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diff docs/scripts/txt/TopologicalPharmacophoreAtomTripletsFingerprints.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/TopologicalPharmacophoreAtomTripletsFingerprints.txt Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,657 @@ +NAME + TopologicalPharmacophoreAtomTripletsFingerprints.pl - Generate + topological pharmacophore atom triplets fingerprints for SD files + +SYNOPSIS + TopologicalPharmacophoreAtomTripletsFingerprints.pl SDFile(s)... + + TopologicalPharmacophoreAtomTripletsFingerprints.pl [--AromaticityModel + *AromaticityModelType*] [--AtomTripletsSetSizeToUse *ArbitrarySize | + FixedSize*] [-a, --AtomTypesToUse *"AtomType1, AtomType2..."*] + [--AtomTypesWeight *"AtomType1, Weight1, AtomType2, Weight2..."*] + [--CompoundID *DataFieldName or LabelPrefixString*] [--CompoundIDLabel + *text*] [--CompoundIDMode] [--DataFields *"FieldLabel1, + FieldLabel2,..."*] [-d, --DataFieldsMode *All | Common | Specify | + CompoundID*] [--DistanceBinSize *number*] [-f, --Filter *Yes | No*] + [--FingerprintsLabelMode *FingerprintsLabelOnly | + FingerprintsLabelWithIDs*] [--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 pharmacophore atom triplets fingerprints [ Ref 66, + Ref 68-71 ] 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. + + Based on the values specified for --AtomTypesToUse, pharmacophore atom + types are assigned to all non-hydrogen atoms in a molecule and a + distance matrix is generated. Using --MinDistance, --MaxDistance, and + --DistanceBinSize values, a binned distance matrix is generated with + lower bound on the distance bin as the distance in distance matrix; the + lower bound on the distance bin is also used as the distance between + atom pairs for generation of atom triplet identifiers. + + A pharmacophore atom triplets basis set is generated for all unique atom + triplets constituting atom pairs binned distances between --MinDistance + and --MaxDistance. The value of --UseTriangleInequality determines + whether the triangle inequality test is applied during generation of + atom triplets basis set. The lower distance bound, along with specified + pharmacophore types, is used during generation of atom triplet IDs. + + Let: + + P = Valid pharmacophore atom type + + Px = Pharmacophore atom x + Py = Pharmacophore atom y + Pz = Pharmacophore atom z + + Dmin = Minimum distance corresponding to number of bonds between two atoms + Dmax = Maximum distance corresponding to number of bonds between two atoms + D = Distance corresponding to number of bonds between two atom + + Bsize = Distance bin size + Nbins = Number of distance bins + + Dxy = Distance or lower bound of binned distance between Px and Py + Dxz = Distance or lower bound of binned distance between Px and Pz + Dyz = Distance or lower bound of binned distance between Py and Pz + + Then: + + PxDyz-PyDxz-PzDxy = Pharmacophore atom triplet IDs for atom types Px, + Py, and Pz + + For example: H1-H1-H1, H2-HBA-H2 and so on + + For default values of Dmin = 1 , Dmax = 10 and Bsize = 2: + + the number of distance bins, Nbins = 5, are: + + [1, 2] [3, 4] [5, 6] [7, 8] [9 10] + + and atom triplet basis set size is 2692. + + Atom triplet basis set size for various values of Dmin, Dmax and Bsize in + conjunction with usage of triangle inequality is: + + Dmin Dmax Bsize UseTriangleInequality TripletBasisSetSize + 1 10 2 No 4960 + 1 10 2 Yes 2692 [ Default ] + 2 12 2 No 8436 + 2 12 2 Yes 4494 + + Using binned distance matrix and pharmacohore atom types, occurrence of + unique pharmacohore atom triplets is counted. + + The final pharmacophore atom triples count along with atom pair + identifiers involving all non-hydrogen atoms constitute pharmacophore + topological atom triplets fingerprints of the molecule. + + For *ArbitrarySize* value of --AtomTripletsSetSizeToUse option, the + fingerprint vector correspond to only those topological pharmacophore + atom triplets which are present and have non-zero count. However, for + *FixedSize* value of --AtomTripletsSetSizeToUse option, the fingerprint + vector contains all possible valid topological pharmacophore atom + triplets with both zero and non-zero count values. + + Example of *SD* file containing topological pharmacophore atom triplets + fingerprints