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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/PathLengthFingerprints.txt Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,911 @@ +NAME + PathLengthFingerprints.pl - Generate atom path length based fingerprints + for SD files + +SYNOPSIS + PathLengthFingerprints.pl SDFile(s)... + + PathLengthFingerprints.pl [--AromaticityModel *AromaticityModelType*] + [-a, --AtomIdentifierType *AtomicInvariantsAtomTypes*] + [--AtomicInvariantsToUse *"AtomicInvariant1,AtomicInvariant2..."*] + [--FunctionalClassesToUse *"FunctionalClass1,FunctionalClass2..."*] + [--BitsOrder *Ascending | Descending*] [-b, --BitStringFormat + *BinaryString | HexadecimalString*] [--CompoundID *DataFieldName or + LabelPrefixString*] [--CompoundIDLabel *text*] [--CompoundIDMode + *DataField | MolName | LabelPrefix | MolNameOrLabelPrefix*] + [--DataFields *"FieldLabel1,FieldLabel2,... "*] [-d, --DataFieldsMode + *All | Common | Specify | CompoundID*] [--DetectAromaticity *Yes | No*] + [-f, --Filter *Yes | No*] [--FingerprintsLabel *text*] [--fold *Yes | + No*] [--FoldedSize *number*] [-h, --help] [-i, --IgnoreHydrogens *Yes | + No*] [-k, --KeepLargestComponent *Yes | No*] [-m, --mode *PathLengthBits + | PathLengthCount*] [--MinPathLength *number*] [--MaxPathLength + *number*] [-n, --NumOfBitsToSetPerPath *number*] [--OutDelim *comma | + tab | semicolon*] [--output *SD | FP | text | all*] [-q, --quote *Yes | + No*] [-r, --root *RootName*] [-p, --PathMode *AtomPathsWithoutRings | + AtomPathsWithRings | AllAtomPathsWithoutRings | AllAtomPathsWithRings*] + [-s, --size *number*] [-u, --UseBondSymbols *Yes | No*] + [--UsePerlCoreRandom *Yes | No*] [--UseUniquePaths *Yes | No*] [-q, + --quote *Yes | No*] [-r, --root *RootName*] [-v, --VectorStringFormat + *IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | + ValuesAndIDsPairsString*] [-w, --WorkingDir dirname] SDFile(s)... + +DESCRIPTION + Generate atom path length fingerprints for *SDFile(s)* and create + appropriate SD, FP or CSV/TSV text file(s) containing fingerprints + bit-vector or 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 path length + fingerprints corresponding to following -a, --AtomIdentifierTypes: + + AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, + FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, + SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes + + Based on the values specified for -p, --PathMode, --MinPathLength and + --MaxPathLength, all appropriate atom paths are generated for each atom + in the molecule and collected in a list and the list is filtered to + remove any structurally duplicate paths as indicated by the value of + --UseUniquePaths option. + + For each atom path in the filtered atom paths list, an atom path string + is created using value of -a, --AtomIdentifierType and specified values + to use for a particular atom identifier type. Value of -u, + --UseBondSymbols controls whether bond order symbols are used during + generation of atom path string. For each atom path, only + lexicographically smaller atom path strings are kept. + + For *PathLengthBits* value of -m, --mode option, each atom path is + hashed to a 32 bit unsigned integer key using TextUtil::HashCode + function. Using the hash key as a seed for a random number generator, a + random integer value between 0 and --Size is used to set corresponding + bits in the fingerprint bit-vector string. Value of + --NumOfBitsToSetPerPath option controls the number of time a random + number is generated to set corresponding bits. + + For * PathLengthCount* value of -m, --mode option, the number of times + an atom path appears is tracked and a fingerprints count-string + corresponding to count of atom paths is generated. + + Example of *SD* file containing path length fingerprints string data: + + ... ... + ... ... + $$$$ + ... ... + ... ... + ... ... + 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + ... ... + 2 3 1 0 0 0 0 + ... ... + M END + > <CmpdID> + Cmpd1 + + > <PathLengthFingerprints> + FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt + h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66 + 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028 + 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462 + 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a + aa0660a11014a011d46 + + $$$$ + ... ... + ... ... + + Example of *FP* file containing path length fingerprints string data: + + # + # Package = MayaChemTools 7.4 + # ReleaseDate = Oct 21, 2010 + # + # TimeStamp = Mon Mar 7 15:14:01 2011 + # + # FingerprintsStringType = FingerprintsBitVector + # + # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:... + # Size = 1024 + # BitStringFormat = HexadecimalString + # BitsOrder = Ascending + # + Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510... + Cmpd2 000000249400840040100042011001001980410c000000001010088001120... + ... ... + ... .. + + Example of CSV *Text* file containing pathlength fingerprints string + data: + + "CompoundID","PathLengthFingerprints" + "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes + :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4 + 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030 + 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..." + ... ... + ... ... + + The current release of MayaChemTools generates the following types of + path length fingerprints bit-vector and vector strings: + + FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng + th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110 + 0100010101011000101001011100110001000010001001101000001001001001001000 + 0010110100000111001001000001001010100100100000000011000000101001011100 + 0010000001000101010100000100111100110111011011011000000010110111001101 + 0101100011000000010001000011000010100011101100001000001000100000000... + + FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng + th1:MaxLength8;1024;HexadecimalString;Ascending;48caa1315d82d91122b029 + 42861c9409a4208182d12015509767bd0867653604481a8b1288000056090583603078 + 9cedae54e26596889ab121309800900490515224208421502120a0dd9200509723ae89 + 00024181b86c0122821d4e4880c38620dab280824b455404009f082003d52c212b4e6d + 6ea05280140069c780290c43 + + FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength + 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2 + C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X + 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1 + 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO + 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C.... + + FingerprintsVector;PathLengthCount:DREIDINGAtomTypes:MinLength1:MaxLen + gth8;410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_ + 1 N_3 1 N_R 1 O_2 2 O_3 3 C_2=O_2 2 C_2C_3 1 C_2C_R 1 C_2N_3 1 C_2O_3 + 1 C_3C_3 7 C_3C_R 1 C_3N_R 1 C_3O_3 2 C_R:C_R 21 C_R:N_R 2 C_RC_R 2 C + _RF_ 1 C_RN_3 1 C_2C_3C_3 1 C_2C_R:C_R 2 C_2N_3C_R 1 C_3C_2=O_2 1 C_3C + _2O_3 1 C_3C_3C_3 5 C_3C_3C_R 2 C_3C_3N_R 1 C_3C_3O_3 4 C_3C_R:C_R ... + + FingerprintsVector;PathLengthCount:EStateAtomTypes:MinLength1:MaxLengt + h8;454;NumericalValues;IDsAndValuesPairsString;aaCH 14 aasC 8 aasN 1 d + O 2 dssC 2 sCH3 2 sF 1 sOH 3 ssCH2 4 ssNH 1 sssCH 3 aaCH:aaCH 10 aaCH: + aasC 8 aasC:aasC 3 aasC:aasN 2 aasCaasC 2 aasCdssC 1 aasCsF 1 aasCssNH + 1 aasCsssCH 1 aasNssCH2 1 dO=dssC 2 dssCsOH 1 dssCssCH2 1 dssCssNH 1 + sCH3sssCH 2 sOHsssCH 2 ssCH2ssCH2 1 ssCH2sssCH 4 aaCH:aaCH:aaCH 6 a... + + FingerprintsVector;PathLengthCount:FunctionalClassAtomTypes:MinLength1 + :MaxLength8;404;NumericalValues;IDsAndValuesPairsString;Ar 22 Ar.HBA 1 + HBA 2 HBA.HBD 3 HBD 1 Hal 1 NI 1 None 10 Ar.HBA:Ar 2 Ar.HBANone 1 Ar: + Ar 21 ArAr 2 ArHBD 1 ArHal 1 ArNone 2 HBA.HBDNI 1 HBA.HBDNone 2 HBA=NI + 1 HBA=None 1 HBDNone 1 NINone 1 NoneNone 7 Ar.HBA:Ar:Ar 2 Ar.HBA:ArAr + 1 Ar.HBA:ArNone 1 Ar.HBANoneNone 1 