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diff docs/scripts/txt/TopologicalAtomTripletsFingerprints.txt @ 0:4816e4a8ae95 draft default tip
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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/txt/TopologicalAtomTripletsFingerprints.txt Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,696 @@ +NAME + TopologicalAtomTripletsFingerprints.pl - Generate topological atom + triplets fingerprints for SD files + +SYNOPSIS + TopologicalAtomTripletsFingerprints.pl SDFile(s)... + + TopologicalAtomTripletsFingerprints.pl [--AromaticityModel + *AromaticityModelType*] [-a, --AtomIdentifierType + *AtomicInvariantsAtomTypes*] [--AtomicInvariantsToUse + *"AtomicInvariant,AtomicInvariant..."*] [--FunctionalClassesToUse + *"FunctionalClass1,FunctionalClass2..."*] [--CompoundID *DataFieldName + or LabelPrefixString*] [--CompoundIDLabel *text*] [--CompoundIDMode] + [--DataFields *"FieldLabel1,FieldLabel2,..."*] [-d, --DataFieldsMode + *All | Common | Specify | CompoundID*] [-f, --Filter *Yes | No*] + [--FingerprintsLabel *text*] [-h, --help] [-k, --KeepLargestComponent + *Yes | No*] [--MinDistance *number*] [--MaxDistance *number*] + [--OutDelim *comma | tab | semicolon*] [--output *SD | FP | text | all*] + [-o, --overwrite] [-q, --quote *Yes | No*] [-r, --root *RootName*] [-u, + --UseTriangleInequality *Yes | No*] [-v, --VectorStringFormat + *ValuesString, IDsAndValuesString | IDsAndValuesPairsString | + ValuesAndIDsString | ValuesAndIDsPairsString*] [-w, --WorkingDir + dirname] SDFile(s)... + +DESCRIPTION + Generate topological atom triplets fingerprints for *SDFile(s)* and + create appropriate SD, FP or CSV/TSV text file(s) containing + fingerprints vector strings corresponding to molecular fingerprints. + + Multiple SDFile names are separated by spaces. The valid file extensions + are *.sdf* and *.sd*. All other file names are ignored. All the SD files + in a current directory can be specified either by **.sdf* or the current + directory name. + + The current release of MayaChemTools supports generation of topological + atom triplets fingerprints corresponding to following -a, + --AtomIdentifierTypes: + + AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, + FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, + SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes + + Based on the values specified for -a, --AtomIdentifierType and + --AtomicInvariantsToUse, 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 --MinDistance and --MaxDistance are identified + and counted. An atom triplet identifier is generated for each unique + atom triplet; the format of the atom triplet identifier is: + + <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 + + The atom triplet identifiers for all unique atom triplets corresponding + to non-hydrogen atoms constitute topological atom triplets fingerprints + of the molecule. + + Example of *SD* file containing topological atom triplets fingerprints + string data: + + ... ... + ... ... + $$$$ + ... ... + ... ... + ... ... + 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + ... ... + 2 3 1 0 0 0 0 + ... ... + M END + > <CmpdID> + Cmpd1 + + > <TopologicalAtomTripletsFingerprints> + FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:Mi + nDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1.B + O1.H3-D1-C.X1.BO1.H3-D1-C.X3.BO3.H1-D2 C.X1.BO1.H3-D1-C.X2.BO2.H2-D10-C + .X3.BO4-D9 C.X1.BO1.H3-D1-C.X2.BO2.H2-D3-N.X3.BO3-D4 C.X1.BO1.H3-D1...; + 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 2 + 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8 8 ... + + $$$$ + ... ... + ... ... + + Example of *FP* file containing topological atom triplets fingerprints + string data: + + # + # 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... + ... ... + ... .. + + Example of CSV *Text* file containing topological atom triplets + fingerprints string data: + + "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 ... + ... ... + ... ... + + The current release of MayaChemTools generates the following types of + topological atom triplets fingerprints vector strings: + + 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-... + +OPTIONS + --AromaticityModel *MDLAromaticityModel | TriposAromaticityModel | + MMFFAromaticityModel | ChemAxonBasicAromaticityModel | + ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | + MayaChemToolsAromaticityModel* + Specify aromaticity model to use during detection of aromaticity. + Possible