string data: + + ... ... + ... ... + $$$$ + ... ... + ... ... + ... ... + 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + ... ... + 2 3 1 0 0 0 0 + ... ... + M END + > <CmpdID> + Cmpd1 + + > <TopologicalPharmacophoreAtomTripletsFingerprints> + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize: + MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1- + Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1 + -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1- + HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...; + 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23 + 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1 + 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ... + + $$$$ + ... ... + ... ... + + Example of *FP* file containing topological pharmacophore atom triplets + fingerprints string data: + + # + # Package = MayaChemTools 7.4 + # Release Date = Oct 21, 2010 + # + # TimeStamp = Fri Mar 11 15:38:58 2011 + # + # FingerprintsStringType = FingerprintsVector + # + # Description = TopologicalPharmacophoreAtomTriplets:ArbitrarySize:M... + # VectorStringFormat = IDsAndValuesString + # VectorValuesType = NumericalValues + # + Cmpd1 696;Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1...;;46 106... + Cmpd2 251;H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-H1-NI1...;4 1 3 1 1 2 2... + ... ... + ... .. + + Example of CSV *Text* file containing topological pharmacophore atom + triplets fingerprints string data: + + "CompoundID","TopologicalPharmacophoreAtomTripletsFingerprints" + "Cmpd1","FingerprintsVector;TopologicalPharmacophoreAtomTriplets:Arbitr + arySize:MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesStri + ng;Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HB + A1 Ar1-H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA + 1 H1-HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 A...; + 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23 + 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1 + 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ... + ... ... + ... ... + + The current release of MayaChemTools generates the following types of + topological pharmacophore atom triplets fingerprints vector strings: + + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize: + MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1- + Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1 + -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1- + HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...; + 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23 + 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1 + 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ... + + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD + istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106 + 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0 + 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26 + 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0 + 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ... + + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD + istance1:MaxDistance10;2692;OrderedNumericalValues;IDsAndValuesString; + Ar1-Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-Ar1-NI1 Ar1-Ar1-P + I1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1-H1-HBD1 Ar1-H1-NI1 Ar1-H1-PI1 Ar1-HBA1-HB + A1 Ar1-HBA1-HBD1 Ar1-HBA1-NI1 Ar1-HBA1-PI1 Ar1-HBD1-HBD1 Ar1-HBD1-...; + 46 106 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 + 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 + 132 26 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 ... + +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. + + --AtomTripletsSetSizeToUse *ArbitrarySize | FixedSize* + Atom triplets set size to use during generation of topological + pharmacophore atom triplets fingerprints. + + Possible values: *ArbitrarySize | FixedSize*; Default value: + *ArbitrarySize*. + + For *ArbitrarySize* value of --AtomTripletsSetSizeToUse option, the + fingerprint vector correspond to only those topological + pharmacophore atom triplets which are present and have non-zero + count. However, for *FixedSize* value of --AtomTripletsSetSizeToUse + option, the fingerprint vector contains all possible valid + topological pharmacophore atom triplets with both zero and non-zero + count values. + + -a, --AtomTypesToUse *"AtomType1,AtomType2,..."