Ar:Ar.HBA:Ar 1 Ar:Ar.HBANone 2 ... + + FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt + h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1 + 8 COO 1 CR 9 F 1 N5 1 NC=O 1 O=CN 1 O=CO 1 OC=O 1 OR 2 C5A:C5B 2 C5A:N + 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1 + CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR + OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ... + + FingerprintsVector;PathLengthCount:SLogPAtomTypes:MinLength1:MaxLength + 8;518;NumericalValues;IDsAndValuesPairsString;C1 5 C10 1 C11 1 C14 1 C + 18 14 C20 4 C21 2 C22 1 C5 2 CS 2 F 1 N11 1 N4 1 O10 1 O2 3 O9 1 C10C1 + 1 C10N11 1 C11C1 2 C11C21 1 C14:C18 2 C14F 1 C18:C18 10 C18:C20 4 C18 + :C22 2 C1C5 1 C1CS 4 C20:C20 1 C20:C21 1 C20:N11 1 C20C20 2 C21:C21 1 + C21:N11 1 C21C5 1 C22N4 1 C5=O10 1 C5=O9 1 C5N4 1 C5O2 1 CSO2 2 C10... + + FingerprintsVector;PathLengthCount:SYBYLAtomTypes:MinLength1:MaxLength + 8;412;NumericalValues;IDsAndValuesPairsString;C.2 2 C.3 9 C.ar 22 F 1 + N.am 1 N.ar 1 O.2 1 O.3 2 O.co2 2 C.2=O.2 1 C.2=O.co2 1 C.2C.3 1 C.2C. + ar 1 C.2N.am 1 C.2O.co2 1 C.3C.3 7 C.3C.ar 1 C.3N.ar 1 C.3O.3 2 C.ar:C + .ar 21 C.ar:N.ar 2 C.arC.ar 2 C.arF 1 C.arN.am 1 C.2C.3C.3 1 C.2C.ar:C + .ar 2 C.2N.amC.ar 1 C.3C.2=O.co2 1 C.3C.2O.co2 1 C.3C.3C.3 5 C.3C.3... + + FingerprintsVector;PathLengthCount:TPSAAtomTypes:MinLength1:MaxLength8 + ;331;NumericalValues;IDsAndValuesPairsString;N21 1 N7 1 None 34 O3 2 O + 4 3 N21:None 2 N21None 1 N7None 2 None:None 21 None=O3 2 NoneNone 13 N + oneO4 3 N21:None:None 2 N21:NoneNone 2 N21NoneNone 1 N7None:None 2 N7N + one=O3 1 N7NoneNone 1 None:N21:None 1 None:N21None 2 None:None:None 20 + None:NoneNone 12 NoneN7None 1 NoneNone=O3 2 NoneNoneNone 8 NoneNon... + + FingerprintsVector;PathLengthCount:UFFAtomTypes:MinLength1:MaxLength8; + 410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_ 1 N_ + 3 1 N_R 1 O_2 2 O_3 3 C_2=O_2 2 C_2C_3 1 C_2C_R 1 C_2N_3 1 C_2O_3 1 C_ + 3C_3 7 C_3C_R 1 C_3N_R 1 C_3O_3 2 C_R:C_R 21 C_R:N_R 2 C_RC_R 2 C_RF_ + 1 C_RN_3 1 C_2C_3C_3 1 C_2C_R:C_R 2 C_2N_3C_R 1 C_3C_2=O_2 1 C_3C_2O_3 + 1 C_3C_3C_3 5 C_3C_3C_R 2 C_3C_3N_R 1 C_3C_3O_3 4 C_3C_R:C_R 1 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. + + This option is ignored during *No* value of --DetectAromaticity + option. + + -a, --AtomIdentifierType *AtomicInvariantsAtomTypes | DREIDINGAtomTypes + | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | + SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes* + Specify atom identifier type to use for assignment of atom types to + hydrogen and/or non-hydrogen atoms during calculation of atom types + fingerprints. Possible values in the current release are: + *AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, + FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, + SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*. Default value: + *AtomicInvariantsAtomTypes*. + + -a, --AtomIdentifierType *AtomicInvariantsAtomTypes | DREIDINGAtomTypes + | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | + SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes* + Specify atom identifier type to use during generation of atom path + strings corresponding to path length fingerprints. Possible values + in the current release are: *AtomicInvariantsAtomTypes, + DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, + MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, + UFFAtomTypes*. Default value: *AtomicInvariantsAtomTypes*. + + --AtomicInvariantsToUse *"AtomicInvariant1,AtomicInvariant2..."