Mercurial > repos > deepakjadmin > mayatool3_test3
diff mayachemtools/docs/scripts/man1/TopologicalAtomTripletsFingerprints.1 @ 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/scripts/man1/TopologicalAtomTripletsFingerprints.1 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,822 @@ +.\" 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 "TOPOLOGICALATOMTRIPLETSFINGERPRINTS 1" +.TH TOPOLOGICALATOMTRIPLETSFINGERPRINTS 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" +TopologicalAtomTripletsFingerprints.pl \- Generate topological atom triplets fingerprints for SD files +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +TopologicalAtomTripletsFingerprints.pl SDFile(s)... +.PP +TopologicalAtomTripletsFingerprints.pl [\fB\-\-AromaticityModel\fR \fIAromaticityModelType\fR] +[\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes\fR] +[\fB\-\-AtomicInvariantsToUse\fR \fI\*(L"AtomicInvariant,AtomicInvariant...\*(R"\fR] +[\fB\-\-FunctionalClassesToUse\fR \fI\*(L"FunctionalClass1,FunctionalClass2...\*(R"\fR] +[\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR] [\fB\-\-CompoundIDLabel\fR \fItext\fR] +[\fB\-\-CompoundIDMode\fR] [\fB\-\-DataFields\fR \fI\*(L"FieldLabel1,FieldLabel2,...\*(R"\fR] +[\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR] [\fB\-f, \-\-Filter\fR \fIYes | No\fR] +[\fB\-\-FingerprintsLabel\fR \fItext\fR] [\fB\-h, \-\-help\fR] [\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR] +[\fB\-\-MinDistance\fR \fInumber\fR] [\fB\-\-MaxDistance\fR \fInumber\fR] +[\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR] [\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR] [\fB\-o, \-\-overwrite\fR] +[\fB\-q, \-\-quote\fR \fIYes | No\fR] [\fB\-r, \-\-root\fR \fIRootName\fR] [\fB\-u, \-\-UseTriangleInequality\fR \fIYes | No\fR] +[\fB\-v, \-\-VectorStringFormat\fR \fIValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR] +[\fB\-w, \-\-WorkingDir\fR dirname] SDFile(s)... +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +Generate topological atom triplets fingerprints for \fISDFile(s)\fR and create +appropriate \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) containing fingerprints vector strings corresponding to +molecular fingerprints. +.PP +Multiple SDFile names are separated by spaces. The valid file extensions are \fI.sdf\fR +and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a current directory +can be specified either by \fI*.sdf\fR or the current directory name. +.PP +The current release of MayaChemTools supports generation of topological atom triplets +fingerprints corresponding to following \fB\-a, \-\-AtomIdentifierTypes\fR: +.PP +.Vb 3 +\& AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +\& FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, +\& SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes +.Ve +.PP +Based on the values specified for \fB\-a, \-\-AtomIdentifierType\fR and \fB\-\-AtomicInvariantsToUse\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 +pairs within \fB\-\-MinDistance\fR and \fB\-\-MaxDistance\fR are identified and counted. An atom triplet +identifier is generated for each unique atom triplet; the format of the 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 +Example of \fI\s-1SD\s0\fR file containing topological atom triplets fingerprints string data: +.PP +.Vb 10 +\& ... ... +\& ... ... +\& $$$$ +\& ... ... +\& ... ... +\& ... ... +\& 41 44 0 0 0 0 0 0 0 0999 V2000 +\& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +\& ... ... +\& 2 3 1 0 0 0 0 +\& ... ... +\& M END +\& > <CmpdID> +\& Cmpd1 +\& +\& > <TopologicalAtomTripletsFingerprints> +\& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:Mi +\& nDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1.B +\& O1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D10\-C +\& .X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1...; +\& 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 2 +\& 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8 8 ... +\& +\& $$$$ +\& ... ... +\& ... ... +.Ve +.PP +Example of \fI\s-1FP\s0\fR file containing topological atom triplets fingerprints string data: +.PP +.Vb 10 +\& # +\& # Package = MayaChemTools 7.4 +\& # Release Date = Oct 21, 2010 +\& # +\& # TimeStamp = Fri Mar 11 15:24:01 2011 +\& # +\& # FingerprintsStringType = FingerprintsVector +\& # +\& # Description = TopologicalAtomTriplets:AtomicInvariantsAtomTypes:Mi... +\& # VectorStringFormat = IDsAndValuesString +\& # VectorValuesType = NumericalValues +\& # +\& Cmpd1 3096;C.X1.BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2...;1 2 2 2 2... +\& Cmpd2 1093;C.X1.BO1.H3\-D1\-C.X1.BO1.H3\-D3\-C.X2.BO2.H2\-D4...;2 2 2 2 2... +\& ... ... +\& ... .. +.Ve +.PP +Example of \s-1CSV\s0 \fIText\fR file containing topological atom triplets fingerprints string data: +.PP +.Vb 9 +\& "CompoundID","TopologicalAtomTripletsFingerprints" +\& "Cmpd1","FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAto +\& mTypes:MinDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesStri +\& ng;C.X1.BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2 +\& .H2\-D10\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1....; +\& 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 8 ... +\& ... ... +\& ... ... +.Ve +.