* + Pharmacophore atom types to use during generation of topological + phramacophore atom triplets. It's a list of comma separated valid + pharmacophore atom types. + + Possible values for pharmacophore atom types are: *Ar, CA, H, HBA, + HBD, Hal, NI, PI, RA*. Default value [ Ref 71 ] : + *HBD,HBA,PI,NI,H,Ar*. + + The pharmacophore atom types abbreviations correspond to: + + HBD: HydrogenBondDonor + HBA: HydrogenBondAcceptor + PI : PositivelyIonizable + NI : NegativelyIonizable + Ar : Aromatic + Hal : Halogen + H : Hydrophobic + RA : RingAtom + CA : ChainAtom + + *AtomTypes::FunctionalClassAtomTypes* module is used to assign + pharmacophore 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*. + + --DistanceBinSize *number* + Distance bin size used to bin distances between atom pairs in atom + triplets. Default value: *2*. Valid values: positive integers. + + For default --MinDistance and --MaxDistance values of 1 and 10 with + --DistanceBinSize of 2 [ Ref 70 ], the following 5 distance bins are + generated: + + [1, 2] [3, 4] [5, 6] [7, 8] [9 10] + + The lower distance bound on the distance bin is uses to bin the + distance between atom pairs in atom triplets. So in the previous + example, atom pairs with distances 1 and 2 fall in first distance + bin, atom pairs with distances 3 and 4 fall in second distance bin + and so on. + + In order to distribute distance bins of equal size, the last bin is + allowed to go past --MaxDistance by up to distance bin size. For + example, --MinDistance and --MaxDistance values of 2 and 10 with + --DistanceBinSize of 2 generates the following 6 distance bins: + + [2, 3] [4, 5] [6, 7] [8, 9] [10 11] + + -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. + + --FingerprintsLabelMode *FingerprintsLabelOnly | + FingerprintsLabelWithIDs* + Specify how fingerprints label is generated in conjunction with + --FingerprintsLabel option value: use fingerprints label generated + only by --FingerprintsLabel option value or append topological atom + pair count value IDs to --FingerprintsLabel option value. + + Possible values: *FingerprintsLabelOnly | FingerprintsLabelWithIDs*. + Default value: *FingerprintsLabelOnly*. + + Topological atom pairs IDs appended to --FingerprintsLabel value + during *FingerprintsLabelWithIDs* values of --FingerprintsLabelMode + correspond to atom pair count values in fingerprint vector string. + + *FingerprintsLabelWithIDs* value of --FingerprintsLabelMode is + ignored during *ArbitrarySize* value of --AtomTripletsSetSizeToUse + option and topological atom triplets IDs not appended to the label. + + --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: *TopologicalPharmacophoreAtomTripletsFingerprints*. + + -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 corresponding to atom + triplets for generating topological pharmacophore atom triplets. + Default value: *1*. Valid values: positive integers and less than + --MaxDistance. + + --MaxDistance *number* + Maximum bond distance between atom pairs corresponding to atom + triplets for generating topological pharmacophore 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><TopologicalPharmacophoreAtomTripletsFP>.<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 basis set generation. Possible values: *Yes or No*. + Default value: *Yes*. + + 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 PxDyz-PyDxz-PzDxy 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 *ValuesString, 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: + *ValuesString, IDsAndValuesString | IDsAndValuesPairsString | + ValuesAndIDsString | ValuesAndIDsPairsString*. Defaultvalue: + *ValuesString*. + + Default value during *FixedSize* value of --AtomTripletsSetSizeToUse + option: *ValuesString*. Default value during *ArbitrarySize* value + of --AtomTripletsSetSizeToUse option: *IDsAndValuesString*. + + *ValuesString* option value is not allowed for *ArbitrarySize* value + of --AtomTripletsSetSizeToUse option. + + Examples: + + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:ArbitrarySize: + MinDistance1:MaxDistance10;696;NumericalValues;IDsAndValuesString;Ar1- + Ar1-Ar1 Ar1-Ar1-H1 Ar1-Ar1-HBA1 Ar1-Ar1-HBD1 Ar1-H1-H1 Ar1-H1-HBA1 Ar1 + -H1-HBD1 Ar1-HBA1-HBD1 H1-H1-H1 H1-H1-HBA1 H1-H1-HBD1 H1-HBA1-HBA1 H1- + HBA1-HBD1 H1-HBA1-NI1 H1-HBD1-NI1 HBA1-HBA1-NI1 HBA1-HBD1-NI1 Ar1-...; + 46 106 8 3 83 11 4 1 21 5 3 1 2 2 1 1 1 100 101 18 11 145 132 26 14 23 + 28 3 3 5 4 61 45 10 4 16 20 7 5 1 3 4 5 3 1 1 1 1 5 4 2 1 2 2 2 1 1 1 + 119 123 24 15 185 202 41 25 22 17 3 5 85 95 18 11 23 17 3 1 1 6 4 ... + + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD + istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesString;46 106 + 8 3 0 0 83 11 4 0 0 0 1 0 0 0 0 0 0 0 0 21 5 3 0 0 1 2 2 0 0 1 0 0 0 + 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 101 18 11 0 0 145 132 26 + 14 0 0 23 28 3 3 0 0 5 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 61 45 10 4 0 + 0 16 20 7 5 1 0 3 4 5 3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 5 ... + + FingerprintsVector;TopologicalPharmacophoreAtomTriplets:FixedSize:MinD + istance1:MaxDistance10;2692;OrderedNumericalValues;ValuesAndIDsPairsSt + ring;46 Ar1-Ar1-Ar1 106 Ar1-Ar1-H1 8 Ar1-Ar1-HBA1 3 Ar1-Ar1-HBD1 0 Ar1 + -Ar1-NI1 0 Ar1-Ar1-PI1 83 Ar1-H1-H1 11 Ar1-H1-HBA1 4 Ar1-H1-HBD1 0 Ar1 + -H1-NI1 0 Ar1-H1-PI1 0 Ar1-HBA1-HBA1 1 Ar1-HBA1-HBD1 0 Ar1-HBA1-NI1 0 + Ar1-HBA1-PI1 0 Ar1-HBD1-HBD1 0 Ar1-HBD1-NI1 0 Ar1-HBD1-PI1 0 Ar1-NI... + + -w, --WorkingDir *DirName* + Location of working directory. Default value: current directory. + +EXAMPLES + To generate topological pharmacophore atom triplets fingerprints of + arbitrary size corresponding to 5 distance bins spanning distances from + 1 through 10 using default atoms with distances satisfying triangle + inequality and create a SampleTPATFP.csv file containing sequential + compound IDs along with fingerprints vector strings data in ValuesString + format, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl -r SampleTPATFP + -o Sample.sdf + + To generate topological pharmacophore atom triplets fingerprints of + fixed size corresponding to 5 distance bins spanning distances from 1 + through 10 using default atoms with distances satisfying triangle + inequality and create a SampleTPATFP.csv file containing sequential + compound IDs along with fingerprints vector strings data in ValuesString + format, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl + --AtomTripletsSetSizeToUse FixedSize -r SampleTPATFP -o Sample.sdf + + To generate topological pharmacophore atom triplets fingerprints of + arbitrary size corresponding to 5 distance bins spanning distances from + 1 through 10 using default atoms with distances satisfying triangle + inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and + SampleTPATFP.csv files with CSV file containing sequential compound IDs + along with fingerprints vector strings data in ValuesString format, + type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --output all + -r SampleTPATFP -o Sample.sdf + + To generate topological pharmacophore atom triplets fingerprints of + arbitrary size corresponding to 5 distance bins spanning distances from + 1 through 10 using default atoms with distances satisfying triangle + inequality and create a SampleTPATFP.csv file containing sequential + compound IDs along with fingerprints vector strings data in ValuesString + format and atom triplets IDs in the fingerprint data column label + starting with Fingerprints, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl + --FingerprintsLabelMode FingerprintsLabelWithIDs --FingerprintsLabel + Fingerprints -r SampleTPATFP -o Sample.sdf + + To generate topological pharmacophore atom triplets fingerprints of + arbitrary size corresponding to 5 distance bins spanning distances from + 1 through 10 using default atoms with distances not satisfying triangle + inequality and create a SampleTPATFP.csv file containing sequential + compound IDs along with fingerprints vector strings data in ValuesString + format, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl + --UseTriangleInequality No -r SampleTPATFP -o Sample.sdf + + To generate topological pharmacophore atom triplets fingerprints of + arbitrary size corresponding to 6 distance bins spanning distances from + 1 through 12 using default atoms with distances satisfying triangle + inequality and create a SampleTPATFP.csv file containing sequential + compound IDs along with fingerprints vector strings