values in the current release are: *MDLAromaticityModel, + TriposAromaticityModel, MMFFAromaticityModel, + ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, + DaylightAromaticityModel or MayaChemToolsAromaticityModel*. Default + value: *MayaChemToolsAromaticityModel*. + + The supported aromaticity model names along with model specific + control parameters are defined in AromaticityModelsData.csv, which + is distributed with the current release and is available under + lib/data directory. Molecule.pm module retrieves data from this file + during class instantiation and makes it available to method + DetectAromaticity for detecting aromaticity corresponding to a + specific model. + + -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: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, + FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, + SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*. Default value: + *AtomicInvariantsAtomTypes*. + + --AtomicInvariantsToUse *"AtomicInvariant,AtomicInvariant..."* + This value is used during *AtomicInvariantsAtomTypes* value of a, + --AtomIdentifierType option. It's a list of comma separated valid + atomic invariant atom types. + + Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB, + TB, H, Ar, RA, FC, MN, SM*. Default value: *AS,X,BO,H,FC*. + + The atomic invariants abbreviations correspond to: + + 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) + + Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class + corresponds to: + + AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n> + + Except for AS 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. + + In addition to usage of abbreviations for specifying atomic + invariants, the following descriptive words are also allowed: + + 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 + + *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign + atomic invariant atom types. + + --FunctionalClassesToUse *"FunctionalClass1,FunctionalClass2..."* + This value is used during *FunctionalClassAtomTypes* value of a, + --AtomIdentifierType option. It's a list of comma separated valid + functional classes. + + Possible values for atom functional classes are: *Ar, CA, H, HBA, + HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]: + *HBD,HBA,PI,NI,Ar,Hal*. + + The functional class abbreviations correspond to: + + 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 + + *AtomTypes::FunctionalClassAtomTypes* module is used to assign + functional class atom types. It uses following definitions [ Ref + 60-61, Ref 65-66 ]: + + HydrogenBondDonor: NH, NH2, OH + HydrogenBondAcceptor: N[!H], O + PositivelyIonizable: +, NH2 + NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH + + --CompoundID *DataFieldName or LabelPrefixString* + This value is --CompoundIDMode specific and indicates how compound + ID is generated. + + For *DataField* value of --CompoundIDMode option, it corresponds to + datafield label name whose value is used as compound ID; otherwise, + it's a prefix string used for generating compound IDs like + LabelPrefixString<Number>. Default value, *Cmpd*, generates compound + IDs which look like Cmpd<Number>. + + Examples for *DataField* value of --CompoundIDMode: + + MolID + ExtReg + + Examples for *LabelPrefix* or *MolNameOrLabelPrefix* value of + --CompoundIDMode: + + Compound + + The value specified above generates compound IDs which correspond to + Compound<Number> instead of default value of Cmpd<Number>. + + --CompoundIDLabel *text* + Specify compound ID column label for CSV/TSV text file(s) used + during *CompoundID* value of --DataFieldsMode option. Default value: + *CompoundID*. + + --CompoundIDMode *DataField | MolName | LabelPrefix | + MolNameOrLabelPrefix* + Specify how to generate compound IDs and write to FP or CSV/TSV text + file(s) along with generated fingerprints for *FP | text | all* + values of --output option: use a *SDFile(s)* datafield value; use + molname line from *SDFile(s)*; generate a sequential ID with + specific prefix; use combination of both MolName and LabelPrefix + with usage of LabelPrefix values for empty molname lines. + + Possible values: *DataField | MolName | LabelPrefix | + MolNameOrLabelPrefix*. Default value: *LabelPrefix*. + + For *MolNameAndLabelPrefix* value of --CompoundIDMode, molname line + in *SDFile(s)* takes precedence over sequential compound IDs + generated using *LabelPrefix* and only empty molname values are + replaced with sequential compound IDs. + + This is only used for *CompoundID* value of --DataFieldsMode option. + + --DataFields *"FieldLabel1,FieldLabel2,..."