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| date | Wed, 20 Jan 2016 12:15:15 -0500 |
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<html> <head> <title>MayaChemTools:Documentation:PathLengthFingerprints.pl</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <div class="DocNav"> <table width="100%" border=0 cellpadding=0 cellspacing=2> <tr align="left" valign="top"><td width="33%" align="left"><a href="./MolFilesToSD.html" title="MolFilesToSD.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./SDFilesToHTML.html" title="SDFilesToHTML.html">Next</a></td><td width="34%" align="middle"><strong>PathLengthFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/PathLengthFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/PathLengthFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/PathLengthFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/PathLengthFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/PathLengthFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> </table> </div> <p> </p> <h2>NAME</h2> <p>PathLengthFingerprints.pl - Generate atom path length based fingerprints for SD files</p> <p> </p> <h2>SYNOPSIS</h2> <p>PathLengthFingerprints.pl SDFile(s)...</p> <p>PathLengthFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>] [<strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes</em>] [<strong>--AtomicInvariantsToUse</strong> <em>"AtomicInvariant1,AtomicInvariant2..."</em>] [<strong>--FunctionalClassesToUse</strong> <em>"FunctionalClass1,FunctionalClass2..."</em>] [<strong>--BitsOrder</strong> <em>Ascending | Descending</em>] [<strong>-b, --BitStringFormat</strong> <em>BinaryString | HexadecimalString</em>] [<strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em>] [<strong>--CompoundIDLabel</strong> <em>text</em>] [<strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>] [<strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,... "</em>] [<strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em>] [<strong>--DetectAromaticity</strong> <em>Yes | No</em>] [<strong>-f, --Filter</strong> <em>Yes | No</em>] [<strong>--FingerprintsLabel</strong> <em>text</em>] [<strong>--fold</strong> <em>Yes | No</em>] [<strong>--FoldedSize</strong> <em>number</em>] [<strong>-h, --help</strong>] [<strong>-i, --IgnoreHydrogens</strong> <em>Yes | No</em>] [<strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em>] [<strong>-m, --mode</strong> <em>PathLengthBits | PathLengthCount</em>] [<strong>--MinPathLength</strong> <em>number</em>] [<strong>--MaxPathLength</strong> <em>number</em>] [<strong>-n, --NumOfBitsToSetPerPath</strong> <em>number</em>] [<strong>--OutDelim</strong> <em>comma | tab | semicolon</em>] [<strong>--output</strong> <em>SD | FP | text | all</em>] [<strong>-q, --quote</strong> <em>Yes | No</em>] [<strong>-r, --root</strong> <em>RootName</em>] [<strong>-p, --PathMode</strong> <em>AtomPathsWithoutRings | AtomPathsWithRings | AllAtomPathsWithoutRings | AllAtomPathsWithRings</em>] [<strong>-s, --size</strong> <em>number</em>] [<strong>-u, --UseBondSymbols</strong> <em>Yes | No</em>] [<strong>--UsePerlCoreRandom</strong> <em>Yes | No</em>] [<strong>--UseUniquePaths</strong> <em>Yes | No</em>] [<strong>-q, --quote</strong> <em>Yes | No</em>] [<strong>-r, --root</strong> <em>RootName</em>] [<strong>-v, --VectorStringFormat</strong> <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em>] [<strong>-w, --WorkingDir</strong> dirname] SDFile(s)...</p> <p> </p> <h2>DESCRIPTION</h2> <p>Generate atom path length fingerprints for <em>SDFile(s)</em> and create appropriate SD, FP or CSV/TSV text file(s) containing fingerprints bit-vector or vector strings corresponding to molecular fingerprints.</p> <p>Multiple SDFile names are separated by spaces. The valid file extensions are <em>.sdf</em> and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory can be specified either by <em>*.sdf</em> or the current directory name.</p> <p>The current release of MayaChemTools supports generation of path length fingerprints corresponding to following <strong>-a, --AtomIdentifierTypes</strong>:</p> <div class="OptionsBox"> AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, <br/> FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, <br/> SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</div> <p>Based on the values specified for <strong>-p, --PathMode</strong>, <strong>--MinPathLength</strong> and <strong>--MaxPathLength</strong>, 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 <strong>--UseUniquePaths</strong> option.