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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/TopologicalPharmacophoreAtomPairsFingerprints.txt Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,710 @@ +NAME + TopologicalPharmacophoreAtomPairsFingerprints.pl - Generate topological + pharmacophore atom pairs fingerprints for SD files + +SYNOPSIS + TopologicalPharmacophoreAtomPairsFingerprints.pl SDFile(s)... + + TopologicalPharmacophoreAtomPairsFingerprints.pl [--AromaticityModel + *AromaticityModelType*] [--AtomPairsSetSizeToUse *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*] [-f, --Filter *Yes | No*] [--FingerprintsLabelMode + *FingerprintsLabelOnly | FingerprintsLabelWithIDs*] [--FingerprintsLabel + *text*] [--FuzzifyAtomPairsCount *Yes | No*] [--FuzzificationMode + *FuzzyBinning | FuzzyBinSmoothing*] [--FuzzificationMethodology + *FuzzyBinning | FuzzyBinSmoothing*] [--FuzzFactor *number*] [-h, --help] + [-k, --KeepLargestComponent *Yes | No*] [--MinDistance *number*] + [--MaxDistance *number*] [-n, --NormalizationMethodology *None | + ByHeavyAtomsCount | ByAtomTypesCount*] [--OutDelim *comma | tab | + semicolon*] [--output *SD | FP | text | all*] [-o, --overwrite] [-q, + --quote *Yes | No*] [-r, --root *RootName*] [--ValuesPrecision *number*] + [-v, --VectorStringFormat *ValuesString, IDsAndValuesString | + IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString*] + [-w, --WorkingDir dirname] SDFile(s)... + +DESCRIPTION + Generate topological pharmacophore atom pairs fingerprints [ Ref 60-62, + Ref 65, Ref 68 ] 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. A pharmacophore atom pairs basis set is + initialized for all unique possible pairs within --MinDistance and + --MaxDistance range. + + Let: + + P = Valid pharmacophore atom type + + Px = Pharmacophore atom type x + Py = Pharmacophore atom type y + + 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 atoms + + Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at + distance Dn + + P = Number of pharmacophore atom types to consider + PPDn = Number of possible unique pharmacophore atom pairs at a distance Dn + + PPT = Total number of possible pharmacophore atom pairs at all distances + between Dmin and Dmax + + Then: + + PPD = (P * (P - 1))/2 + P + + PPT = ((Dmax - Dmin) + 1) * ((P * (P - 1))/2 + P) + = ((Dmax - Dmin) + 1) * PPD + + So for default values of Dmin = 1, Dmax = 10 and P = 5, + + PPD = (5 * (5 - 1))/2 + 5 = 15 + PPT = ((10 - 1) + 1) * 15 = 150 + + The pharmacophore atom pairs bais set includes 150 values. + + The atom pair IDs correspond to: + + Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at + distance Dn + + For example: H-D1-H, H-D2-HBA, PI-D5-PI and so on + + Using distance matrix and pharmacohore atom types, occurrence of unique + pharmacohore atom pairs is counted. The contribution of each atom type + to atom pair interaction is optionally weighted by specified + --AtomTypesWeight before assigning its count to appropriate distance + bin. Based on --NormalizationMethodology option, pharmacophore atom + pairs count is optionally normalized. Additionally, pharmacohore atom + pairs count is optionally fuzzified before or after the normalization + controlled by values of --FuzzifyAtomPairsCount, --FuzzificationMode, + --FuzzificationMethodology and --FuzzFactor options. + + The final pharmacophore atom pairs count along with atom pair + identifiers involving all non-hydrogen atoms, with optional + normalization and fuzzification, constitute pharmacophore topological + atom pairs fingerprints of the molecule. + + For *ArbitrarySize* value of --AtomPairsSetSizeToUse option, the + fingerprint vector correspond to only those topological pharmacophore + atom pairs which are present and have non-zero count. However, for + *FixedSize* value of --AtomPairsSetSizeToUse option, the fingerprint + vector contains all possible valid topological pharmacophore atom pairs + with both zero and non-zero count values. + + Example of *SD* file containing topological pharmacophore atom pairs + fingerprints string data: + + ... ... + ... ... + $$$$ + ... ... + ... ... + ... ... + 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + ... ... + 2 3 1 0 0 0 0 + ... ... + M END + > <CmpdID> + Cmpd1 + + > <TopologicalPharmacophoreAtomPairsFingerprints> + FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min + Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H + -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2- + HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D...; + 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 3 + 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1 + + $$$$ + ... ... + ... ... + + Example of *FP* file containing topological pharmacophore atom pairs + fingerprints string data: + + # + # Package = MayaChemTools 7.4 + # Release Date = Oct 21, 2010 + # + # TimeStamp = Fri Mar 11 15:32:48 2011 + # + # FingerprintsStringType = FingerprintsVector + # + # Description = TopologicalPharmacophoreAtomPairs:ArbitrarySize:MinDistance1:MaxDistance10 + # VectorStringFormat = IDsAndValuesString + # VectorValuesType = NumericalValues + # + Cmpd1 54;H-D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA...;18 1 2... + Cmpd2 61;H-D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA...;5 1 2 ... + ... ... + ... .. + + Example of CSV *Text* file containing topological pharmacophore atom + pairs fingerprints string data: + + "CompoundID","TopologicalPharmacophoreAtomPairsFingerprints" + "Cmpd1","FingerprintsVector;TopologicalPharmacophoreAtomPairs:Arbitrary + Size:MinDistance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H + -D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA H + BA-D2-HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4...; + 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 3 + 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1" + ... ... + ... ... + + The current release of MayaChemTools generates the following types of + topological pharmacophore atom pairs fingerprints vector strings: + + FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min + Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H + -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2- + HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H + BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...; + 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 + 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1 + + FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist + ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0 + 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1 + 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0 + 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0 + 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18... + + FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist + ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H-D1 + -H H-D1-HBA H-D1-HBD H-D1-NI H-D1-PI HBA-D1-HBA HBA-D1-HBD HBA-D1-NI H + BA-D1-PI HBD-D1-HBD HBD-D1-NI HBD-D1-PI NI-D1-NI NI-D1-PI PI-D1-PI H-D + 2-H H-D2-HBA H-D2-HBD H-D2-NI H-D2-PI HBA-D2-HBA HBA-D2-HBD HBA-D2...; + 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 + 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 + 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 + +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. + + --AtomPairsSetSizeToUse *ArbitrarySize | FixedSize* + Atom pairs set size to use during generation of topological + pharmacophore atom pairs fingerprints. + + Possible values: *ArbitrarySize | FixedSize*; Default value: + *ArbitrarySize*. + + For *ArbitrarySize* value of --AtomPairsSetSizeToUse option, the + fingerprint vector correspond to only those topological + pharmacophore atom pairs which are present and have non-zero count. + However, for *FixedSize* value of --AtomPairsSetSizeToUse option, + the fingerprint vector contains all possible valid topological + pharmacophore atom pairs with both zero and non-zero count values. + + -a, --AtomTypesToUse *"AtomType1,AtomType2,..."* + Pharmacophore atom types to use during generation of topological + phramacophore atom pairs. 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 60-62 ] : + *HBD,HBA,PI,NI,H*. + + 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 + + --AtomTypesWeight *"AtomType1,Weight1,AtomType2,Weight2..."