* + 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*. + + 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 + + Examples: + + Benzene: Using value of *AS* for --AtomicInvariantsToUse, *Yes* for + UseBondSymbols, and * AllAtomPathsWithRings* for -p, --PathMode, + atom path strings generated are: + + C C:C C:C:C C:C:C:C C:C:C:C:C C:C:C:C:C:C C:C:C:C:C:C:C + + And using *AS,X,BO* for --AtomicInvariantsToUse generates following + atom path strings: + + C.X2.BO3 C.X2.BO3:C.X2.BO3 C.X2.BO3:C.X2.BO3:C.X2.BO3 + C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3 + C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3 + C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3 + C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3 + + Urea: Using value of *AS* for --AtomicInvariantsToUse, *Yes* for + UseBondSymbols, and * AllAtomPathsWithRings* for -p, --PathMode, + atom path strings are: + + C N O C=O CN NC=O NCN + + And using *AS,X,BO* for --AtomicInvariantsToUse generates following + atom path strings: + + C.X3.BO4 N.X1.BO1 O.X1.BO2 C.X3.BO4=O.X1.BO2 + C.X3.BO4N.X1.BO1 N.X1.BO1C.X3.BO4=O.X1.BO2 + N.X1.BO1C.X3.BO4N.X1.BO1 + + --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 + + --BitsOrder *Ascending | Descending* + Bits order to use during generation of fingerprints bit-vector + string for *PathLengthBits* value of -m, --mode option. Possible + values: *Ascending, Descending*. Default: *Ascending*. + + *Ascending* bit order which corresponds to first bit in each byte as + the lowest bit as opposed to the highest bit. + + Internally, bits are stored in *Ascending* order using Perl vec + function. Regardless of machine order, big-endian or little-endian, + vec function always considers first string byte as the lowest byte + and first bit within each byte as the lowest bit. + + -b, --BitStringFormat *BinaryString | HexadecimalString* + Format of fingerprints bit-vector string data in output SD, FP or + CSV/TSV text file(s) specified by --output used during + *PathLengthBits* value of -m, --mode option. Possible values: + *BinaryString, HexadecimalString*. Default value: + *HexadecimalString*. + + *BinaryString* corresponds to an ASCII string containing 1s and 0s. + *HexadecimalString* contains bit values in ASCII hexadecimal format. + + Examples: + + FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng + th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110 + 0100010101011000101001011100110001000010001001101000001001001001001000 + 0010110100000111001001000001001010100100100000000011000000101001011100 + 0010000001000101010100000100111100110111011011011000000010110111001101 + 0101100011000000010001000011000010100011101100001000001000100000000... + + FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng + th1:MaxLength8;1024;HexadecimalString;Ascending;48caa1315d82d91122b029 + 42861c9409a4208182d12015509767bd0867653604481a8b1288000056090583603078 + 9cedae54e26596889ab121309800900490515224208421502120a0dd9200509723ae89 + 00024181b86c0122821d4e4880c38620dab280824b455404009f082003d52c212b4e6d + 6ea05280140069c780290c43 + + --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 FP or CSV/TSV text file(s) used + during *CompoundID* value of --DataFieldsMode option. Default: + *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: *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*. + + --DetectAromaticity *Yes | No* + Detect aromaticity before generating fingerprints. Possible values: + *Yes or No*. Default value: *Yes*. + + *No* --DetectAromaticity forces usage of atom and bond aromaticity + values from *SDFile(s)* and skips the step which detects and assigns + aromaticity. + + *No* --DetectAromaticity value is only allowed uring + *AtomicInvariantsAtomTypes* value of -a, --AtomIdentifierType + options; for all possible values -a, --AtomIdentifierType values, it + must be *Yes*. + + -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: *PathLenghFingerprints*. + + --fold *Yes | No* + Fold fingerprints to increase bit density during *PathLengthBits* + value of -m, --mode option. Possible values: *Yes or No*. Default + value: *No*. + + --FoldedSize *number* + Size of folded fingerprint during *PathLengthBits* value of -m, + --mode option. Default value: *256*. Valid values correspond to any + positive integer which is less than -s, --size and meets