Sp +Sets atomic invariants to use during \fIAtomicInvariantsAtomTypes\fR value of \fIAtomIdentifierType\fR +for atom neighborhood fingerprints generation and returns \fIAtomNeighborhoodsFingerprints\fR. +.Sp +Possible values for atomic invariants are: \fI\s-1AS\s0, X, \s-1BO\s0, \s-1LBO\s0, \s-1SB\s0, \s-1DB\s0, \s-1TB\s0, +H, Ar, \s-1RA\s0, \s-1FC\s0, \s-1MN\s0, \s-1SM\s0\fR. Default value: \fI\s-1AS\s0,X,BO,H,FC\fR. +.Sp +The atomic invariants abbreviations correspond to: +.Sp +.Vb 1 +\& AS = Atom symbol corresponding to element symbol +\& +\& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms +\& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms +\& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms +\& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms +\& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms +\& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms +\& H<n> = Number of implicit and explicit hydrogens for atom +\& Ar = Aromatic annotation indicating whether atom is aromatic +\& RA = Ring atom annotation indicating whether atom is a ring +\& FC<+n/\-n> = Formal charge assigned to atom +\& MN<n> = Mass number indicating isotope other than most abundant isotope +\& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or +\& 3 (triplet) +.Ve +.Sp +Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to: +.Sp +.Vb 1 +\& AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/\-n>.MN<n>.SM<n> +.Ve +.Sp +Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are +optional. Atom type specification doesn't include atomic invariants with zero or undefined values. +.Sp +In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words +are also allowed: +.Sp +.Vb 12 +\& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors +\& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms +\& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms +\& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms +\& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms +\& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms +\& H : NumOfImplicitAndExplicitHydrogens +\& Ar : Aromatic +\& RA : RingAtom +\& FC : FormalCharge +\& MN : MassNumber +\& SM : SpinMultiplicity +.Ve +.Sp +\&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant +atom types. +.IP "\fBSetFunctionalClassesToUse\fR" 4 +.IX Item "SetFunctionalClassesToUse" +.Vb 2 +\& $AtomNeighborhoodsFingerprints\->SetFunctionalClassesToUse($ValuesRef); +\& $AtomNeighborhoodsFingerprints\->SetFunctionalClassesToUse(@Values); +.Ve +.Sp +Sets functional classes invariants to use during \fIFunctionalClassAtomTypes\fR value of \fIAtomIdentifierType\fR +for atom neighborhoods fingerprints generation and returns \fIAtomNeighborhoodsFingerprints\fR. +.Sp +Possible values for atom functional classes are: \fIAr, \s-1CA\s0, H, \s-1HBA\s0, \s-1HBD\s0, Hal, \s-1NI\s0, \s-1PI\s0, \s-1RA\s0\fR. +Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR. +.Sp +The functional class abbreviations correspond to: +.Sp +.Vb 9 +\& HBD: HydrogenBondDonor +\& HBA: HydrogenBondAcceptor +\& PI : PositivelyIonizable +\& NI : NegativelyIonizable +\& Ar : Aromatic +\& Hal : Halogen +\& H : Hydrophobic +\& RA : RingAtom +\& CA : ChainAtom +\& +\& Functional class atom type specification for an atom corresponds to: +\& +\& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None +.Ve +.Sp +\&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom +types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]: +.Sp +.Vb 4 +\& HydrogenBondDonor: NH, NH2, OH +\& HydrogenBondAcceptor: N[!H], O +\& PositivelyIonizable: +, NH2 +\& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH +.Ve +.IP "\fBSetMaxNeighborhoodRadius\fR" 4 +.IX Item "SetMaxNeighborhoodRadius" +.Vb 1 +\& $AtomNeighborhoodsFingerprints\->SetMaxNeighborhoodRadius($Radius); +.Ve +.Sp +Sets maximum neighborhood radius to use during atom neighborhood fingerprints generation and +returns \fIAtomNeighborhoodsFingerprints\fR. +.IP "\fBSetMinNeighborhoodRadius\fR" 4 +.IX Item "SetMinNeighborhoodRadius" +.Vb 1 +\& $AtomNeighborhoodsFingerprints\->SetMinNeighborhoodRadius($Radius); +.Ve +.Sp +Sets minimum neighborhood radius to use during atom neighborhood fingerprints generation and +returns \fIAtomNeighborhoodsFingerprints\fR. +.IP "\fBStringifyAtomNeighborhoodsFingerprints\fR" 4 +.IX Item "StringifyAtomNeighborhoodsFingerprints" +.Vb 1 +\& $String = $Fingerprints\->StringifyAtomNeighborhoodsFingerprints(); +.Ve +.Sp +Returns a string containing information about \fIAtomNeighborhoodsFingerprints\fR object. +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +Fingerprints.pm, FingerprintsStringUtil.pm, AtomTypesFingerprints.pm, EStateIndiciesFingerprints.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.