* + Weights of specified pharmacophore atom types to use during + calculation of their contribution to atom pair count. Default value: + *None*. Valid values: real numbers greater than 0. In general it's + comma delimited list of valid atom type and its weight. + + The weight values allow to increase the importance of specific + pharmacophore atom type in the generated fingerprints. A weight + value of 0 for an atom type eliminates its contribution to atom pair + count where as weight value of 2 doubles its contribution. + + --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. + + --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 --AtomPairsSetSizeToUse + option and topological atom pairs 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: *TopologicalPharmacophoreAtomPairsFingerprints*. + + --FuzzifyAtomPairsCount *Yes | No* + To fuzzify or not to fuzzify atom pairs count. Possible values: *Yes + or No*. Default value: *No*. + + --FuzzificationMode *BeforeNormalization | AfterNormalization* + When to fuzzify atom pairs count. Possible values: + *BeforeNormalization | AfterNormalizationYes*. Default value: + *AfterNormalization*. + + --FuzzificationMethodology *FuzzyBinning | FuzzyBinSmoothing* + How to fuzzify atom pairs count. Possible values: *FuzzyBinning | + FuzzyBinSmoothing*. Default value: *FuzzyBinning*. + + In conjunction with values for options --FuzzifyAtomPairsCount, + --FuzzificationMode and --FuzzFactor, --FuzzificationMethodology + option is used to fuzzify pharmacophore atom pairs count. + + Let: + + Px = Pharmacophore atom type x + Py = Pharmacophore atom type y + PPxy = Pharmacophore atom pair between atom type Px and Py + + PPxyDn = Pharmacophore atom pairs count between atom type Px and Py + at distance Dn + PPxyDn-1 = Pharmacophore atom pairs count between atom type Px and Py + at distance Dn - 1 + PPxyDn+1 = Pharmacophore atom pairs count between atom type Px and Py + at distance Dn + 1 + + FF = FuzzFactor for FuzzyBinning and FuzzyBinSmoothing + + Then: + + For *FuzzyBinning*: + + PPxyDn = PPxyDn (Unchanged) + + PPxyDn-1 = PPxyDn-1 + PPxyDn * FF + PPxyDn+1 = PPxyDn+1 + PPxyDn * FF + + For *FuzzyBinSmoothing*: + + PPxyDn = PPxyDn - PPxyDn * 2FF for Dmin < Dn < Dmax + PPxyDn = PPxyDn - PPxyDn * FF for Dn = Dmin or Dmax + + PPxyDn-1 = PPxyDn-1 + PPxyDn * FF + PPxyDn+1 = PPxyDn+1 + PPxyDn * FF + + In both fuzzification schemes, a value of 0 for FF implies no + fuzzification of occurrence counts. A value of 1 during + *FuzzyBinning* corresponds to maximum fuzzification of occurrence + counts; however, a value of 1 during *FuzzyBinSmoothing* ends up + completely distributing the value over the previous and next + distance bins. + + So for default value of --FuzzFactor (FF) 0.15, the occurrence count + of pharmacohore atom pairs at distance Dn during FuzzyBinning is + left unchanged and the counts at distances Dn -1 and Dn + 1 are + incremented by PPxyDn * 0.15. + + And during *FuzzyBinSmoothing* the occurrence counts at Distance Dn + is scaled back using multiplicative factor of (1 - 2*0.15) and the + occurrence counts at distances Dn -1 and Dn + 1 are incremented by + PPxyDn * 0.15. In otherwords, occurrence bin count is smoothed out + by distributing it over the previous and next distance value. + + --FuzzFactor *number* + Specify by how much to fuzzify atom pairs count. Default value: + *0.15*. Valid values: For *FuzzyBinning* value of + --FuzzificationMethodology option: *between 0 and 1.0*; For + *FuzzyBinSmoothing* value of --FuzzificationMethodology option: + *between 0 and 0.5*. + + -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 + pharmacophore atom pairs. Default value: *1*. Valid values: positive + integers including 0 and less than --MaxDistance. + + --MaxDistance *number* + Maximum bond distance between atom pairs for generating topological + pharmacophore atom pairs. Default value: *10*. Valid values: + positive integers and greater than --MinDistance. + + -n, --NormalizationMethodology *None | ByHeavyAtomsCount | + ByAtomTypesCount* + Normalization methodology to use for scaling the occurrence count of + pharmacophore atom pairs within specified distance range. Possible + values: *None, ByHeavyAtomsCount or ByAtomTypesCount*. Default + value: *None*. + + --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><TopologicalPharmacophoreAtomPairsFP>.