the + criteria for its value. + + Examples: + + 128 + 512 + + -h, --help + Print this help message + + -i, --IgnoreHydrogens *Yes | No* + Ignore hydrogens during fingerprints generation. Possible values: + *Yes or No*. Default value: *Yes*. + + For *yes* value of -i, --IgnoreHydrogens, any explicit hydrogens are + also used for generation of atoms path lengths and fingerprints; + implicit hydrogens are still ignored. + + -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. + + -m, --mode *PathLengthBits | PathLengthCount* + Specify type of path length fingerprints to generate for molecules + in *SDFile(s)*. Possible values: *PathLengthBits, PathLengthCount*. + Default value: *PathLengthBits*. + + For *PathLengthBits* value of -m, --mode option, a fingerprint + bit-vector string containing zeros and ones is generated and for + *PathLengthCount* value, a fingerprint vector string corresponding + to number of atom paths is generated. + + --MinPathLength *number* + Minimum atom path length to include in fingerprints. Default value: + *1*. Valid values: positive integers and less than --MaxPathLength. + Path length of 1 correspond to a path containing only one atom. + + --MaxPathLength *number* + Maximum atom path length to include in fingerprints. Default value: + *8*. Valid values: positive integers and greater than + --MinPathLength. + + -n, --NumOfBitsToSetPerPath *number* + Number of bits to set per path during generation of fingerprints + bit-vector string for *PathLengthBits* value of -m, --mode option. + Default value: *1*. Valid values: positive integers. + + --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. + + -p, --PathMode *AtomPathsWithoutRings | AtomPathsWithRings | + AllAtomPathsWithoutRings | AllAtomPathsWithRings* + Specify type of atom paths to use for generating pathlength + fingerprints for molecules in *SDFile(s)*. Possible + values:*AtomPathsWithoutRings, AtomPathsWithRings, + AllAtomPathsWithoutRings, AllAtomPathsWithRings*. Default value: + *AllAtomPathsWithRings*. + + For molecules with no rings, first two and last two options are + equivalent and generate same set of atom paths starting from each + atom with length between --MinPathLength and --MaxPathLength. + However, all these four options can result in the same set of final + atom paths for molecules containing fused, bridged or spiro rings. + + For molecules containing rings, atom paths starting from each atom + can be traversed in four different ways: + + *AtomPathsWithoutRings* - Atom paths containing no rings and without + sharing of bonds in traversed paths. + + *AtomPathsWithRings* - Atom paths containing rings and without any + sharing of bonds in traversed paths. + + *AllAtomPathsWithoutRings* - All possible atom paths containing no + rings and without any sharing of bonds in traversed paths. + + *AllAtomPathsWithRings* - All possible atom paths containing rings + and with sharing of bonds in traversed paths. + + Atom path traversal is terminated at the ring atom. + + Based on values specified for for -p, --PathMode, --MinPathLength + and --MaxPathLength, all appropriate atom paths are generated for + each atom in the molecule and collected in a list. + + For each atom path in the filtered atom paths list, an atom path + string is created using value of -a, --AtomIdentifierType and + specified values to use for a particular atom identifier type. Value + of -u, --UseBondSymbols controls whether bond order symbols are used + during generation of atom path string. Atom symbol corresponds to + element symbol and characters used to represent bond order are: *1 - + None; 2 - '='; 3 - '#'; 1.5 or aromatic - ':'; others: bond order + value*. By default, bond symbols are included in atom path strings. + Exclusion of bond symbols in atom path strings results in + fingerprints which correspond purely to atom paths without + considering bonds. + + UseUniquePaths controls the removal of