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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/man1/TopologicalAtomPairsFingerprints.1 Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,796 @@ +.\" 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++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +TopologicalAtomPairsFingerprints.pl \- Generate topological atom pairs fingerprints for SD files +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +TopologicalAtomPairsFingerprints.pl SDFile(s)... +.PP +TopologicalAtomPairsFingerprints.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\-v, \-\-VectorStringFormat\fR \fIValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR] +[\fB\-w, \-\-WorkingDir\fR dirname] SDFile(s)... +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +Generate topological atom pairs fingerprints [ Ref 57, Ref 59, Ref 72 ] 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 pairs +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 pair +identifier is generated for each unique atom pair; the format of the atom pair identifier is: +.PP +.Vb 1 +\& <AtomType1>\-D<n>\-<AtomType2> +\& +\& AtomType1, AtomType2: Atom types assigned to atom1 and atom2 +\& D: Distance between atom1 and atom2 +\& +\& where AtomType1 <= AtomType2 +.Ve +.PP +The atom pair identifiers for all unique atom pairs corresponding to non-hydrogen atoms constitute +topological atom pairs fingerprints of the molecule. +.PP +Example of \fI\s-1SD\s0\fR file containing topological atom pairs fingerprints string data: +.PP +.Vb 10 +\& ... ... +\& ... ... +\& $$$$ +\& ... ... +\& ... ... +\& ... ... +\& 41 44 0 0 0 0 0 0 0 0999 V2000 +\& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +\& ... ... +\& 2 3 1 0 0 0 0 +\& ... ... +\& M END +\& > <CmpdID> +\& Cmpd1 +\& +\& > <TopologicalAtomPairsFingerprints> +\& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi +\& stance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1.H +\& 3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3.H1 +\& C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-C.X2...; +\& 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1 +\& 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1 ... +\& +\& $$$$ +\& ... ... +\& ... ... +.Ve +.PP +Example of \fI\s-1FP\s0\fR file containing topological atom pairs fingerprints string data: +.PP +.Vb 10 +\& # +\& # Package = MayaChemTools 7.4 +\& # Release Date = Oct 21, 2010 +\& # +\& # TimeStamp = Fri Mar 11 15:04:36 2011 +\& # +\& # FingerprintsStringType = FingerprintsVector +\& # +\& # Description = TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi... +\& # VectorStringFormat = IDsAndValuesString +\& # VectorValuesType = NumericalValues +\& # +\& Cmpd1 223;C.X1.BO1.H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2...;1 1... +\& Cmpd2 128;C.X1.BO1.H3\-D1\-C.X2.BO2.H2 C.X1.BO1.H3\-D1\-C.X3.BO4...;1 1... +\& ... ... +\& ... .. +.Ve +.PP +Example of \s-1CSV\s0 \fIText\fR file containing topological atom pairs fingerprints string data: +.PP +.Vb 9 +\& "CompoundID","TopologicalAtomPairsFingerprints" +\& "Cmpd1","FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTy +\& pes:MinDistance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C +\& .X1.BO1.H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X +\& 3.BO3.H1C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1...; +\& 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1 +\& 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1 ... +\& ... ... +\& ... ... +.Ve +.PP +The current release of MayaChemTools generates the following types of topological atom pairs +fingerprints vector