<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. + + --ValuesPrecision *number* + Precision of atom pairs count real values which might be generated + after normalization or fuzzification. Default value: up to *2* + decimal places. Valid values: positive integers. + + -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*. + + Default value during *FixedSize* value of --AtomPairsSetSizeToUse + option: *ValuesString*. Default value during *ArbitrarySize* value + of --AtomPairsSetSizeToUse option: *IDsAndValuesString*. + + *ValuesString* option value is not allowed for *ArbitrarySize* value + of --AtomPairsSetSizeToUse option. + + Examples: + + FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min + Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H + -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2- + HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H + BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...; + 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 + 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1 + + FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist + ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0 + 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1 + 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0 + 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0 + 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18... + + FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist + ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H-D1 + -H H-D1-HBA H-D1-HBD H-D1-NI H-D1-PI HBA-D1-HBA HBA-D1-HBD HBA-D1-NI H + BA-D1-PI HBD-D1-HBD HBD-D1-NI HBD-D1-PI NI-D1-NI NI-D1-PI PI-D1-PI H-D + 2-H H-D2-HBA H-D2-HBD H-D2-NI H-D2-PI HBA-D2-HBA HBA-D2-HBD HBA-D2...; + 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 + 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 + 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 + + -w, --WorkingDir *DirName* + Location of working directory. Default value: current directory. + +EXAMPLES + To generate topological pharmacophore atom pairs fingerprints of + arbitrary size corresponding to distances from 1 through 10 using + default atom types with no weighting, normalization, and fuzzification + of atom pairs count and create a SampleTPAPFP.csv file containing + sequential compound IDs along with fingerprints vector strings data in + ValuesString format, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl -r SampleTPAPFP + -o Sample.sdf + + To generate topological pharmacophore atom pairs fingerprints of fixed + size corresponding to distances from 1 through 10 using default atom + types with no weighting, normalization, and fuzzification of atom pairs + count and create a SampleTPAPFP.csv file containing sequential compound + IDs along with fingerprints vector strings data in ValuesString format, + type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl + --AtomPairsSetSizeToUse FixedSize -r SampleTPAPFP-o Sample.sdf + + To generate topological pharmacophore atom pairs fingerprints of + arbitrary size corresponding to distances from 1 through 10 using + default atom types with no weighting, normalization, and fuzzification + of atom pairs count and create SampleTPAPFP.sdf, SampleTPAPFP.fpf and + SampleTPAPFP.csv files containing sequential compound IDs in CSV file + along with fingerprints vector strings data in ValuesString format, + type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --output all + -r SampleTPAPFP -o Sample.sdf + + To generate topological pharmacophore atom pairs fingerprints of + arbitrary size corresponding to distances from 1 through 10 using + default atom types with no weighting, normalization, and fuzzification + of atom pairs count and create a SampleTPAPFP.csv file containing + sequential compound IDs along with fingerprints vector strings data in + IDsAndValuesPairsString format, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --VectorStringFormat + IDsAndValuesPairsString -r SampleTPAPFP -o Sample.sdf + + To generate topological pharmacophore atom pairs fingerprints of + arbitrary size corresponding to distances from 1 through 6 using default + atom types with no weighting, normalization, and fuzzification of atom + pairs count and create a SampleTPAPFP.csv file containing sequential + compound IDs along with fingerprints vector strings data in ValuesString + format, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1 + -MaxDistance 6 -r SampleTPAPFP -o Sample.sdf + + To generate topological pharmacophore atom pairs fingerprints of + arbitrary size corresponding to distances from 1 through 10 using + "HBD,HBA,PI,NI" atom types with double the