structurally duplicate atom + path strings are removed from the list. + + For *PathLengthBits* value of -m, --mode option, each atom path is + hashed to a 32 bit unsigned integer key using TextUtil::HashCode + function. Using the hash key as a seed for a random number + generator, a random integer value between 0 and --Size is used to + set corresponding bits in the fingerprint bit-vector string. Value + of --NumOfBitsToSetPerPaths option controls the number of time a + random number is generated to set corresponding bits. + + For * PathLengthCount* value of -m, --mode option, the number of + times an atom path appears is tracked and a fingerprints + count-string corresponding to count of atom paths is generated. + + For molecule containing rings, combination of -p, --PathMode and + --UseBondSymbols allows generation of up to 8 different types of + atom path length strings: + + AllowSharedBonds AllowRings UseBondSymbols + + 0 0 1 - AtomPathsNoCyclesWithBondSymbols + 0 1 1 - AtomPathsWithCyclesWithBondSymbols + + 1 0 1 - AllAtomPathsNoCyclesWithBondSymbols + 1 1 1 - AllAtomPathsWithCyclesWithBondSymbols + [ DEFAULT ] + + 0 0 0 - AtomPathsNoCyclesNoBondSymbols + 0 1 0 - AtomPathsWithCyclesNoBondSymbols + + 1 0 0 - AllAtomPathsNoCyclesNoBondSymbols + 1 1 0 - AllAtomPathsWithCyclesNoWithBondSymbols + + Default atom path length fingerprints generation for molecules + containing rings with *AllAtomPathsWithRings* value for -p, + --PathMode, *Yes* value for --UseBondSymbols, *2* value for + --MinPathLength and *8* value for --MaxPathLength is the most time + consuming. Combinations of other options can substantially speed up + fingerprint generation for molecules containing complex ring + systems. + + Additionally, value for option -a, --AtomIdentifierType in + conjunction with corresponding specified values for atom types + changes the nature of atom path length strings and the fingerprints. + + -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><PathLengthFP>.<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. + + -s, --size *number* + Size of fingerprints. Default value: *1024*. Valid values correspond + to any positive integer which satisfies the following criteria: + power of 2, >= 32 and <= 2 ** 32. + + Examples: + + 256 + 512 + 2048 + + -u, --UseBondSymbols *Yes | No* + Specify whether to use bond symbols for atom paths during generation + of atom path strings. Possible values: *Yes or No*. Default value: + *Yes*. + + *No* value option for -u, --UseBondSymbols allows the generation of + fingerprints corresponding purely to atoms disregarding all bonds. + + --UsePerlCoreRandom *Yes | No* + Specify whether to use Perl CORE::rand or MayaChemTools + MathUtil::random function during random number generation for + setting bits in fingerprints bit-vector strings. Possible values: + *Yes or No*. Default value: *Yes*. + + *No* value option for --UsePerlCoreRandom allows the generation of + fingerprints bit-vector strings which are same across different + platforms. + + The random number generator implemented in MayaChemTools is a + variant of linear congruential generator (LCG) as described by + Miller et al. [ Ref 120 ]. It is also referred to as Lehmer random + number generator or Park-Miller random number generator. + + Unlike Perl's core random number generator function rand, the random + number generator implemented in MayaChemTools, MathUtil::random, + generates consistent random values across different platforms for a + specific random seed and leads to generation of portable + fingerprints bit-vector strings. + + --UseUniquePaths *Yes | No* + Specify whether to use structurally unique atom paths during + generation of atom path strings. Possible values: *Yes or No*. + Default value: *Yes*. + + *No* value option for --UseUniquePaths allows usage of all atom + paths generated by -p, --PathMode option value for generation of + atom path strings leading to duplicate