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diff mayachemtools/docs/modules/man3/TopologicalAtomTripletsFingerprints.3 @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/man3/TopologicalAtomTripletsFingerprints.3 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,516 @@ +.\" 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. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +TopologicalAtomTripletsFingerprints +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +use Fingerprints::TopologicalAtomTripletsFingerprints; +.PP +use Fingerprints::TopologicalAtomTripletsFingerprints qw(:all); +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +\&\fBTopologicalAtomTripletsFingerprints\fR [ Ref 57, Ref 59, Ref 72 ] class provides the following methods: +.PP +new, GenerateFingerprints, GetAtomTripletIDs, GetDescription, +SetAtomIdentifierType, SetAtomicInvariantsToUse, SetFunctionalClassesToUse, +SetMaxDistance, SetMinDistance, StringifyTopologicalAtomTripletsFingerprints +.PP +\&\fBTopologicalAtomTripletsFingerprints\fR is derived from \fBFingerprints\fR class which in turn +is derived from \fBObjectProperty\fR base class that provides methods not explicitly defined +in \fBTopologicalAtomTripletsFingerprints\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 \fBTopologicalAtomTripletsFingerprints\fR +corresponding to following \fBAtomtomIdentifierTypes\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 +parameters such as \fBAtomicInvariantsToUse\fR and \fBFunctionalClassesToUse\fR, initial +atom types are assigned to all non-hydrogen atoms in a molecule. Using the distance +matrix for the molecule and initial atom types assigned to non-hydrogen atoms, all unique atom +triplets within \fBMinDistance\fR and \fBMaxDistance\fR are identified and counted. An atom triplet +identifier is generated for each unique atom triplet; the format of atom triplet identifier is: +.PP +.Vb 1 +\& <ATx>\-Dyz\-<ATy>\-Dxz\-<ATz>\-Dxy +\& +\& ATx, ATy, ATz: Atom types assigned to atom x, atom y, and atom z +\& Dxy: Distance between atom x and atom y +\& Dxz: Distance between atom x and atom z +\& Dyz: Distance between atom y and atom z +\& +\& where <AT1>\-D23 <= <AT2>\-D13 <= <AT3>\-D12 +.Ve +.PP +The atom triplet identifiers for all unique atom triplets corresponding to non-hydrogen atoms constitute +topological atom triplets fingerprints of the molecule. +.PP +The current release of MayaChemTools generates the following types of topological atom triplets +fingerprints vector strings: +.PP +.Vb 7 +\& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M +\& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1 +\& .BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D1 +\& 0\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1 +\& \-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3....; +\& 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 +\& 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8... +\& +\& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M +\& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString +\& ;C.X1.BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 1 C.X1.BO1.H3\-D1\-C.X2.BO +\& 2.H2\-D10\-C.X3.BO4\-D9 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 2 C.X +\& 1.BO1.H3\-D1\-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2 +\& \-D6\-C.X3.BO3.H1\-D5 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3.BO3.H1\-D7 2... +\& +\& FingerprintsVector;TopologicalAtomTriplets:DREIDINGAtomTypes:MinDistan +\& ce1:MaxDistance10;2377;NumericalValues;IDsAndValuesString;C_2\-D1\-C_2\-D +\& 9\-C_3\-D10 C_2\-D1\-C_2\-D9\-C_R\-D10 C_2\-D1\-C_3\-D1\-C_3\-D2 C_2\-D1\-C_3\-D10\-C_ +\& 3\-D9 C_2\-D1\-C_3\-D2\-C_3\-D3 C_2\-D1\-C_3\-D2\-C_R\-D3 C_2\-D1\-C_3\-D3\-C_3\-D4 C_ +\& 2\-D1\-C_3\-D3\-N_R\-D4 C_2\-D1\-C_3\-D3\-O_3\-D2 C_2\-D1\-C_3\-D4\-C_3\-D5 C_2\-D...; +\& 1 1 1 2 1 1 3 1 1 2 2 1 1 1 1 1 1 1 1 2 1 3 4 5 1 1 6 4 2 2 3 1 1 1 2 +\& 2 1 2 1 1 2 2 2 1 2 1 2 1 1 3 3 2 6 4 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1... +\& +\& FingerprintsVector;TopologicalAtomTriplets:EStateAtomTypes:MinDistance +\& 1:MaxDistance10;3298;NumericalValues;IDsAndValuesString;aaCH\-D1\-aaCH\-D +\& 1\-aaCH\-D2 aaCH\-D1\-aaCH\-D1\-aasC\-D2 aaCH\-D1\-aaCH\-D10\-aaCH\-D9 aaCH\-D1\-aaC +\& H\-D10\-aasC\-D9 aaCH\-D1\-aaCH\-D2\-aaCH\-D3 aaCH\-D1\-aaCH\-D2\-aasC\-D1 aaCH\-D1\- +\& aaCH\-D2\-aasC\-D3 aaCH\-D1\-aaCH\-D3\-aasC\-D2 aaCH\-D1\-aaCH\-D4\-aasC\-D5 aa...; +\& 6 4 24 4 16 8 8 4 8 8 8 12 10 14 4 16 24 4 12 2 2 4 1 10 2 2 15 2 2 2 +\& 2 2 2 14 4 2 2 2 2 1 2 10 2 2 4 1 2 4 8 3 3 3 4 6 4 2 2 3 3 1 1 1 2 1 +\& 2 2 4 2 3 2 1 2 4 5 3 2 2 1 2 4 3 2 8 12 6 2 2 4 4 7 1 4 2 4 2 2 2 ... +\& +\& FingerprintsVector;TopologicalAtomTriplets:FunctionalClassAtomTypes:Mi +\& nDistance1:MaxDistance10;2182;NumericalValues;IDsAndValuesString;Ar\-D1 +\& \-Ar\-D1\-Ar\-D2 Ar\-D1\-Ar\-D1\-Ar.HBA\-D2 Ar\-D1\-Ar\-D10\-Ar\-D9 Ar\-D1\-Ar\-D10\-Hal +\& \-D9 Ar\-D1\-Ar\-D2\-Ar\-D2 Ar\-D1\-Ar\-D2\-Ar\-D3 Ar\-D1\-Ar\-D2\-Ar.HBA\-D1 Ar\-D1\-Ar +\& \-D2\-Ar.HBA\-D2 Ar\-D1\-Ar\-D2\-Ar.HBA\-D3 Ar\-D1\-Ar\-D2\-HBD\-D1 Ar\-D1\-Ar\-D2...; +\& 27 1 32 2 2 63 3 2 1 2 1 2 3 1 1 40 3 1 2 2 2 2 4 2 2 47 4 2 2 1 2 1 5 +\& 2 2 51 4 3 1 3 1 9 1 1 50 3 3 4 1 9 50 2 2 3 3 5 45 1 1 1 2 1 2 2 3 3 +\& 4 4 3 2 1 1 3 4 5 5 3 1 2 3 2 3 5 7 2 7 3 7 1 1 2 2 2 2 3 1 4 3 1 2... +\& +\& FingerprintsVector;TopologicalAtomTriplets:MMFF94AtomTypes:MinDistance +\& 1:MaxDistance10;2966;NumericalValues;IDsAndValuesString;C5A\-D1\-C5A\-D1\- +\& N5\-D2 C5A\-D1\-C5A\-D2\-C5B\-D2 C5A\-D1\-C5A\-D3\-CB\-D2 C5A\-D1\-C5A\-D3\-CR\-D2 C5A +\& \-D1\-C5B\-D1\-C5B\-D2 C5A\-D1\-C5B\-D2\-C=ON\-D1 C5A\-D1\-C5B\-D2\-CB\-D1 C5A\-D1\-C5B +\& \-D3\-C=ON\-D2 C5A\-D1\-C5B\-D3\-CB\-D2 C5A\-D1\-C=ON\-D3\-NC=O\-D2 C5A\-D1\-C=ON\-D3\- +\& O=CN\-D2 C5A\-D1\-C=ON\-D4\-NC=O\-D3 C5A\-D1\-C=ON\-D4\-O=CN\-D3 C5A\-D1\-CB\-D1\-... +\& +\& FingerprintsVector;TopologicalAtomTriplets:SLogPAtomTypes:MinDistance1 +\& :MaxDistance10;3710;NumericalValues;IDsAndValuesString;C1\-D1\-C1\-D1\-C11 +\& \-D2 C1\-D1\-C1\-D1\-CS\-D2 C1\-D1\-C1\-D10\-C5\-D9 C1\-D1\-C1\-D3\-C10\-D2 C1\-D1\-C1\-D +\& 3\-C5\-D2 C1\-D1\-C1\-D3\-CS\-D2 C1\-D1\-C1\-D3\-CS\-D4 C1\-D1\-C1\-D4\-C10\-D5 C1\-D1\-C +\& 1\-D4\-C11\-D5 C1\-D1\-C1\-D5\-C10\-D4 C1\-D1\-C1\-D5\-C5\-D4 C1\-D1\-C1\-D6\-C11\-D7 C1 +\& \-D1\-C1\-D6\-CS\-D5 C1\-D1\-C1\-D6\-CS\-D7 C1\-D1\-C1\-D8\-C11\-D9 C1\-D1\-C1\-D8\-CS... +\& +\& FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1 +\& :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2\-D1\-C.2\-D9\-C +\& .3\-D10 C.2\-D1\-C.2\-D9\-C.ar\-D10 C.2\-D1\-C.3\-D1\-C.3\-D2 C.2\-D1\-C.3\-D10\-C.3\- +\& D9 C.2\-D1\-C.3\-D2\-C.3\-D3 C.2\-D1\-C.3\-D2\-C.ar\-D3 