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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/man1/PathLengthFingerprints.1 Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,1014 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +PathLengthFingerprints.pl \- Generate atom path length based fingerprints for SD files +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +PathLengthFingerprints.pl SDFile(s)... +.PP +PathLengthFingerprints.pl [\fB\-\-AromaticityModel\fR \fIAromaticityModelType\fR] +[\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes\fR] +[\fB\-\-AtomicInvariantsToUse\fR \fI\*(L"AtomicInvariant1,AtomicInvariant2...\*(R"\fR] +[\fB\-\-FunctionalClassesToUse\fR \fI\*(L"FunctionalClass1,FunctionalClass2...\*(R"\fR] +[\fB\-\-BitsOrder\fR \fIAscending | Descending\fR] [\fB\-b, \-\-BitStringFormat\fR \fIBinaryString | HexadecimalString\fR] +[\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR] [\fB\-\-CompoundIDLabel\fR \fItext\fR] +[\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR] +[\fB\-\-DataFields\fR \fI\*(L"FieldLabel1,FieldLabel2,... \*(R"\fR] [\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR] +[\fB\-\-DetectAromaticity\fR \fIYes | No\fR] [\fB\-f, \-\-Filter\fR \fIYes | No\fR] [\fB\-\-FingerprintsLabel\fR \fItext\fR] +[\fB\-\-fold\fR \fIYes | No\fR] [\fB\-\-FoldedSize\fR \fInumber\fR] [\fB\-h, \-\-help\fR] +[\fB\-i, \-\-IgnoreHydrogens\fR \fIYes | No\fR] [\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR] +[\fB\-m, \-\-mode\fR \fIPathLengthBits | PathLengthCount\fR] +[\fB\-\-MinPathLength\fR \fInumber\fR] [\fB\-\-MaxPathLength\fR \fInumber\fR] [\fB\-n, \-\-NumOfBitsToSetPerPath\fR \fInumber\fR] +[\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR] +[\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR] [\fB\-q, \-\-quote\fR \fIYes | No\fR] [\fB\-r, \-\-root\fR \fIRootName\fR] +[\fB\-p, \-\-PathMode\fR \fIAtomPathsWithoutRings | AtomPathsWithRings | AllAtomPathsWithoutRings | AllAtomPathsWithRings\fR] +[\fB\-s, \-\-size\fR \fInumber\fR] [\fB\-u, \-\-UseBondSymbols\fR \fIYes | No\fR] [\fB\-\-UsePerlCoreRandom\fR \fIYes | No\fR] +[\fB\-\-UseUniquePaths\fR \fIYes | No\fR] [\fB\-q, \-\-quote\fR \fIYes | No\fR] [\fB\-r, \-\-root\fR \fIRootName\fR] +[\fB\-v, \-\-VectorStringFormat\fR \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR] +[\fB\-w, \-\-WorkingDir\fR dirname] SDFile(s)... +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +Generate atom path length fingerprints for \fISDFile(s)\fR and create appropriate \s-1SD\s0, \s-1FP\s0 or +\&\s-1CSV/TSV\s0 text file(s) containing fingerprints bit-vector or vector strings corresponding to +molecular fingerprints. +.PP +Multiple SDFile names are separated by spaces. The valid file extensions are \fI.sdf\fR +and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a current directory +can be specified either by \fI*.sdf\fR or the current directory name. +.PP +The current release of MayaChemTools supports generation of path length fingerprints +corresponding to following \fB\-a, \-\-AtomIdentifierTypes\fR: +.PP +.Vb 3 +\& AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +\& FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, +\& SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes +.Ve +.PP +Based on the values specified for \fB\-p, \-\-PathMode\fR, \fB\-\-MinPathLength\fR and \fB\-\-MaxPathLength\fR, +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 +\&\fB\-\-UseUniquePaths\fR option. +.PP +For each atom path in the filtered atom paths list, an atom path string is created using value of +\&\fB\-a, \-\-AtomIdentifierType\fR and specified values to use for a particular atom identifier type. +Value of \fB\-u, \-\-UseBondSymbols\fR 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. +.PP +For \fIPathLengthBits\fR value of \fB\-m, \-\-mode\fR