weighting for "HBD,HBA" and + normalization by HeavyAtomCount but no fuzzification of atom pairs count + and create a SampleTPAPFP.csv file containing sequential compound IDs + along with fingerprints vector strings data in ValuesString format, + type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1 + -MaxDistance 10 --AtomTypesToUse "HBD,HBA,PI, NI" --AtomTypesWeight + "HBD,2,HBA,2,PI,1,NI,1" --NormalizationMethodology ByHeavyAtomsCount + --FuzzifyAtomPairsCount No -r SampleTPAPFP -o Sample.sdf + + To generate topological pharmacophore atom pairs fingerprints of + arbitrary size corresponding to distances from 1 through 10 using + "HBD,HBA,PI,NI,H" atom types with no weighting of atom types and + normalization but with fuzzification of atom pairs count using + FuzzyBinning methodology with FuzzFactor value 0.15 and create a + SampleTPAPFP.csv file containing sequential compound IDs along with + fingerprints vector strings data in ValuesString format, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1 + --MaxDistance 10 --AtomTypesToUse "HBD,HBA,PI, NI,H" --AtomTypesWeight + "HBD,1,HBA,1,PI,1,NI,1,H,1" --NormalizationMethodology None + --FuzzifyAtomPairsCount Yes --FuzzificationMethodology FuzzyBinning + --FuzzFactor 0.5 -r SampleTPAPFP -o Sample.sdf + + To generate topological pharmacophore atom pairs fingerprints of + arbitrary size corresponding to distances distances from 1 through 10 + using default atom types with no weighting, normalization, and + fuzzification of atom pairs count and create a SampleTPAPFP.csv file + containing compound ID from molecule name line along with fingerprints + vector strings data, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode + CompoundID -CompoundIDMode MolName -r SampleTPAPFP -o Sample.sdf + + To generate topological pharmacophore atom pairs fingerprints of + arbitrary size corresponding to distances from 1 through 10 using + default atom types with no weighting, normalization, and fuzzification + of atom pairs count and create a SampleTPAPFP.csv file containing + compound IDs using specified data field along with fingerprints vector + strings data, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode + CompoundID -CompoundIDMode DataField --CompoundID Mol_ID + -r SampleTPAPFP -o Sample.sdf + + To generate topological pharmacophore atom pairs fingerprints of + arbitrary size corresponding to distances from 1 through 10 using + default atom types with no weighting, normalization, and fuzzification + of atom pairs count and create a SampleTPAPFP.csv file containing + compound ID using combination of molecule name line and an explicit + compound prefix along with fingerprints vector strings data, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode + CompoundID -CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTPAPFP -o Sample.sdf + + To generate topological pharmacophore atom pairs fingerprints of + arbitrary size corresponding to distances from 1 through 10 using + default atom types with no weighting, normalization, and fuzzification + of atom pairs count and create a SampleTPAPFP.csv file containing + specific data fields columns along with fingerprints vector strings + data, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode + Specify --DataFields Mol_ID -r SampleTPAPFP -o Sample.sdf + + To generate topological pharmacophore atom pairs fingerprints of + arbitrary size corresponding to distances from 1 through 10 using + default atom types with no weighting, normalization, and fuzzification + of atom pairs count and create a SampleTPAPFP.csv file containing common + data fields columns along with fingerprints vector strings data, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode + Common -r SampleTPAPFP -o Sample.sdf + + To generate topological pharmacophore atom pairs fingerprints of + arbitrary size corresponding to distances from 1 through 10 using + default atom types with no weighting, normalization, and fuzzification + of atom pairs count and create SampleTPAPFP.sdf, SampleTPAPFP.fpf, and + SampleTPAPFP.csv files containing all data fields columns in CSV file + along with fingerprints data, type: + + % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode + All --output all -r SampleTPAPFP -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, + 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. +