path count during + *PathLengthCount* value of -m, --mode option. It doesn't change + fingerprint string generated during *PathLengthBits* value of -m, + --mode. + + For example, during *AllAtomPathsWithRings* value of -p, --PathMode + option, benzene has 12 linear paths of length 2 and 12 cyclic paths + length of 7, but only 6 linear paths of length 2 and 1 cyclic path + of length 7 are structurally unique. + + -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 used during + *PathLengthCount* value of -m, --mode option. Possible values: + *IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | + ValuesAndIDsPairsString*. Defaultvalue: *IDsAndValuesString*. + + Examples: + + FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength + 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2 + C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X + 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1 + 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO + 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C.... + + FingerprintsVector;PathLengthCount:EStateAtomTypes:MinLength1:MaxLengt + h8;454;NumericalValues;IDsAndValuesPairsString;aaCH 14 aasC 8 aasN 1 d + O 2 dssC 2 sCH3 2 sF 1 sOH 3 ssCH2 4 ssNH 1 sssCH 3 aaCH:aaCH 10 aaCH: + aasC 8 aasC:aasC 3 aasC:aasN 2 aasCaasC 2 aasCdssC 1 aasCsF 1 aasCssNH + 1 aasCsssCH 1 aasNssCH2 1 dO=dssC 2 dssCsOH 1 dssCssCH2 1 dssCssNH 1 + sCH3sssCH 2 sOHsssCH 2 ssCH2ssCH2 1 ssCH2sssCH 4 aaCH:aaCH:aaCH 6 a... + + -w, --WorkingDir *DirName* + Location of working directory. Default: current directory. + +EXAMPLES + To generate path length fingerprints corresponding to all unique paths + from length 1 through 8 in hexadecimal bit-vector string format of size + 1024 and create a SamplePLFPHex.csv file containing sequential compound + IDs along with fingerprints bit-vector strings data, type: + + % PathLengthFingerprints.pl -o -r SamplePLFPHex Sample.sdf + + To generate path length fingerprints corresponding to all unique paths + from length 1 through 8 in hexadecimal bit-vector string format of size + 1024 and create SamplePLFPHex.sdf, SamplePLFPHex.fpf, and + SamplePLFPHex.csv files containing sequential compound IDs in CSV file + along with fingerprints bit-vector strings data, type: + + % PathLengthFingerprints.pl --output all -o -r SamplePLFPHex Sample.sdf + + To generate path length fingerprints corresponding to all unique paths + from length 1 through 8 in binary bit-vector string format of size 1024 + and create a SamplePLFPBin.csv file containing sequential compound IDs + along with fingerprints bit-vector strings data, type: + + % PathLengthFingerprints.pl --BitStringFormat BinaryString --size 2048 + -o -r SamplePLFPBin Sample.sdf + + To generate path length fingerprints corresponding to count of all + unique paths from length 1 through 8 in IDsAndValuesString format and + create a SamplePLFPCount.csv file containing sequential compound IDs + along with fingerprints vector strings data, type: + + % PathLengthFingerprints.pl -m PathLengthCount -o -r SamplePLFPCount + Sample.sdf + + To generate path length fingerprints corresponding to count of all + unique paths from length 1 through 8 in IDsAndValuesString format using + E-state atom types and create a SamplePLFPCount.csv file containing + sequential compound IDs along with fingerprints vector strings data, + type: + + % PathLengthFingerprints.pl -m PathLengthCount --AtomIdentifierType + EStateAtomTypes -o -r SamplePLFPCount Sample.sdf + + To generate path length fingerprints corresponding to count of all + unique paths from length 1 through 8 in IDsAndValuesString format using + SLogP atom types and create a SamplePLFPCount.csv file containing + sequential compound IDs along with fingerprints vector strings data, + type: + + % PathLengthFingerprints.pl -m PathLengthCount --AtomIdentifierType + SLogPAtomTypes -o -r SamplePLFPCount Sample.sdf + + To generate path