option, each atom path is hashed to a 32 bit unsigned +integer key using \fBTextUtil::HashCode\fR function. Using the hash key as a seed for a random number +generator, a random integer value between 0 and \fB\-\-Size\fR is used to set corresponding bits +in the fingerprint bit-vector string. Value of \fB\-\-NumOfBitsToSetPerPath\fR option controls the number +of time a random number is generated to set corresponding bits. +.PP +For \fI PathLengthCount\fR value of \fB\-m, \-\-mode\fR option, the number of times an atom path appears +is tracked and a fingerprints count-string corresponding to count of atom paths is generated. +.PP +Example of \fI\s-1SD\s0\fR file containing path length fingerprints string data: +.PP +.Vb 10 +\& ... ... +\& ... ... +\& $$$$ +\& ... ... +\& ... ... +\& ... ... +\& 41 44 0 0 0 0 0 0 0 0999 V2000 +\& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +\& ... ... +\& 2 3 1 0 0 0 0 +\& ... ... +\& M END +\& > <CmpdID> +\& Cmpd1 +\& +\& > <PathLengthFingerprints> +\& FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt +\& h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66 +\& 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028 +\& 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462 +\& 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a +\& aa0660a11014a011d46 +\& +\& $$$$ +\& ... ... +\& ... ... +.Ve +.PP +Example of \fI\s-1FP\s0\fR file containing path length fingerprints string data: +.PP +.Vb 10 +\& # +\& # 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... +\& ... ... +\& ... .. +.Ve +.PP +Example of \s-1CSV\s0 \fIText\fR file containing pathlength fingerprints string data: +.PP +.Vb 7 +\& "CompoundID","PathLengthFingerprints" +\& "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes +\& :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4 +\& 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030 +\& 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..." +\& ... ... +\& ... ... +.Ve +.PP +The current release of MayaChemTools generates the following types of path length +fingerprints bit-vector and vector strings: +.PP +.Vb 6 +\& 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... +.Ve +.SH "OPTIONS" +.IX Header "OPTIONS" +.IP "\fB\-\-AromaticityModel\fR \fIMDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel\fR" 4 +.IX Item "--AromaticityModel MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel" +Specify aromaticity model to use during detection of aromaticity. Possible values in the current +release are: \fIMDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel, +ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel +or MayaChemToolsAromaticityModel\fR. Default value: \fIMayaChemToolsAromaticityModel\fR. +.Sp +The supported aromaticity model names along with model specific control parameters +are defined in \fBAromaticityModelsData.csv\fR, which is distributed with the current release +and is available under \fBlib/data\fR directory. \fBMolecule.pm\fR module retrieves data from +this file during class instantiation and makes it available to method \fBDetectAromaticity\fR +for detecting aromaticity corresponding to a specific model. +.Sp +This option is ignored during \fINo\fR value of \fB\-\-DetectAromaticity\fR option. +.IP "\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes\fR" 4 +.IX Item "-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: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, +TPSAAtomTypes, UFFAtomTypes\fR. Default value: \fIAtomicInvariantsAtomTypes\fR. +.IP "\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes\fR" 4 +.IX Item "-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: +\&\fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, +TPSAAtomTypes, UFFAtomTypes\fR. Default value: \fIAtomicInvariantsAtomTypes\fR. +.ie n .IP "\fB\-\-AtomicInvariantsToUse\fR \fI""AtomicInvariant1,AtomicInvariant2...""