</p> <p>For each atom path in the filtered atom paths list, an atom path string is created using value of <strong>-a, --AtomIdentifierType</strong> and specified values to use for a particular atom identifier type. Value of <strong>-u, --UseBondSymbols</strong> 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.</p> <p>For <em>PathLengthBits</em> value of <strong>-m, --mode</strong> option, each atom path is hashed to a 32 bit unsigned integer key using <strong>TextUtil::HashCode</strong> function. Using the hash key as a seed for a random number generator, a random integer value between 0 and <strong>--Size</strong> is used to set corresponding bits in the fingerprint bit-vector string. Value of <strong>--NumOfBitsToSetPerPath</strong> option controls the number of time a random number is generated to set corresponding bits.</p> <p>For <em> PathLengthCount</em> value of <strong>-m, --mode</strong> option, the number of times an atom path appears is tracked and a fingerprints count-string corresponding to count of atom paths is generated.</p> <p>Example of <em>SD</em> file containing path length fingerprints string data:</p> <div class="OptionsBox"> ... ... <br/> ... ... <br/> $$$$ <br/> ... ... <br/> ... ... <br/> ... ... <br/> 41 44 0 0 0 0 0 0 0 0999 V2000 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 <br/> ... ... <br/> 2 3 1 0 0 0 0 <br/> ... ... <br/> M END <br/> > <CmpdID> <br/> Cmpd1</div> <div class="OptionsBox"> > <PathLengthFingerprints> <br/> FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt <br/> h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66 <br/> 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028 <br/> 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462 <br/> 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a <br/> aa0660a11014a011d46</div> <div class="OptionsBox"> $$$$ <br/> ... ... <br/> ... ...</div> <p>Example of <em>FP</em> file containing path length fingerprints string data:</p> <div class="OptionsBox"> # <br/> # Package = MayaChemTools 7.4 <br/> # ReleaseDate = Oct 21, 2010 <br/> # <br/> # TimeStamp = Mon Mar 7 15:14:01 2011 <br/> # <br/> # FingerprintsStringType = FingerprintsBitVector <br/> # <br/> # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:... <br/> # Size = 1024 <br/> # BitStringFormat = HexadecimalString <br/> # BitsOrder = Ascending <br/> # <br/> Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510... <br/> Cmpd2 000000249400840040100042011001001980410c000000001010088001120... <br/> ... ... <br/> ... ..</div> <p>Example of CSV <em>Text</em> file containing pathlength fingerprints string data:</p> <div class="OptionsBox"> "CompoundID","PathLengthFingerprints" <br/> "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes <br/> :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4 <br/> 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030 <br/> 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..." <br/> ... ... <br/> ... ...</div> <p>The current release of MayaChemTools generates the following types of path length fingerprints bit-vector and vector strings:</p> <div class="OptionsBox"> FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng <br/> th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110 <br/> 0100010101011000101001011100110001000010001001101000001001001001001000 <br/> 0010110100000111001001000001001010100100100000000011000000101001011100 <br/> 0010000001000101010100000100111100110111011011011000000010110111001101 <br/> 0101100011000000010001000011000010100011101100001000001000100000000...</div> <div class="OptionsBox"> FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng <br/> th1:MaxLength8;1024;HexadecimalString;Ascending;48caa1315d82d91122b029 <br/> 42861c9409a4208182d12015509767bd0867653604481a8b1288000056090583603078 <br/> 9cedae54e26596889ab121309800900490515224208421502120a0dd9200509723ae89 <br/> 00024181b86c0122821d4e4880c38620dab280824b455404009f082003d52c212b4e6d <br/> 6ea05280140069c780290c43</div> <div class="OptionsBox"> FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength <br/> 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2 <br/> 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 <br/> 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1 <br/> 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO <br/> 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....