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 +.SH "OPTIONS" +.IX Header "OPTIONS" +.IP "\fB\-\-AromaticityModel\fR \fIMDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel\fR" 4 +.IX Item "--AromaticityModel MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel" +Specify aromaticity model to use during detection of aromaticity. Possible values in the current +release are: \fIMDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel, +ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel +or MayaChemToolsAromaticityModel\fR. Default value: \fIMayaChemToolsAromaticityModel\fR. +.Sp +The supported aromaticity model names along with model specific control parameters +are defined in \fBAromaticityModelsData.csv\fR, which is distributed with the current release +and is available under \fBlib/data\fR directory. \fBMolecule.pm\fR module retrieves data from +this file during class instantiation and makes it available to method \fBDetectAromaticity\fR +for detecting aromaticity corresponding to a specific model. +.IP "\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes\fR" 4 +.IX Item "-a, --AtomIdentifierType AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes" +Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen +atoms during calculation of topological atom triplets fingerprints. Possible values in the current +release are: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, +TPSAAtomTypes, UFFAtomTypes\fR. Default value: \fIAtomicInvariantsAtomTypes\fR. +.ie n .IP "\fB\-\-AtomicInvariantsToUse\fR \fI""AtomicInvariant,AtomicInvariant...""\fR" 4 +.el .IP "\fB\-\-AtomicInvariantsToUse\fR \fI``AtomicInvariant,AtomicInvariant...''\fR" 4 +.IX Item "--AtomicInvariantsToUse AtomicInvariant,AtomicInvariant..." +This value is used during \fIAtomicInvariantsAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR +option. It's a list of comma separated valid atomic invariant atom types. +.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. +.ie n .IP "\fB\-\-FunctionalClassesToUse\fR \fI""FunctionalClass1,FunctionalClass2...""\fR" 4 +.el .IP "\fB\-\-FunctionalClassesToUse\fR \fI``FunctionalClass1,FunctionalClass2...''\fR" 4 +.IX Item "--FunctionalClassesToUse FunctionalClass1,FunctionalClass2..." +This value is used during \fIFunctionalClassAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR +option. It's a list of comma separated valid functional classes. +.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 +.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 "\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR" 4 +.IX Item "--CompoundID DataFieldName or LabelPrefixString" +This value is \fB\-\-CompoundIDMode\fR specific and indicates how compound \s-1ID\s0 is generated. +.Sp +For \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option, it corresponds to datafield label name +whose value is used as compound \s-1ID\s0; otherwise, it's a prefix string used for generating compound +IDs like LabelPrefixString<Number>. Default value, \fICmpd\fR, generates compound IDs which +look like Cmpd<Number>. +.Sp +Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR: +.Sp +.Vb 2 +\& MolID +\& ExtReg +.Ve +.Sp +Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR: +.Sp +.Vb 1 +\& Compound +.Ve +.Sp +The value specified above generates compound IDs which correspond to Compound<Number> +instead of default value of Cmpd<Number>. +.IP "\fB\-\-CompoundIDLabel\fR \fItext\fR" 4 +.IX Item "--CompoundIDLabel text" +Specify compound \s-1ID\s0 column label for \s-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value +of \fB\-\-DataFieldsMode\fR option. Default value: \fICompoundID\fR. +.IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4 +.IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix" +Specify how to generate compound IDs and write to \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) along with generated +fingerprints for \fI\s-1FP\s0 | text | all\fR values of \fB\-\-output\fR option: use a \fISDFile(s)\fR datafield value; +use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0 with specific prefix; use combination +of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines. +.Sp +Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR. +Default value: \fILabelPrefix\fR. +.Sp +For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes +precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname +values are replaced with sequential compound IDs. +.Sp +This is only used for \fICompoundID\fR value of \fB\-\-DataFieldsMode\fR option. +.ie n .IP "\fB\-\-DataFields\fR \fI""FieldLabel1,FieldLabel2,...""\fR" 4 +.el .IP "\fB\-\-DataFields\fR \fI``FieldLabel1,FieldLabel2,...''