\fR" 4 +.el .IP "\fB\-\-AtomicInvariantsToUse\fR \fI``AtomicInvariant1,AtomicInvariant2...''\fR" 4 +.IX Item "--AtomicInvariantsToUse AtomicInvariant1,AtomicInvariant2..." +This value is used during \fIAtomicInvariantsAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR +option. It's a list of comma separated valid atomic invariant atom types. +.Sp +Possible values for atomic invariants are: \fI\s-1AS\s0, X, \s-1BO\s0, \s-1LBO\s0, \s-1SB\s0, \s-1DB\s0, \s-1TB\s0, +H, Ar, \s-1RA\s0, \s-1FC\s0, \s-1MN\s0, \s-1SM\s0\fR. Default value: \fI\s-1AS\s0\fR. +.Sp +The atomic invariants abbreviations correspond to: +.Sp +.Vb 1 +\& 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) +.Ve +.Sp +Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to: +.Sp +.Vb 1 +\& AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/\-n>.MN<n>.SM<n> +.Ve +.Sp +Except for \s-1AS\s0 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. +.Sp +In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words +are also allowed: +.Sp +.Vb 12 +\& 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 +.Ve +.Sp +Examples: +.Sp +\&\fBBenzene\fR: Using value of \fI\s-1AS\s0\fR for \fB\-\-AtomicInvariantsToUse\fR, \fIYes\fR for \fBUseBondSymbols\fR, +and \fI AllAtomPathsWithRings\fR for \fB\-p, \-\-PathMode\fR, atom path strings generated are: +.Sp +.Vb 1 +\& 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 +.Ve +.Sp +And using \fI\s-1AS\s0,X,BO\fR for \fB\-\-AtomicInvariantsToUse\fR generates following atom path +strings: +.Sp +.Vb 5 +\& 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 +.Ve +.Sp +\&\fBUrea\fR: Using value of \fI\s-1AS\s0\fR for \fB\-\-AtomicInvariantsToUse\fR, \fIYes\fR for \fBUseBondSymbols\fR, +and \fI AllAtomPathsWithRings\fR for \fB\-p, \-\-PathMode\fR, atom path strings are: +.Sp +.Vb 1 +\& C N O C=O CN NC=O NCN +.Ve +.Sp +And using \fI\s-1AS\s0,X,BO\fR for \fB\-\-AtomicInvariantsToUse\fR generates following atom path +strings: +.Sp +.Vb 3 +\& 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 +.Ve +.ie n .IP "\fB\-\-FunctionalClassesToUse\fR \fI""FunctionalClass1,FunctionalClass2...""\fR" 4 +.el .IP "\fB\-\-FunctionalClassesToUse\fR \fI``FunctionalClass1,FunctionalClass2...''\fR" 4 +.IX Item "--FunctionalClassesToUse FunctionalClass1,FunctionalClass2..." +This value is used during \fIFunctionalClassAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR +option. It's a list of comma separated valid functional classes. +.Sp +Possible values for atom functional classes are: \fIAr, \s-1CA\s0, H, \s-1HBA\s0, \s-1HBD\s0, Hal, \s-1NI\s0, \s-1PI\s0, \s-1RA\s0\fR. +Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR. +.Sp +The functional class abbreviations correspond to: +.Sp +.Vb 9 +\& 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 +.Ve +.Sp +\&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom +types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]: +.Sp +.Vb 4 +\& HydrogenBondDonor: NH, NH2, OH +\& HydrogenBondAcceptor: N[!H], O +\& PositivelyIonizable: +, NH2 +\& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH +.Ve +.IP "\fB\-\-BitsOrder\fR \fIAscending | Descending\fR" 4 +.IX Item "--BitsOrder Ascending | Descending" +Bits order to use during generation of fingerprints bit-vector string for \fIPathLengthBits\fR value of +\&\fB\-m, \-\-mode\fR option. Possible values: \fIAscending, Descending\fR. Default: \fIAscending\fR. +.Sp +\&\fIAscending\fR bit order which corresponds to first bit in each byte as the lowest bit as +opposed to the highest bit. +.Sp +Internally, bits are stored in \fIAscending\fR 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. +.IP "\fB\-b, \-\-BitStringFormat\fR \fIBinaryString | HexadecimalString\fR" 4 +.IX Item "-b, --BitStringFormat BinaryString | HexadecimalString" +Format