* + Comma delimited list of *SDFiles(s)* data fields to extract and + write to CSV/TSV text file(s) along with generated fingerprints for + *text | all* values of --output option. + + This is only used for *Specify* value of --DataFieldsMode option. + + Examples: + + Extreg + MolID,CompoundName + + -d, --DataFieldsMode *All | Common | Specify | CompoundID* + Specify how data fields in *SDFile(s)* are transferred to output + CSV/TSV text file(s) along with generated fingerprints for *text | + all* values of --output option: transfer all SD data field; transfer + SD data files common to all compounds; extract specified data + fields; generate a compound ID using molname line, a compound + prefix, or a combination of both. Possible values: *All | Common | + specify | CompoundID*. Default value: *CompoundID*. + + -f, --Filter *Yes | No* + Specify whether to check and filter compound data in SDFile(s). + Possible values: *Yes or No*. Default value: *Yes*. + + 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. + + --FingerprintsLabel *text* + SD data label or text file column label to use for fingerprints + string in output SD or CSV/TSV text file(s) specified by --output. + Default value: *TopologicalAtomTripletsFingerprints*. + + -h, --help + Print this help message. + + -k, --KeepLargestComponent *Yes | No* + Generate fingerprints for only the largest component in molecule. + Possible values: *Yes or No*. Default value: *Yes*. + + 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. + + --MinDistance *number* + Minimum bond distance between atom triplets for generating + topological atom triplets. Default value: *1*. Valid values: + positive integers and less than --MaxDistance. + + --MaxDistance *number* + Maximum bond distance between atom triplets for generating + topological atom triplets. Default value: *10*. Valid values: + positive integers and greater than --MinDistance. + + --OutDelim *comma | tab | semicolon* + Delimiter for output CSV/TSV text file(s). Possible values: *comma, + tab, or semicolon* Default value: *comma* + + --output *SD | FP | text | all* + Type of output files to generate. Possible values: *SD, FP, text, or + all*. Default value: *text*. + + -o, --overwrite + Overwrite existing files. + + -q, --quote *Yes | No* + Put quote around column values in output CSV/TSV text file(s). + Possible values: *Yes or No*. Default value: *Yes*. + + -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 SD, FP, comma/semicolon, and tab delimited text + files, respectively.This option is ignored for multiple input files. + + -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: *Yes or No*. Default + value: *No*. + + 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. + + 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 + + -v, --VectorStringFormat *IDsAndValuesString | IDsAndValuesPairsString | + ValuesAndIDsString | ValuesAndIDsPairsString* + Format of fingerprints vector string data in output SD, FP or + CSV/TSV text file(s) specified by --output option. Possible values: + *IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | + ValuesAndIDsPairsString*. Default value: *IDsAndValuesString*. + + Examples: + + 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... + + -w, --WorkingDir *DirName* + Location of working directory. Default value: current directory. + +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: + + % TopologicalAtomTripletsFingerprints.pl -r SampleTATFP -o Sample.sdf + + 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 CSV file + along with fingerprints vector strings data, type: + + % TopologicalAtomTripletsFingerprints.pl --output all -r SampleTATFP + -o Sample.sdf + + 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: + + % TopologicalAtomTripletsFingerprints.pl --VectorStringFormat + IDsAndValuesPairsString -r SampleTATFP -o Sample.sdf + + To generate topological atom triplets fingerprints corresponding to bond + distances from 1 through 10 using DREIDING atom types in + IDsAndValuesString format and create a SampleTATFP.csv file containing + sequential compound IDs along with fingerprints vector strings data, + type: + + % TopologicalAtomTripletsFingerprints.pl -a DREIDINGAtomTypes + -r SampleTATFP -o Sample.sdf + + 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: + + % TopologicalAtomTripletsFingerprints.pl -a EStateAtomTypes + -r SampleTATFP -o Sample.sdf + + 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: + + % TopologicalAtomTripletsFingerprints.pl -a FunctionalClassAtomTypes + -r SampleTATFP -o Sample.sdf + + To generate topological atom triplets fingerprints corresponding to bond + distances from 1 through 10 using DREIDING atom types in + IDsAndValuesString format and create a SampleTATFP.csv file containing + sequential compound IDs along with fingerprints vector strings data, + type: + + % TopologicalAtomTripletsFingerprints.pl -a DREIDINGAtomTypes + -r SampleTATFP -o Sample.sdf + + To generate topological atom triplets fingerprints corresponding to bond + distances from 1 through 10 using MM94 atom types in IDsAndValuesString + format and create a SampleTATFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % TopologicalAtomTripletsFingerprints.pl -a MMFF94AtomTypes + -r SampleTATFP -o Sample.sdf + + 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: + + % TopologicalAtomTripletsFingerprints.pl -a SLogPAtomTypes + -r SampleTATFP -o Sample.sdf + + To generate topological atom triplets fingerprints corresponding to bond + distances from 1 through 10 using SYBYL atom types in IDsAndValuesString + format and create a SampleTATFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % TopologicalAtomTripletsFingerprints.pl -a SYBYLAtomTypes + -r SampleTATFP -o Sample.sdf + + To generate topological atom triplets fingerprints corresponding to bond + distances from 1 through 10 using TPSA atom types in IDsAndValuesString + format and create a SampleTATFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % TopologicalAtomTripletsFingerprints.pl -a TPSAAtomTypes + -r SampleTATFP -o Sample.sdf + + To generate topological atom triplets fingerprints corresponding to bond + distances from 1 through 10 using UFF atom types in IDsAndValuesString + format and create a SampleTATFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % TopologicalAtomTripletsFingerprints.pl -a UFFAtomTypes + -r SampleTATFP -o Sample.sdf + + 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: + + % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes + --MinDistance 1 --MaxDistance 6 -r SampleTATFP -o Sample.sdf + + To generate topological atom triplets fingerprints corresponding to bond + distances from 1 through 10 using only AS,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: + + % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes + --AtomicInvariantsToUse "AS,X" --MinDistance 1 --MaxDistance 6 + -r SampleTATFP -o Sample.sdf + + 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 ID from molecule name line along with fingerprints vector + strings data, type: + + % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode MolName + -r SampleTATFP -o Sample.sdf + + 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: + + % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID + Mol_ID -r SampleTATFP -o Sample.sdf + + 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 ID using combination of molecule name line and an explicit + compound prefix along with fingerprints vector strings data, type: + + % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTATFP -o Sample.sdf + + 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: + + % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode Specify --DataFields Mol_ID -r SampleTATFP + -o Sample.sdf + + 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: + + % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode Common -r SampleTATFP -o Sample.sdf + + 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 CSV file + along with fingerprints data, type: + + % TopologicalAtomTripletsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode All --output all -r SampleTATFP + -o Sample.sdf + +AUTHOR + Manish Sud <msud@san.rr.com> + +SEE ALSO + InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, + AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl, + MACCSKeysFingerprints.pl, PathLengthFingerprints.pl, + TopologicalAtomTorsionsFingerprints.pl, + TopologicalPharmacophoreAtomPairsFingerprints.pl, + TopologicalPharmacophoreAtomTripletsFingerprints.pl + +COPYRIGHT + Copyright (C) 2015 Manish Sud. All rights reserved. + + This file is part of MayaChemTools. + + MayaChemTools is free software; you can redistribute it and/or modify it + under the terms of the GNU Lesser General Public License as published by + the Free Software Foundation; either version 3 of the License, or (at + your option) any later version. +