C.2\-D1\-C.3\-D3\-C.3\-D4 C.2 +\& \-D1\-C.3\-D3\-N.ar\-D4 C.2\-D1\-C.3\-D3\-O.3\-D2 C.2\-D1\-C.3\-D4\-C.3\-D5 C.2\-D1\-C. +\& 3\-D5\-C.3\-D6 C.2\-D1\-C.3\-D5\-O.3\-D4 C.2\-D1\-C.3\-D6\-C.3\-D7 C.2\-D1\-C.3\-D7... +\& +\& FingerprintsVector;TopologicalAtomTriplets:TPSAAtomTypes:MinDistance1: +\& MaxDistance10;1007;NumericalValues;IDsAndValuesString;N21\-D1\-N7\-D3\-Non +\& e\-D4 N21\-D1\-N7\-D5\-None\-D4 N21\-D1\-None\-D1\-None\-D2 N21\-D1\-None\-D2\-None\-D +\& 2 N21\-D1\-None\-D2\-None\-D3 N21\-D1\-None\-D3\-None\-D4 N21\-D1\-None\-D4\-None\-D5 +\& N21\-D1\-None\-D4\-O3\-D3 N21\-D1\-None\-D4\-O4\-D3 N21\-D1\-None\-D5\-None\-D6 N21\- +\& D1\-None\-D6\-None\-D7 N21\-D1\-None\-D6\-O4\-D5 N21\-D1\-None\-D7\-None\-D8 N21\-... +\& +\& FingerprintsVector;TopologicalAtomTriplets:UFFAtomTypes:MinDistance1:M +\& axDistance10;2377;NumericalValues;IDsAndValuesString;C_2\-D1\-C_2\-D9\-C_3 +\& \-D10 C_2\-D1\-C_2\-D9\-C_R\-D10 C_2\-D1\-C_3\-D1\-C_3\-D2 C_2\-D1\-C_3\-D10\-C_3\-D9 +\& C_2\-D1\-C_3\-D2\-C_3\-D3 C_2\-D1\-C_3\-D2\-C_R\-D3 C_2\-D1\-C_3\-D3\-C_3\-D4 C_2\-D1\- +\& C_3\-D3\-N_R\-D4 C_2\-D1\-C_3\-D3\-O_3\-D2 C_2\-D1\-C_3\-D4\-C_3\-D5 C_2\-D1\-C_3\-D5\- +\& C_3\-D6 C_2\-D1\-C_3\-D5\-O_3\-D4 C_2\-D1\-C_3\-D6\-C_3\-D7 C_2\-D1\-C_3\-D7\-C_3\-... +.Ve +.SS "\s-1METHODS\s0" +.IX Subsection "METHODS" +.IP "\fBnew\fR" 4 +.IX Item "new" +.Vb 2 +\& $NewTopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( +\& %NamesAndValues); +.Ve +.Sp +Using specified \fITopologicalAtomTripletsFingerprints\fR property names and values hash, \fBnew\fR +method creates a new object and returns a reference to newly created \fBTopologicalAtomTripletsFingerprints\fR +object. By default, the following properties are initialized: +.Sp +.Vb 8 +\& Molecule = \*(Aq\*(Aq +\& Type = \*(AqTopologicalAtomTriplets\*(Aq +\& MinDistance = 1 +\& MaxDistance = 10 +\& UseTriangleInequality = 1 +\& AtomIdentifierType = \*(Aq\*(Aq +\& AtomicInvariantsToUse = [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq] +\& FunctionalClassesToUse = [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq] +.Ve +.Sp +Examples: +.Sp +.Vb 4 +\& $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqAtomicInvariantsAtomTypes\*(Aq); +\& +\& $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqMinDistance\*(Aq => 1, +\& \*(AqMaxDistance\*(Aq => 10, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqAtomicInvariantsAtomTypes\*(Aq, +\& \*(AqAtomicInvariantsToUse\*(Aq => +\& [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq] ); +\& +\& $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqDREIDINGAtomTypes\*(Aq); +\& +\& $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqMMFF94AtomTypes\*(Aq); +\& +\& $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqTPSAAtomTypes\*(Aq); +\& +\& $TopologicalAtomTripletsFingerprints = new TopologicalAtomTripletsFingerprints( +\& \*(AqMolecule\*(Aq => $Molecule, +\& \*(AqMinDistance\*(Aq => 1, +\& \*(AqMaxDistance\*(Aq => 10, +\& \*(AqAtomIdentifierType\*(Aq => +\& \*(AqFunctionalClassAtomTypes\*(Aq, +\& \*(AqFunctionalClassesToUse\*(Aq => +\& [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq]); +\& +\& $TopologicalAtomTripletsFingerprints\->GenerateFingerprints(); +\& print "$TopologicalAtomTripletsFingerprints\en"; +.Ve +.IP "\fBGetDescription\fR" 4 +.IX Item "GetDescription" +.Vb 