of fingerprints bit-vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by +\&\fB\-\-output\fR used during \fIPathLengthBits\fR value of \fB\-m, \-\-mode\fR option. Possible +values: \fIBinaryString, HexadecimalString\fR. Default value: \fIHexadecimalString\fR. +.Sp +\&\fIBinaryString\fR corresponds to an \s-1ASCII\s0 string containing 1s and 0s. \fIHexadecimalString\fR +contains bit values in \s-1ASCII\s0 hexadecimal format. +.Sp +Examples: +.Sp +.Vb 6 +\& 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 +.Ve +.IP "\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR" 4 +.IX Item "--CompoundID DataFieldName or LabelPrefixString" +This value is \fB\-\-CompoundIDMode\fR specific and indicates how compound \s-1ID\s0 is generated. +.Sp +For \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option, it corresponds to datafield label name +whose value is used as compound \s-1ID\s0; otherwise, it's a prefix string used for generating compound +IDs like LabelPrefixString<Number>. Default value, \fICmpd\fR, generates compound IDs which +look like Cmpd<Number>. +.Sp +Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR: +.Sp +.Vb 2 +\& MolID +\& ExtReg +.Ve +.Sp +Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR: +.Sp +.Vb 1 +\& Compound +.Ve +.Sp +The value specified above generates compound IDs which correspond to Compound<Number> +instead of default value of Cmpd<Number>. +.IP "\fB\-\-CompoundIDLabel\fR \fItext\fR" 4 +.IX Item "--CompoundIDLabel text" +Specify compound \s-1ID\s0 column label for \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value +of \fB\-\-DataFieldsMode\fR option. Default: \fICompoundID\fR. +.IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4 +.IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix" +Specify how to generate compound IDs and write to \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) along with generated +fingerprints for \fI\s-1FP\s0 | text | all\fR values of \fB\-\-output\fR option: use a \fISDFile(s)\fR datafield value; +use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0 with specific prefix; use combination +of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines. +.Sp +Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR. +Default: \fILabelPrefix\fR. +.Sp +For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes +precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname +values are replaced with sequential compound IDs. +.Sp +This is only used for \fICompoundID\fR value of \fB\-\-DataFieldsMode\fR option. +.ie n .IP "\fB\-\-DataFields\fR \fI""FieldLabel1,FieldLabel2,... ""\fR" 4 +.el .IP "\fB\-\-DataFields\fR \fI``FieldLabel1,FieldLabel2,... ''\fR" 4 +.IX Item "--DataFields FieldLabel1,FieldLabel2,... " +Comma delimited list of \fISDFiles(s)\fR data fields to extract and write to \s-1CSV/TSV\s0 text file(s) along +with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option. +.Sp +This is only used for \fISpecify\fR value of \fB\-\-DataFieldsMode\fR option. +.Sp +Examples: +.Sp +.Vb 2 +\& Extreg +\& MolID,CompoundName +.Ve +.IP "\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR" 4 +.IX Item "-d, --DataFieldsMode All | Common | Specify | CompoundID" +Specify how data fields in \fISDFile(s)\fR are transferred to output \s-1CSV/TSV\s0 text file(s) along +with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option: transfer all \s-1SD\s0 +data field; transfer \s-1SD\s0 data files common to all compounds; extract specified data fields; +generate a compound \s-1ID\s0 using molname line, a compound prefix, or a combination of both. +Possible values: \fIAll | Common | specify | CompoundID\fR. Default value: \fICompoundID\fR. +.IP "\fB\-\-DetectAromaticity\fR \fIYes | No\fR" 4 +.IX Item "--DetectAromaticity Yes | No" +Detect aromaticity before generating fingerprints. Possible values: \fIYes or No\fR. +Default value: \fIYes\fR. +.Sp +\&\fINo\fR \fB\-\-DetectAromaticity\fR forces usage of atom and bond aromaticity values +from \fISDFile(s)\fR and skips the step which detects and assigns aromaticity. +.Sp +\&\fINo\fR \fB\-\-DetectAromaticity\fR value is only allowed uring \fIAtomicInvariantsAtomTypes\fR +value of \fB\-a, \-\-AtomIdentifierType\fR options; for all possible values \fB\-a, \-\-AtomIdentifierType\fR +values, it must be \fIYes\fR. +.IP "\fB\-f, \-\-Filter\fR \fIYes | No\fR" 4 +.IX Item "-f, --Filter Yes | No" +Specify whether to check and filter compound data in SDFile(s). Possible values: \fIYes or No\fR. +Default value: \fIYes\fR. +.Sp +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. +.IP "\fB\-\-FingerprintsLabel\fR \fItext\fR" 4 +.IX Item "--FingerprintsLabel text" +\&\s-1SD\s0 data label or text file column label to use for fingerprints string in output \s-1SD\s0 or +\&\s-1CSV/TSV\s0 text file(s) specified by \fB\-\-output\fR. Default value: \fIPathLenghFingerprints\fR. +.IP "\fB\-\-fold\fR \fIYes | No\fR" 4 +.IX Item "--fold Yes | No" +Fold fingerprints to increase bit density during \fIPathLengthBits\fR value of +\&\fB\-m, \-\-mode\fR option. Possible values: \fIYes or No\fR. Default value: \fINo\fR. +.IP "\fB\-\-FoldedSize\fR \fInumber\fR" 4 +.IX Item "--FoldedSize number" +Size of folded fingerprint during \fIPathLengthBits\fR value of \fB\-m, \-\-mode\fR option. Default +value: \fI256\fR. Valid values correspond to any positive integer which is less than +\&\fB\-s, \-\-size\fR and meets the criteria for its value. +.Sp +Examples: +.Sp +.Vb 2 +\& 128 +\& 512 +.Ve +.IP "\fB\-h, \-\-help\fR" 4 +.IX Item "-h, --help" +Print this help message +.IP "\fB\-i, \-\-IgnoreHydrogens\fR \fIYes | No\fR" 4 +.IX Item "-i, --IgnoreHydrogens Yes | No" +Ignore hydrogens during fingerprints generation. Possible values: \fIYes or No\fR. +Default value: \fIYes\fR. +.Sp +For \fIyes\fR value of \fB\-i, \-\-IgnoreHydrogens\fR, any explicit hydrogens are also used for +generation of atoms path lengths and fingerprints; implicit hydrogens are still ignored. +.IP "\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR" 4 +.IX Item "-k, --KeepLargestComponent Yes | No" +Generate fingerprints for only the largest component in molecule. Possible values: +\&\fIYes or No\fR. Default value: \fIYes\fR. +.Sp +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. +.IP "\fB\-m, \-\-mode\fR \fIPathLengthBits | PathLengthCount\fR" 4 +.IX Item "-m, --mode PathLengthBits | PathLengthCount" +Specify type of path length fingerprints to generate for molecules in \fISDFile(s)\fR. Possible +values: \fIPathLengthBits, PathLengthCount\fR. Default value: \fIPathLengthBits\fR. +.Sp +For \fIPathLengthBits\fR value of \fB\-m, \-\-mode\fR option, a fingerprint bit-vector string containing +zeros and ones is generated and for \fIPathLengthCount\fR value, a fingerprint vector string +corresponding to number of atom paths is generated. +.IP "\fB\-\-MinPathLength\fR \fInumber\fR" 4 +.IX Item "--MinPathLength number" +Minimum atom path length to include in fingerprints. Default value: \fI1\fR. Valid values: +positive integers and less than \fB\-\-MaxPathLength\fR. Path length of 1 correspond to +a path containing only one atom. +.IP "\fB\-\-MaxPathLength\fR \fInumber\fR" 4 +.IX Item "--MaxPathLength number" +Maximum atom path length to include in fingerprints. Default value: \fI8\fR. Valid values: +positive integers and greater than \fB\-\-MinPathLength\fR. +.IP "\fB\-n, \-\-NumOfBitsToSetPerPath\fR \fInumber\fR" 4 +.IX Item "-n, --NumOfBitsToSetPerPath number" +Number of bits to set per path during generation of fingerprints bit-vector string for \fIPathLengthBits\fR +value of \fB\-m, \-\-mode\fR option. Default value: \fI1\fR. Valid values: positive integers. +.IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4 +.IX Item "--OutDelim comma | tab | semicolon" +Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR +Default value: \fIcomma\fR. +.IP "\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR" 4 +.IX Item "--output SD | FP | text | all" +Type of output files to generate. Possible values: \fI\s-1SD\s0, \s-1FP\s0, text, or all\fR. Default value: \fItext\fR. +.IP "\fB\-o, \-\-overwrite\fR" 4 +.IX Item "-o, --overwrite" +Overwrite existing files. +.IP "\fB\-p, \-\-PathMode\fR \fIAtomPathsWithoutRings | AtomPathsWithRings | AllAtomPathsWithoutRings | AllAtomPathsWithRings\fR" 4 +.IX Item "-p, --PathMode AtomPathsWithoutRings | AtomPathsWithRings | AllAtomPathsWithoutRings | AllAtomPathsWithRings" +Specify type of atom paths to use for generating pathlength fingerprints for molecules in +\&\fISDFile(s)\fR. Possible values:\fIAtomPathsWithoutRings, AtomPathsWithRings, +AllAtomPathsWithoutRings, AllAtomPathsWithRings\fR. Default value: \fIAllAtomPathsWithRings\fR. +.Sp +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 \fB\-\-MinPathLength\fR +and \fB\-\-MaxPathLength\fR. However, all these four options can result in the same set of +final atom paths for molecules containing fused, bridged or spiro rings. +.Sp +For molecules containing rings, atom paths starting from each atom can be traversed in +four different ways: +.Sp +\&\fIAtomPathsWithoutRings\fR \- Atom paths containing no rings and without sharing of bonds +in traversed paths. +.Sp +\&\fIAtomPathsWithRings\fR \- Atom paths containing rings and without any sharing of bonds in +traversed paths. +.Sp +\&\fIAllAtomPathsWithoutRings\fR \- All possible atom paths containing no rings and without any +sharing of bonds in traversed paths. +.Sp +\&\fIAllAtomPathsWithRings\fR \- All possible atom paths containing rings and with sharing of +bonds in traversed paths. +.Sp +Atom path traversal is terminated at the ring atom. +.Sp +Based on values specified for for \fB\-p, \-\-PathMode\fR, \fB\-\-MinPathLength\fR and +\&\fB\-\-MaxPathLength\fR, all appropriate atom paths are generated for each atom in the molecule +and collected in a list. +.Sp +For each atom path in the filtered atom paths list, an atom path string is created using value of +\&\fB\-a, \-\-AtomIdentifierType\fR and specified values to use for a particular atom identifier type. +Value of \fB\-u, \-\-UseBondSymbols\fR 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: \fI1 \- None; 2 \- '='; 3 \- '#'; 1.5 or aromatic \- ':'; others: bond order value\fR. 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. +.Sp +\&\fBUseUniquePaths\fR controls the removal of structurally duplicate atom path strings are removed +from the list. +.Sp +For \fIPathLengthBits\fR value of \fB\-m, \-\-mode\fR option, each atom path is hashed to a 32 bit unsigned +integer key using \fBTextUtil::HashCode\fR function. Using the hash key as a seed for a random number +generator, a random integer value between 0 and \fB\-\-Size\fR is used to set corresponding bits +in the fingerprint bit-vector string. Value of \fB\-\-NumOfBitsToSetPerPaths\fR option controls the number +of time a random number is generated to set corresponding bits. +.Sp +For \fI PathLengthCount\fR value of \fB\-m, \-\-mode\fR option, the number of times an atom path appears +is tracked and a fingerprints count-string corresponding to count of atom paths is generated. +.Sp +For molecule containing rings, combination of \fB\-p, \-\-PathMode\fR and \fB\-\-UseBondSymbols\fR allows +generation of up to 8 different types of atom path length strings: +.Sp +.Vb 1 +\& 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 +.Ve +.Sp +Default atom path length fingerprints generation for molecules containing rings with +\&\fIAllAtomPathsWithRings\fR value for \fB\-p, \-\-PathMode\fR, \fIYes\fR value for \fB\-\-UseBondSymbols\fR, +\&\fI2\fR value for \fB\-\-MinPathLength\fR and \fI8\fR value for \fB\-\-MaxPathLength\fR is the most time +consuming. Combinations of other options can substantially speed up fingerprint generation +for molecules containing complex ring systems. +.Sp +Additionally, value for option \fB\-a, \-\-AtomIdentifierType\fR in conjunction with corresponding specified +values for atom types changes the nature of atom path length strings and the fingerprints. +.IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4 +.IX Item "-q, --quote Yes | No" +Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values: +\&\fIYes or No\fR. Default value: \fIYes\fR. +.IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4 +.IX Item "-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 \s-1SD\s0, \s-1FP\s0, comma/semicolon, and tab +delimited text files, respectively.This option is ignored for multiple input files. +.IP "\fB\-s, \-\-size\fR \fInumber\fR" 4 +.IX Item "-s, --size number" +Size of fingerprints. Default value: \fI1024\fR. Valid values correspond to any positive +integer which satisfies the following criteria: power of 2, >= 32 and <= 2 ** 32. +.Sp +Examples: +.Sp +.Vb 3 +\& 256 +\& 512 +\& 2048 +.Ve +.IP "\fB\-u, \-\-UseBondSymbols\fR \fIYes | No\fR" 4 +.IX Item "-u, --UseBondSymbols Yes | No" +Specify whether to use bond symbols for atom paths during generation of atom path strings. +Possible values: \fIYes or No\fR. Default value: \fIYes\fR. +.Sp +\&\fINo\fR value option for \fB\-u, \-\-UseBondSymbols\fR allows the generation of fingerprints corresponding +purely to atoms disregarding all bonds. +.IP "\fB\-\-UsePerlCoreRandom\fR \fIYes | No\fR" 4 +.IX Item "--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: \fIYes or No\fR. Default value: \fIYes\fR. +.Sp +\&\fINo\fR value option for \fB\-\-UsePerlCoreRandom\fR allows the generation of fingerprints +bit-vector strings which are same across different platforms. +.Sp +The random number generator implemented in MayaChemTools is a variant of +linear congruential generator (\s-1LCG\s0) as described by Miller et al. [ Ref 120 ]. +It is also referred to as Lehmer random number generator or Park-Miller +random number generator. +.Sp +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. +.IP "\fB\-\-UseUniquePaths\fR \fIYes | No\fR" 4 +.IX Item "--UseUniquePaths Yes | No" +Specify whether to use structurally unique atom paths during generation of atom path strings. +Possible values: \fIYes or No\fR. Default value: \fIYes\fR. +.Sp +\&\fINo\fR value option for \fB\-\-UseUniquePaths\fR allows usage of all atom paths generated by +\&\fB\-p, \-\-PathMode\fR option value for generation of atom path strings leading to duplicate +path count during \fIPathLengthCount\fR value of \fB\-m, \-\-mode\fR option. It doesn't change fingerprint +string generated during \fIPathLengthBits\fR value of \fB\-m, \-\-mode\fR. +.Sp +For example, during \fIAllAtomPathsWithRings\fR value of \fB\-p, \-\-PathMode\fR 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. +.IP "\fB\-v, \-\-VectorStringFormat\fR \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR" 4 +.IX Item "-v, --VectorStringFormat IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString" +Format of fingerprints vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by +\&\fB\-\-output\fR used during \fIPathLengthCount\fR value of \fB\-m, \-\-mode\fR option. Possible +values: \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | +ValuesAndIDsPairsString\fR. Defaultvalue: \fIIDsAndValuesString\fR. +.Sp +Examples: +.Sp +.Vb 6 +\& 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... +.Ve +.IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4 +.IX Item "-w, --WorkingDir DirName" +Location of working directory. Default: current directory. +.SH "EXAMPLES" +.IX Header "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: +.PP +.Vb 1 +\& % PathLengthFingerprints.pl \-o \-r SamplePLFPHex Sample.sdf +.Ve +.PP +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 \s-1CSV\s0 file along with fingerprints bit-vector strings data, type: +.PP +.Vb 1 +\& % PathLengthFingerprints.pl \-\-output all \-o \-r SamplePLFPHex Sample.sdf +.Ve +.PP +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: +.PP +.Vb 2 +\& % PathLengthFingerprints.pl \-\-BitStringFormat BinaryString \-\-size 2048 +\& \-o \-r SamplePLFPBin Sample.sdf +.Ve +.PP +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: +.PP +.Vb 2 +\& % PathLengthFingerprints.pl \-m PathLengthCount \-o \-r SamplePLFPCount +\& Sample.sdf +.Ve +.PP +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: +.PP +.Vb 2 +\& % PathLengthFingerprints.pl \-m PathLengthCount \-\-AtomIdentifierType +\& EStateAtomTypes \-o \-r SamplePLFPCount Sample.sdf +.Ve +.PP +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: +.PP +.Vb 2 +\& % PathLengthFingerprints.pl \-m PathLengthCount \-\-AtomIdentifierType +\& SLogPAtomTypes \-o \-r SamplePLFPCount Sample.sdf +.Ve +.PP +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: +.PP +.Vb 2 +\& % PathLengthFingerprints.pl \-m PathLengthCount \-\-VectorStringFormat +\& ValuesAndIDsPairsString \-o \-r SamplePLFPCount Sample.sdf +.Ve +.PP +To generate path length fingerprints corresponding to count of all unique paths from +length 1 through 8 in IDsAndValuesString format using \s-1AS\s0,X,BO as atomic invariants and +create a SamplePLFPCount.csv file containing sequential compound IDs along with fingerprints +vector strings data, type: +.PP +.Vb 3 +\& % PathLengthFingerprints.pl \-m PathLengthCount \-\-AtomIdentifierType +\& AtomicInvariantsAtomTypes \-\-AtomicInvariantsToUse "AS,X,BO" \-o +\& \-r SamplePLFPCount Sample.sdf +.Ve +.PP +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: +.PP +.Vb 3 +\& % PathLengthFingerprints.pl \-m PathLengthCount \-\-UseUniquePaths No +\& \-o \-\-CompoundIDMode MolName \-r SamplePLFPCount \-\-UseUniquePaths No +\& Sample.sdf +.Ve +.PP +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: +.PP +.Vb 2 +\& % PathLengthFingerprints.pl \-\-output all \-\-Fold Yes \-\-FoldedSize 512 +\& \-o \-r SamplePLFPHex Sample.sdf +.Ve +.PP +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: +.PP +.Vb 2 +\& % PathLengthFingerprints.pl \-p AtomPathsWithoutRings \-\-DataFieldsMode All +\& \-o \-r SamplePLFPHex Sample.sdf +.Ve +.PP +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: +.PP +.Vb 4 +\& % PathLengthFingerprints.pl \-p AtomPathsWithRings \-\-DataFieldsMode +\& CompoundID \-\-CompoundIDMode MolnameOrLabelPrefix \-\-CompoundID Cmpd +\& \-\-CompoundIDLabel MolID \-\-FingerprintsLabel PathLengthFP \-\-OutDelim Tab +\& \-r SamplePLFPHex \-o Sample.sdf +.Ve +.PP +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 \s-1SD\s0 file, type: +.PP +.Vb 2 +\& % PathLengthFingerprints.pl \-m PathLengthCount \-\-DetectAromaticity No +\& \-o \-r SamplePLFPCount Sample.sdf +.Ve +.PP +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: +.PP +.Vb 2 +\& % PathLengthFingerprints.pl \-\-MinPathLength 2 \-\-MaxPathLength 6 +\& \-o \-r SamplePLFPHex Sample.sdf +.Ve +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl, +ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl, +TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl, +TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl +.SH "COPYRIGHT" +.IX Header "COPYRIGHT" +Copyright (C) 2015 Manish Sud. All rights reserved. +.PP +This file is part of MayaChemTools. +.PP +MayaChemTools is free software; you can redistribute it and/or modify it under +the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free +Software Foundation; either version 3 of the License, or (at your option) +any later version.