\fR" 4 +.IX Item "--DataFields FieldLabel1,FieldLabel2,..." +Comma delimited list of \fISDFiles(s)\fR data fields to extract and write to \s-1CSV/TSV\s0 text file(s) along +with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option. +.Sp +This is only used for \fISpecify\fR value of \fB\-\-DataFieldsMode\fR option. +.Sp +Examples: +.Sp +.Vb 2 +\& Extreg +\& MolID,CompoundName +.Ve +.IP "\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR" 4 +.IX Item "-d, --DataFieldsMode All | Common | Specify | CompoundID" +Specify how data fields in \fISDFile(s)\fR are transferred to output \s-1CSV/TSV\s0 text file(s) along +with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option: transfer all \s-1SD\s0 +data field; transfer \s-1SD\s0 data files common to all compounds; extract specified data fields; +generate a compound \s-1ID\s0 using molname line, a compound prefix, or a combination of both. +Possible values: \fIAll | Common | specify | CompoundID\fR. Default value: \fICompoundID\fR. +.IP "\fB\-f, \-\-Filter\fR \fIYes | No\fR" 4 +.IX Item "-f, --Filter Yes | No" +Specify whether to check and filter compound data in SDFile(s). Possible values: \fIYes or No\fR. +Default value: \fIYes\fR. +.Sp +By default, compound data is checked before calculating fingerprints and compounds containing +atom data corresponding to non-element symbols or no atom data are ignored. +.IP "\fB\-\-FingerprintsLabel\fR \fItext\fR" 4 +.IX Item "--FingerprintsLabel text" +\&\s-1SD\s0 data label or text file column label to use for fingerprints string in output \s-1SD\s0 or +\&\s-1CSV/TSV\s0 text file(s) specified by \fB\-\-output\fR. Default value: \fITopologicalAtomTripletsFingerprints\fR. +.IP "\fB\-h, \-\-help\fR" 4 +.IX Item "-h, --help" +Print this help message. +.IP "\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR" 4 +.IX Item "-k, --KeepLargestComponent Yes | No" +Generate fingerprints for only the largest component in molecule. Possible values: +\&\fIYes or No\fR. Default value: \fIYes\fR. +.Sp +For molecules containing multiple connected components, fingerprints can be generated +in two different ways: use all connected components or just the largest connected +component. By default, all atoms except for the largest connected component are +deleted before generation of fingerprints. +.IP "\fB\-\-MinDistance\fR \fInumber\fR" 4 +.IX Item "--MinDistance number" +Minimum bond distance between atom triplets for generating topological atom triplets. Default value: +\&\fI1\fR. Valid values: positive integers and less than \fB\-\-MaxDistance\fR. +.IP "\fB\-\-MaxDistance\fR \fInumber\fR" 4 +.IX Item "--MaxDistance number" +Maximum bond distance between atom triplets for generating topological atom triplets. Default value: +\&\fI10\fR. Valid values: positive integers and greater than \fB\-\-MinDistance\fR. +.IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4 +.IX Item "--OutDelim comma | tab | semicolon" +Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR +Default value: \fIcomma\fR +.IP "\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR" 4 +.IX Item "--output SD | FP | text | all" +Type of output files to generate. Possible values: \fI\s-1SD\s0, \s-1FP\s0, text, or all\fR. Default value: \fItext\fR. +.IP "\fB\-o, \-\-overwrite\fR" 4 +.IX Item "-o, --overwrite" +Overwrite existing files. +.IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4 +.IX Item "-q, --quote Yes | No" +Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values: +\&\fIYes or No\fR. Default value: \fIYes\fR. +.IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4 +.IX Item "-r, --root RootName" +New file name is generated using the root: <Root>.<Ext>. Default for new file names: +<SDFileName><TopologicalAtomTripletsFP>.<Ext>. The file type determines <Ext> value. +The sdf, fpf, csv, and tsv <Ext> values are used for \s-1SD\s0, \s-1FP\s0, comma/semicolon, and tab +delimited text files, respectively.This option is ignored for multiple input files. +.IP "\fB\-u, \-\-UseTriangleInequality\fR \fIYes | No\fR" 4 +.IX Item "-u, --UseTriangleInequality Yes | No" +Specify whether to imply triangle distance inequality test to distances between atom pairs in +atom triplets during generation of atom triplets generation. Possible values: \fIYes or No\fR. +Default value: \fINo\fR. +.Sp +Triangle distance inequality test implies that distance or binned distance between any two atom +pairs in an atom triplet must be less than the sum of distances or binned distances between other +two atoms pairs and greater than the difference of their distances. +.Sp +.Vb 1 +\& For atom triplet ATx\-Dyz\-ATy\-Dxz\-ATz\-Dxy to satisfy triangle inequality: +\& +\& Dyz > |Dxz \- Dxy| and Dyz < Dxz + Dxy +\& Dxz > |Dyz \- Dxy| and Dyz < Dyz + Dxy +\& Dxy > |Dyz \- Dxz| and Dxy < Dyz + Dxz +.Ve +.IP "\fB\-v, \-\-VectorStringFormat\fR \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR" 4 +.IX Item "-v, --VectorStringFormat IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString" +Format of fingerprints vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by +\&\fB\-\-output\fR option. Possible values: \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | +ValuesAndIDsPairsString\fR. Default value: \fIIDsAndValuesString\fR. +.Sp +Examples: +.Sp +.