length fingerprints corresponding to count of all + unique paths from length 1 through 8 in IDsAndValuesString format and + create a SamplePLFPCount.csv file containing sequential compound IDs + along with fingerprints vector strings data, type: + + % PathLengthFingerprints.pl -m PathLengthCount --VectorStringFormat + ValuesAndIDsPairsString -o -r SamplePLFPCount Sample.sdf + + To generate path length fingerprints corresponding to count of all + unique paths from length 1 through 8 in IDsAndValuesString format using + AS,X,BO as atomic invariants and create a SamplePLFPCount.csv file + containing sequential compound IDs along with fingerprints vector + strings data, type: + + % PathLengthFingerprints.pl -m PathLengthCount --AtomIdentifierType + AtomicInvariantsAtomTypes --AtomicInvariantsToUse "AS,X,BO" -o + -r SamplePLFPCount Sample.sdf + + To generate path length fingerprints corresponding to count of all paths + from length 1 through 8 in IDsAndValuesString format and create a + SamplePLFPCount.csv file containing compound IDs from MolName line along + with fingerprints vector strings data, type: + + % PathLengthFingerprints.pl -m PathLengthCount --UseUniquePaths No + -o --CompoundIDMode MolName -r SamplePLFPCount --UseUniquePaths No + Sample.sdf + + To generate path length fingerprints corresponding to all unique paths + from length 1 through 8 in hexadecimal bit-vector string format of size + 512 after folding and create SamplePLFPHex.sdf, SamplePLFPHex.fpf, and + SamplePLFPHex.sdf files containing sequential compound IDs along with + fingerprints bit-vector strings data, type: + + % PathLengthFingerprints.pl --output all --Fold Yes --FoldedSize 512 + -o -r SamplePLFPHex Sample.sdf + + To generate path length fingerprints corresponding to all unique paths + from length 1 through 8 containing no rings and without sharing of bonds + in hexadecimal bit-vector string format of size 1024 and create a + SamplePLFPHex.csv file containing sequential compound IDs along with + fingerprints bit-vector strings data and all data fields, type: + + % PathLengthFingerprints.pl -p AtomPathsWithoutRings --DataFieldsMode All + -o -r SamplePLFPHex Sample.sdf + + To generate path length fingerprints corresponding to all unique paths + from length 1 through 8 containing rings and without sharing of bonds in + hexadecimal bit-vector string format of size 1024 and create a + SamplePLFPHex.tsv file containing compound IDs derived from combination + of molecule name line and an explicit compound prefix along with + fingerprints bit-vector strings data and all data fields, type: + + % PathLengthFingerprints.pl -p AtomPathsWithRings --DataFieldsMode + CompoundID --CompoundIDMode MolnameOrLabelPrefix --CompoundID Cmpd + --CompoundIDLabel MolID --FingerprintsLabel PathLengthFP --OutDelim Tab + -r SamplePLFPHex -o Sample.sdf + + To generate path length fingerprints corresponding to count of all + unique paths from length 1 through 8 in IDsAndValuesString format and + create a SamplePLFPCount.csv file containing sequential compound IDs + along with fingerprints vector strings data using aromaticity specified + in SD file, type: + + % PathLengthFingerprints.pl -m PathLengthCount --DetectAromaticity No + -o -r SamplePLFPCount Sample.sdf + + To generate path length fingerprints corresponding to all unique paths + from length 2 through 6 in hexadecimal bit-vector string format of size + 1024 and create a SamplePLFPHex.csv file containing sequential compound + IDs along with fingerprints bit-vector strings data, type: + + % PathLengthFingerprints.pl --MinPathLength 2 --MaxPathLength 6 + -o -r SamplePLFPHex Sample.sdf + +AUTHOR + Manish Sud <msud@san.rr.com> + +SEE ALSO + InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, + AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl, + MACCSKeysFingerprints.pl, TopologicalAtomPairsFingerprints.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. +