data in ValuesString + format, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl + --UseTriangleInequality Yes --MinDistance 1 --MaxDistance 12 + --DistanceBinSIze 2 -r SampleTPATFP -o Sample.sdf + + To generate topological pharmacophore atom triplets fingerprints of + arbitrary size corresponding to 6 distance bins spanning distances from + 1 through 12 using "HBD,HBA,PI, NI, H, Ar" atoms with distances + satisfying triangle inequality and create a SampleTPATFP.csv file + containing sequential compound IDs along with fingerprints vector + strings data in ValuesString format, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl + --AtomTypesToUse "HBD,HBA,PI,NI,H,Ar" --UseTriangleInequality Yes + --MinDistance 1 --MaxDistance 12 --DistanceBinSIze 2 + --VectorStringFormat ValuesString -r SampleTPATFP -o Sample.sdf + + To generate topological pharmacophore atom triplets fingerprints of + arbitrary size corresponding to 5 distance bins spanning distances from + 1 through 10 using default atoms with distances satisfying triangle + inequality and create a SampleTPATFP.csv file containing sequential + compound IDs from molecule name line along with fingerprints vector + strings data in ValuesString format, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode + CompoundID -CompoundIDMode MolName -r SampleTPATFP -o Sample.sdf + + To generate topological pharmacophore atom triplets fingerprints of + arbitrary size corresponding to 5 distance bins spanning distances from + 1 through 10 using default atoms with distances satisfying triangle + inequality and create a SampleTPATFP.csv file containing sequential + compound IDs using specified data field along with fingerprints vector + strings data in ValuesString format, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode + CompoundID -CompoundIDMode DataField --CompoundID Mol_ID + -r SampleTPATFP -o Sample.sdf + + To generate topological pharmacophore atom triplets fingerprints of + arbitrary size corresponding to 5 distance bins spanning distances from + 1 through 10 using default atoms with distances satisfying triangle + inequality and create a SampleTPATFP.csv file containing sequential + compound IDs using combination of molecule name line and an explicit + compound prefix along with fingerprints vector strings data, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode + CompoundID -CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleSampleTPATFP + -o Sample.sdf + + To generate topological pharmacophore atom triplets fingerprints of + arbitrary size corresponding to 5 distance bins spanning distances from + 1 through 10 using default atoms with distances satisfying triangle + inequality and create a SampleTPATFP.csv file containing specific data + fields columns along with fingerprints vector strings data, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode + Specify --DataFields Mol_ID -r SampleTPATFP -o Sample.sdf + + To generate topological pharmacophore atom triplets fingerprints of + arbitrary size corresponding to 5 distance bins spanning distances from + 1 through 10 using default atoms with distances satisfying triangle + inequality and create a SampleTPATFP.csv file containing common data + fields columns along with fingerprints vector strings data, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode + Common -r SampleTPATFP -o Sample.sdf + + To generate topological pharmacophore atom triplets fingerprints of + arbitrary size corresponding to 5 distance bins spanning distances from + 1 through 10 using default atoms with distances satisfying triangle + inequality and create SampleTPATFP.sdf, SampleTPATFP.fpf and + SampleTPATFP.csv files containing all data fields columns in CSV file + along with fingerprints data, type: + + % TopologicalPharmacophoreAtomTripletsFingerprints.pl --DataFieldsMode + All --output all -r SampleTPATFP -o Sample.sdf + +AUTHOR + Manish Sud <msud@san.rr.com> + +SEE ALSO + InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, + AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl, + MACCSKeysFingerprints.pl, PathLengthFingerprints.pl, + TopologicalAtomPairsFingerprints.pl, + TopologicalAtomTorsionsFingerprints.pl, + TopologicalPharmacophoreAtomPairsFingerprints.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. +