1 +\& $Return = $TopologicalAtomTripletsFingerprints\->GetDescription(); +.Ve +.Sp +Returns a string containing description of topological atom triplets fingerprints. +.IP "\fBGenerateFingerprints\fR" 4 +.IX Item "GenerateFingerprints" +.Vb 1 +\& $TopologicalAtomTripletsFingerprints\->GenerateFingerprints(); +.Ve +.Sp +Generates topological atom triplets fingerprints and returns \fITopologicalAtomTripletsFingerprints\fR. +.IP "\fBGetAtomTripletIDs\fR" 4 +.IX Item "GetAtomTripletIDs" +.Vb 2 +\& $AtomTripletIDsRef = $TopologicalAtomTripletsFingerprints\->GetAtomTripletIDs(); +\& @AtomTripletIDs = $TopologicalAtomTripletsFingerprints\->GetAtomTripletIDs(); +.Ve +.Sp +Returns atom triplet IDs corresponding to atom triplets count values in topological atom triplets +fingerprints vector as an array or reference to an array. +.IP "\fBSetAtomIdentifierType\fR" 4 +.IX Item "SetAtomIdentifierType" +.Vb 1 +\& $TopologicalAtomTripletsFingerprints\->SetAtomIdentifierType($IdentifierType); +.Ve +.Sp +Sets atom \fIIdentifierType\fR to use during atom triplets fingerprints generation and +returns \fITopologicalAtomTripletsFingerprints\fR. +.Sp +Possible values: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, +TPSAAtomTypes, UFFAtomTypes\fR. +.IP "\fBSetAtomicInvariantsToUse\fR" 4 +.IX Item "SetAtomicInvariantsToUse" +.Vb 2 +\& $TopologicalAtomTripletsFingerprints\->SetAtomicInvariantsToUse($ValuesRef); +\& $TopologicalAtomTripletsFingerprints\->SetAtomicInvariantsToUse(@Values); +.Ve +.Sp +Sets atomic invariants to use during \fIAtomicInvariantsAtomTypes\fR value of \fIAtomIdentifierType\fR +for topological atom triplets fingerprints generation and returns \fITopologicalAtomTripletsFingerprints\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 +\& $TopologicalTripletsFingerprints\->SetFunctionalClassesToUse($ValuesRef); +\& $TopologicalTripletsFingerprints\->SetFunctionalClassesToUse(@Values); +.Ve +.Sp +Sets functional classes invariants to use during \fIFunctionalClassAtomTypes\fR value of \fIAtomIdentifierType\fR +for topological atom triplets fingerprints generation and returns \fITopologicalAtomTripletsFingerprints\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 "\fBSetMaxDistance\fR" 4 +.IX Item "SetMaxDistance" +.Vb 1 +\& $TopologicalAtomTripletsFingerprints\->SetMaxDistance($Distance); +.Ve +.Sp +Sets maximum distance to use during topological atom triplets fingerprints generation and +returns \fITopologicalAtomTripletsFingerprints\fR. +.IP "\fBSetMinDistance\fR" 4 +.IX Item "SetMinDistance" +.Vb 1 +\& $TopologicalAtomTripletsFingerprints\->SetMinDistance($Distance); +.Ve +.Sp +Sets minimum distance to use during topological atom triplets fingerprints generation and +returns \fITopologicalAtomTripletsFingerprints\fR. +.IP "\fBStringifyTopologicalAtomTripletsFingerprints\fR" 4 +.IX Item "StringifyTopologicalAtomTripletsFingerprints" +.Vb 2 +\& $String = $TopologicalAtomTripletsFingerprints\-> +\& StringifyTopologicalAtomTripletsFingerprints(); +.Ve +.Sp +Returns a string containing information about \fITopologicalAtomTripletsFingerprints\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, EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm, +MACCSKeys.pm, PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.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.