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... +.Ve +.IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4 +.IX Item "-w, --WorkingDir DirName" +Location of working directory. Default value: current directory. +.SH "EXAMPLES" +.IX Header "EXAMPLES" +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 1 +\& % TopologicalAtomTripletsFingerprints.pl \-r SampleTATFP \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create SampleTATFP.sdf, +SampleTATFP.fpf and SampleTATFP.csv files containing sequential compound IDs in \s-1CSV\s0 file along +with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomTripletsFingerprints.pl \-\-output all \-r SampleTATFP +\& \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesPairsString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomTripletsFingerprints.pl \-\-VectorStringFormat +\& IDsAndValuesPairsString \-r SampleTATFP \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using \s-1DREIDING\s0 atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomTripletsFingerprints.pl \-a DREIDINGAtomTypes +\& \-r SampleTATFP \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using E\-state atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomTripletsFingerprints.pl \-a EStateAtomTypes +\& \-r SampleTATFP \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using functional class atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomTripletsFingerprints.pl \-a FunctionalClassAtomTypes +\& \-r SampleTATFP \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using \s-1DREIDING\s0 atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomTripletsFingerprints.pl \-a DREIDINGAtomTypes +\& \-r SampleTATFP \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using \s-1MM94\s0 atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomTripletsFingerprints.pl \-a MMFF94AtomTypes +\& \-r SampleTATFP \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using SLogP atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomTripletsFingerprints.pl \-a SLogPAtomTypes +\& \-r SampleTATFP \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using \s-1SYBYL\s0 atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomTripletsFingerprints.pl \-a SYBYLAtomTypes +\& \-r SampleTATFP \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using \s-1TPSA\s0 atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomTripletsFingerprints.pl \-a TPSAAtomTypes +\& \-r SampleTATFP \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using \s-1UFF\s0 atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomTripletsFingerprints.pl \-a UFFAtomTypes +\& \-r SampleTATFP \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +6 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-MinDistance 1 \-\-MaxDistance 6 \-r SampleTATFP \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using only \s-1AS\s0,X atomic invariants atom types in IDsAndValuesString format and create a +SampleTATFP.csv file containing sequential compound IDs along with fingerprints vector strings +data, type: +.PP +.Vb 3 +\& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-AtomicInvariantsToUse "AS,X" \-\-MinDistance 1 \-\-MaxDistance 6 +\& \-r SampleTATFP \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing compound \s-1ID\s0 from molecule name line along with fingerprints vector strings +data, type: +.PP +.Vb 3 +\& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolName +\& \-r SampleTATFP \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing compound IDs using specified data field along with fingerprints vector strings +data, type: +.PP +.Vb 3 +\& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode CompoundID \-CompoundIDMode DataField \-\-CompoundID +\& Mol_ID \-r SampleTATFP \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing compound \s-1ID\s0 using combination of molecule name line and an explicit compound +prefix along with fingerprints vector strings data, type: +.PP +.Vb 3 +\& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolnameOrLabelPrefix +\& \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleTATFP \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing specific data fields columns along with fingerprints vector strings +data, type: +.PP +.Vb 3 +\& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode Specify \-\-DataFields Mol_ID \-r SampleTATFP +\& \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv +file containing common data fields columns along with fingerprints vector strings +data, type: +.PP +.Vb 2 +\& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode Common \-r SampleTATFP \-o Sample.sdf +.Ve +.PP +To generate topological atom triplets fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create SampleTATFP.sdf, +SampleTATFP.fpf and SampleTATFP.csv files containing all data fields columns in \s-1CSV\s0 file along with +fingerprints data, type: +.PP +.Vb 3 +\& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode All \-\-output all \-r SampleTATFP +\& \-o Sample.sdf +.Ve +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl, +ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl, +PathLengthFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl, +TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl +.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.