strings: +.PP +.Vb 6 +\& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD +\& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1 +\& .H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3. +\& H1 C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-...; +\& 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1 +\& 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1... +\& +\& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD +\& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X +\& 1.BO1.H3\-D1\-C.X3.BO3.H1 2 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 1 C.X2.BO2.H2\-D1\- +\& C.X3.BO3.H1 4 C.X2.BO2.H2\-D1\-C.X3.BO4 1 C.X2.BO2.H2\-D1\-N.X3.BO3 1 C.X2 +\& .BO3.H1\-D1\-C.X2.BO3.H1 10 C.X2.BO3.H1\-D1\-C.X3.BO4 8 C.X3.BO3.H1\-D1\-C.X +\& 3.BO4 1 C.X3.BO3.H1\-D1\-O.X1.BO1.H1 2 C.X3.BO4\-D1\-C.X3.BO4 6 C.X3.BO... +\& +\& FingerprintsVector;TopologicalAtomPairs:DREIDINGAtomTypes:MinDistance1 +\& :MaxDistance10;157;NumericalValues;IDsAndValuesString;C_2\-D1\-C_3 C_2\-D +\& 1\-C_R C_2\-D1\-N_3 C_2\-D1\-O_2 C_2\-D1\-O_3 C_3\-D1\-C_3 C_3\-D1\-C_R C_3\-D1\-N_ +\& R C_3\-D1\-O_3 C_R\-D1\-C_R C_R\-D1\-F_ C_R\-D1\-N_3 C_R\-D1\-N_R C_2\-D2\-C_3 C_2 +\& 1 1 1 2 1 7 1 1 2 23 1 1 2 1 3 5 5 2 1 5 28 2 3 3 1 1 1 2 4 1 1 4 9 3 +\& 1 4 24 2 4 3 3 4 5 5 14 1 1 2 3 22 1 3 4 4 1 1 1 1 2 2 5 1 4 21 3 1... +\& +\& FingerprintsVector;TopologicalAtomPairs:EStateAtomTypes:MinDistance1:M +\& axDistance10;251;NumericalValues;IDsAndValuesString;aaCH\-D1\-aaCH aaCH\- +\& D1\-aasC aasC\-D1\-aasC aasC\-D1\-aasN aasC\-D1\-dssC aasC\-D1\-sF aasC\-D1\-ssNH +\& aasC\-D1\-sssCH aasN\-D1\-ssCH2 dO\-D1\-dssC dssC\-D1\-sOH dssC\-D1\-ssCH2 d...; +\& 10 8 5 2 1 1 1 1 1 2 1 1 1 2 2 1 4 10 12 2 2 6 3 1 3 2 2 1 1 1 1 1 1 1 +\& 1 1 5 2 1 1 6 12 2 2 2 2 6 1 3 2 2 5 2 2 1 2 1 1 1 1 1 1 3 1 3 19 2... +\& +\& FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi +\& stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar\-D1\-Ar +\& Ar\-D1\-Ar.HBA Ar\-D1\-HBD Ar\-D1\-Hal Ar\-D1\-None Ar.HBA\-D1\-None HBA\-D1\-NI H +\& BA\-D1\-None HBA.HBD\-D1\-NI HBA.HBD\-D1\-None HBD\-D1\-None NI\-D1\-None No...; +\& 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4 +\& 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ... +\& +\& FingerprintsVector;TopologicalAtomPairs:MMFF94AtomTypes:MinDistance1:M +\& axDistance10;227;NumericalValues;IDsAndValuesPairsString;C5A\-D1\-C5B 2 +\& C5A\-D1\-CB 1 C5A\-D1\-CR 1 C5A\-D1\-N5 2 C5B\-D1\-C5B 1 C5B\-D1\-C=ON 1 C5B\-D1\- +\& CB 1 C=ON\-D1\-NC=O 1 C=ON\-D1\-O=CN 1 CB\-D1\-CB 18 CB\-D1\-F 1 CB\-D1\-NC=O 1 +\& COO\-D1\-CR 1 COO\-D1\-O=CO 1 COO\-D1\-OC=O 1 CR\-D1\-CR 7 CR\-D1\-N5 1 CR\-D1\-OR +\& 2 C5A\-D2\-C5A 1 C5A\-D2\-C5B 2 C5A\-D2\-C=ON 1 C5A\-D2\-CB 3 C5A\-D2\-CR 4 ... +\& +\& FingerprintsVector;TopologicalAtomPairs:SLogPAtomTypes:MinDistance1:Ma +\& xDistance10;329;NumericalValues;IDsAndValuesPairsString;C1\-D1\-C10 1 C1 +\& \-D1\-C11 2 C1\-D1\-C5 1 C1\-D1\-CS 4 C10\-D1\-N11 1 C11\-D1\-C21 1 C14\-D1\-C18 2 +\& C14\-D1\-F 1 C18\-D1\-C18 10 C18\-D1\-C20 4 C18\-D1\-C22 2 C20\-D1\-C20 3 C20\-D +\& 1\-C21 1 C20\-D1\-N11 1 C21\-D1\-C21 1 C21\-D1\-C5 1 C21\-D1\-N11 1 C22\-D1\-N4 1 +\& C5\-D1\-N4 1 C5\-D1\-O10 1 C5\-D1\-O2 1 C5\-D1\-O9 1 CS\-D1\-O2 2 C1\-D2\-C1 3... +\& +\& FingerprintsVector;TopologicalAtomPairs:SYBYLAtomTypes:MinDistance1:Ma +\& xDistance10;159;NumericalValues;IDsAndValuesPairsString;C.2\-D1\-C.3 1 C +\& .2\-D1\-C.ar 1 C.2\-D1\-N.am 1 C.2\-D1\-O.2 1 C.2\-D1\-O.co2 2 C.3\-D1\-C.3 7 C. +\& 3\-D1\-C.ar 1 C.3\-D1\-N.ar 1 C.3\-D1\-O.3 2 C.ar\-D1\-C.ar 23 C.ar\-D1\-F 1 C.a +\& r\-D1\-N.am 1 C.ar\-D1\-N.ar 2 C.2\-D2\-C.3 1 C.2\-D2\-C.ar 3 C.3\-D2\-C.3 5 C.3 +\& \-D2\-C.ar 5 C.3\-D2\-N.ar 2 C.3\-D2\-O.3 4 C.3\-D2\-O.co2 2 C.ar\-D2\-C.ar 2... +\& +\& FingerprintsVector;TopologicalAtomPairs:TPSAAtomTypes:MinDistance1:Max +\& Distance10;64;NumericalValues;IDsAndValuesPairsString;N21\-D1\-None 3 N7 +\& \-D1\-None 2 None\-D1\-None 34 None\-D1\-O3 2 None\-D1\-O4 3 N21\-D2\-None 5 N7\- +\& D2\-None 3 N7\-D2\-O3 1 None\-D2\-None 44 None\-D2\-O3 2 None\-D2\-O4 5 O3\-D2\-O +\& 4 1 N21\-D3\-None 7 N7\-D3\-None 4 None\-D3\-None 45 None\-D3\-O3 4 None\-D3\-O4 +\& 5 N21\-D4\-N7 1 N21\-D4\-None 5 N21\-D4\-O3 1 N21\-D4\-O4 1 N7\-D4\-None 4 N... +\& +\& FingerprintsVector;TopologicalAtomPairs:UFFAtomTypes:MinDistance1:MaxD +\& istance10;157;NumericalValues;IDsAndValuesPairsString;C_2\-D1\-C_3 1 C_2 +\& \-D1\-C_R 1 C_2\-D1\-N_3 1 C_2\-D1\-O_2 2 C_2\-D1\-O_3 1 C_3\-D1\-C_3 7 C_3\-D1\-C +\& _R 1 C_3\-D1\-N_R 1 C_3\-D1\-O_3 2 C_R\-D1\-C_R 23 C_R\-D1\-F_ 1 C_R\-D1\-N_3 1 +\& C_R\-D1\-N_R 2 C_2\-D2\-C_3 1 C_2\-D2\-C_R 3 C_3\-D2\-C_3 5 C_3\-D2\-C_R 5 C_3\-D +\& 2\-N_R 2 C_3\-D2\-O_2 1 C_3\-D2\-O_3 5 C_R\-D2\-C_R 28 C_R\-D2\-F_ 2 C_R\-D2\-... +.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 pairs 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 | both\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 | both\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: \fITopologicalAtomPairsFingerprints\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 pairs for generating topological atom pairs. 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 pairs for generating topological atom pairs. 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><TopologicalAtomPairsFP>.<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\-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 6 +\& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD +\& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1 +\& .H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3. +\& H1 C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-...; +\& 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1 +\& 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1... +\& +\& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD +\& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X +\& 1.BO1.H3\-D1\-C.X3.BO3.H1 2 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 1 C.X2.BO2.H2\-D1\- +\& C.X3.BO3.H1 4 C.X2.BO2.H2\-D1\-C.X3.BO4 1 C.X2.BO2.H2\-D1\-N.X3.BO3 1 C.X2 +\& .BO3.H1\-D1\-C.X2.BO3.H1 10 C.X2.BO3.H1\-D1\-C.X3.BO4 8 C.X3.BO3.H1\-D1\-C.X +\& 3.BO4 1 C.X3.BO3.H1\-D1\-O.X1.BO1.H1 2 C.X3.BO4\-D1\-C.X3.BO4 6 C.X3.BO... +.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 pairs fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 1 +\& % TopologicalAtomPairsFingerprints.pl \-r SampleTAPFP \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create SampleTAPFP.sdf, +SampleTAPFP.fpf and SampleTAPFP.csv files containing sequential compound IDs in \s-1CSV\s0 file along +with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomPairsFingerprints.pl \-\-output all \-r SampleTAPFP +\& \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using \s-1DREIDING\s0 atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomPairsFingerprints.pl \-a DREIDINGAtomTypes +\& \-r SampleTAPFP \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using E\-state types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomPairsFingerprints.pl \-a EStateAtomTypes +\& \-r SampleTAPFP \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using \s-1DREIDING\s0 atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomPairsFingerprints.pl \-a DREIDINGAtomTypes +\& \-r SampleTAPFP \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using functional class atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomPairsFingerprints.pl \-a FunctionalClassAtomTypes +\& \-r SampleTAPFP \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using \s-1MMFF94\s0 atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomPairsFingerprints.pl \-a MMFF94AtomTypes +\& \-r SampleTAPFP \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using SLogP atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomPairsFingerprints.pl \-a SLogPAtomTypes +\& \-r SampleTAPFP \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using \s-1SYBYL\s0 atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomPairsFingerprints.pl \-a SYBYLAtomTypes +\& \-r SampleTAPFP \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using \s-1TPSA\s0 atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomPairsFingerprints.pl \-a TPSAAtomTypes +\& \-r SampleTAPFP \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using \s-1UFF\s0 atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomPairsFingerprints.pl \-a UFFAtomTypes +\& \-r SampleTAPFP \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesPairsString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomPairsFingerprints.pl \-\-VectorStringFormat +\& IDsAndValuesPairsString \-r SampleTAPFP \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +6 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type: +.PP +.Vb 2 +\& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-MinDistance 1 \-\-MaxDistance 6 \-r SampleTAPFP \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs 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 +SampleTAPFP.csv file containing sequential compound IDs along with fingerprints vector strings +data, type: +.PP +.Vb 3 +\& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-AtomicInvariantsToUse "AS,X" \-\-MinDistance 1 \-\-MaxDistance 6 +\& \-r SampleTAPFP \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing compound \s-1ID\s0 from molecule name line along with fingerprints vector strings +data, type: +.PP +.Vb 3 +\& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolName +\& \-r SampleTAPFP \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing compound IDs using specified data field along with fingerprints vector strings +data, type: +.PP +.Vb 3 +\& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode CompoundID \-CompoundIDMode DataField \-\-CompoundID +\& Mol_ID \-r SampleTAPFP \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.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 +\& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolnameOrLabelPrefix +\& \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleTAPFP \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing specific data fields columns along with fingerprints vector strings +data, type: +.PP +.Vb 3 +\& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode Specify \-\-DataFields Mol_ID \-r SampleTAPFP +\& \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing common data fields columns along with fingerprints vector strings +data, type: +.PP +.Vb 2 +\& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode Common \-r SampleTAPFP \-o Sample.sdf +.Ve +.PP +To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create SampleTAPFP.sdf, +SampleTAPFP.fpf and SampleTAPFP.csv files containing all data fields columns in \s-1CSV\s0 file along +with fingerprints data, type: +.PP +.Vb 3 +\& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes +\& \-\-DataFieldsMode All \-\-output all \-r SampleTAPFP +\& \-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.