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diff docs/scripts/txt/TopologicalAtomPairsFingerprints.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/TopologicalAtomPairsFingerprints.txt Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,669 @@ +NAME + TopologicalAtomPairsFingerprints.pl - Generate topological atom pairs + fingerprints for SD files + +SYNOPSIS + TopologicalAtomPairsFingerprints.pl SDFile(s)... + + TopologicalAtomPairsFingerprints.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*] [-v, + --VectorStringFormat *ValuesString, IDsAndValuesString | + IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString*] + [-w, --WorkingDir dirname] SDFile(s)... + +DESCRIPTION + Generate topological atom pairs fingerprints [ Ref 57, Ref 59, Ref 72 ] + 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 pairs 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 pair identifier is generated for each unique atom + pair; the format of the atom pair identifier is: + + <AtomType1>-D<n>-<AtomType2> + + AtomType1, AtomType2: Atom types assigned to atom1 and atom2 + D: Distance between atom1 and atom2 + + where AtomType1 <= AtomType2 + + The atom pair identifiers for all unique atom pairs corresponding to + non-hydrogen atoms constitute topological atom pairs fingerprints of the + molecule. + + Example of *SD* file containing topological atom pairs fingerprints + string data: + + ... ... + ... ... + $$$$ + ... ... + ... ... + ... ... + 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + ... ... + 2 3 1 0 0 0 0 + ... ... + M END + > <CmpdID> + Cmpd1 + + > <TopologicalAtomPairsFingerprints> + FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi + stance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1.H + 3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.H1 + C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-C.X2...; + 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1 + 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1 ... + + $$$$ + ... ... + ... ... + + Example of *FP* file containing topological atom pairs fingerprints + string data: + + # + # 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... + ... ... + ... .. + + Example of CSV *Text* file containing topological atom pairs + fingerprints string data: + + "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 ... + ... ... + ... ... + + The current release of MayaChemTools generates the following types of + topological atom pairs fingerprints vector strings: + + 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-... + +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 pairs 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 | both* 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 | + both* 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: *TopologicalAtomPairsFingerprints*. + + -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 pairs for generating topological + atom pairs. Default value: *1*. Valid values: positive integers and + less than --MaxDistance. + + --MaxDistance *number* + Maximum bond distance between atom pairs for generating topological + atom pairs. 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><TopologicalAtomPairsFP>.<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. + + -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;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... + + -w, --WorkingDir *DirName* + Location of working directory. Default value: current directory. + +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: + + % TopologicalAtomPairsFingerprints.pl -r SampleTAPFP -o Sample.sdf + + 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 CSV file + along with fingerprints vector strings data, type: + + % TopologicalAtomPairsFingerprints.pl --output all -r SampleTAPFP + -o Sample.sdf + + To generate topological atom pairs fingerprints corresponding to bond + distances from 1 through 10 using DREIDING atom types in + IDsAndValuesString format and create a SampleTAPFP.csv file containing + sequential compound IDs along with fingerprints vector strings data, + type: + + % TopologicalAtomPairsFingerprints.pl -a DREIDINGAtomTypes + -r SampleTAPFP -o Sample.sdf + + 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: + + % TopologicalAtomPairsFingerprints.pl -a EStateAtomTypes + -r SampleTAPFP -o Sample.sdf + + To generate topological atom pairs fingerprints corresponding to bond + distances from 1 through 10 using DREIDING atom types in + IDsAndValuesString format and create a SampleTAPFP.csv file containing + sequential compound IDs along with fingerprints vector strings data, + type: + + % TopologicalAtomPairsFingerprints.pl -a DREIDINGAtomTypes + -r SampleTAPFP -o Sample.sdf + + 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: + + % TopologicalAtomPairsFingerprints.pl -a FunctionalClassAtomTypes + -r SampleTAPFP -o Sample.sdf + + To generate topological atom pairs fingerprints corresponding to bond + distances from 1 through 10 using MMFF94 atom types in + IDsAndValuesString format and create a SampleTAPFP.csv file containing + sequential compound IDs along with fingerprints vector strings data, + type: + + % TopologicalAtomPairsFingerprints.pl -a MMFF94AtomTypes + -r SampleTAPFP -o Sample.sdf + + 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: + + % TopologicalAtomPairsFingerprints.pl -a SLogPAtomTypes + -r SampleTAPFP -o Sample.sdf + + To generate topological atom pairs fingerprints corresponding to bond + distances from 1 through 10 using SYBYL atom types in IDsAndValuesString + format and create a SampleTAPFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % TopologicalAtomPairsFingerprints.pl -a SYBYLAtomTypes + -r SampleTAPFP -o Sample.sdf + + To generate topological atom pairs fingerprints corresponding to bond + distances from 1 through 10 using TPSA atom types in IDsAndValuesString + format and create a SampleTAPFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % TopologicalAtomPairsFingerprints.pl -a TPSAAtomTypes + -r SampleTAPFP -o Sample.sdf + + To generate topological atom pairs fingerprints corresponding to bond + distances from 1 through 10 using UFF atom types in IDsAndValuesString + format and create a SampleTAPFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % TopologicalAtomPairsFingerprints.pl -a UFFAtomTypes + -r SampleTAPFP -o Sample.sdf + + 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: + + % TopologicalAtomPairsFingerprints.pl --VectorStringFormat + IDsAndValuesPairsString -r SampleTAPFP -o Sample.sdf + + 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: + + % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes + --MinDistance 1 --MaxDistance 6 -r SampleTAPFP -o Sample.sdf + + To generate topological atom pairs fingerprints corresponding to bond + distances from 1 through 10 using only AS,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: + + % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes + --AtomicInvariantsToUse "AS,X" --MinDistance 1 --MaxDistance 6 + -r SampleTAPFP -o Sample.sdf + + 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 ID from molecule name line along with fingerprints vector + strings data, type: + + % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode MolName + -r SampleTAPFP -o Sample.sdf + + 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: + + % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID + Mol_ID -r SampleTAPFP -o Sample.sdf + + 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 ID using combination of molecule name line and an explicit + compound prefix along with fingerprints vector strings data, type: + + % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTAPFP -o Sample.sdf + + 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: + + % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode Specify --DataFields Mol_ID -r SampleTAPFP + -o Sample.sdf + + 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: + + % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode Common -r SampleTAPFP -o Sample.sdf + + 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 CSV file + along with fingerprints data, type: + + % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode All --output all -r SampleTAPFP + -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. +