</div> <div class="OptionsBox"> FingerprintsVector;PathLengthCount:DREIDINGAtomTypes:MinLength1:MaxLen <br/> gth8;410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_ <br/> 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 <br/> 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 <br/> _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 <br/> _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 ...</div> <div class="OptionsBox"> FingerprintsVector;PathLengthCount:EStateAtomTypes:MinLength1:MaxLengt <br/> h8;454;NumericalValues;IDsAndValuesPairsString;aaCH 14 aasC 8 aasN 1 d <br/> O 2 dssC 2 sCH3 2 sF 1 sOH 3 ssCH2 4 ssNH 1 sssCH 3 aaCH:aaCH 10 aaCH: <br/> aasC 8 aasC:aasC 3 aasC:aasN 2 aasCaasC 2 aasCdssC 1 aasCsF 1 aasCssNH <br/> 1 aasCsssCH 1 aasNssCH2 1 dO=dssC 2 dssCsOH 1 dssCssCH2 1 dssCssNH 1 <br/> sCH3sssCH 2 sOHsssCH 2 ssCH2ssCH2 1 ssCH2sssCH 4 aaCH:aaCH:aaCH 6 a...</div> <div class="OptionsBox"> FingerprintsVector;PathLengthCount:FunctionalClassAtomTypes:MinLength1 <br/> :MaxLength8;404;NumericalValues;IDsAndValuesPairsString;Ar 22 Ar.HBA 1 <br/> HBA 2 HBA.HBD 3 HBD 1 Hal 1 NI 1 None 10 Ar.HBA:Ar 2 Ar.HBANone 1 Ar: <br/> Ar 21 ArAr 2 ArHBD 1 ArHal 1 ArNone 2 HBA.HBDNI 1 HBA.HBDNone 2 HBA=NI <br/> 1 HBA=None 1 HBDNone 1 NINone 1 NoneNone 7 Ar.HBA:Ar:Ar 2 Ar.HBA:ArAr <br/> 1 Ar.HBA:ArNone 1 Ar.HBANoneNone 1 Ar:Ar.HBA:Ar 1 Ar:Ar.HBANone 2 ...</div> <div class="OptionsBox"> FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt <br/> h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1 <br/> 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 <br/> 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1 <br/> CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR <br/> OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...</div> <div class="OptionsBox"> FingerprintsVector;PathLengthCount:SLogPAtomTypes:MinLength1:MaxLength <br/> 8;518;NumericalValues;IDsAndValuesPairsString;C1 5 C10 1 C11 1 C14 1 C <br/> 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 <br/> 1 C10N11 1 C11C1 2 C11C21 1 C14:C18 2 C14F 1 C18:C18 10 C18:C20 4 C18 <br/> :C22 2 C1C5 1 C1CS 4 C20:C20 1 C20:C21 1 C20:N11 1 C20C20 2 C21:C21 1 <br/> C21:N11 1 C21C5 1 C22N4 1 C5=O10 1 C5=O9 1 C5N4 1 C5O2 1 CSO2 2 C10...</div> <div class="OptionsBox"> FingerprintsVector;PathLengthCount:SYBYLAtomTypes:MinLength1:MaxLength <br/> 8;412;NumericalValues;IDsAndValuesPairsString;C.2 2 C.3 9 C.ar 22 F 1 <br/> 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. <br/> 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 <br/> .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 <br/> .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...</div> <div class="OptionsBox"> FingerprintsVector;PathLengthCount:TPSAAtomTypes:MinLength1:MaxLength8 <br/> ;331;NumericalValues;IDsAndValuesPairsString;N21 1 N7 1 None 34 O3 2 O <br/> 4 3 N21:None 2 N21None 1 N7None 2 None:None 21 None=O3 2 NoneNone 13 N <br/> oneO4 3 N21:None:None 2 N21:NoneNone 2 N21NoneNone 1 N7None:None 2 N7N <br/> one=O3 1 N7NoneNone 1 None:N21:None 1 None:N21None 2 None:None:None 20 <br/> None:NoneNone 12 NoneN7None 1 NoneNone=O3 2 NoneNoneNone 8 NoneNon...</div> <div class="OptionsBox"> FingerprintsVector;PathLengthCount:UFFAtomTypes:MinLength1:MaxLength8; <br/> 410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_ 1 N_ <br/> 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_ <br/> 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_ <br/> 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 <br/> 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...</div> <p> </p> <h2>OPTIONS</h2> <dl> <dt><strong><strong>--AromaticityModel</strong> <em>MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel</em></strong></dt> <dd> <p>Specify aromaticity model to use during detection of aromaticity. Possible values in the current release are: <em>MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel, ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel or MayaChemToolsAromaticityModel</em>. Default value: <em>MayaChemToolsAromaticityModel</em>.</p> <p>The supported aromaticity model names along with model specific control parameters are defined in <strong>AromaticityModelsData.csv</strong>, which is distributed with the current release and is available under <strong>lib/data</strong> directory. <strong>Molecule.pm</strong> module retrieves data from this file during class instantiation and makes it available to method <strong>DetectAromaticity</strong> for detecting aromaticity corresponding to a specific model.</p> <p>This option is ignored during <em>No</em> value of <strong>--DetectAromaticity</strong> option.</p> </dd> <dt><strong><strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes</em></strong></dt> <dd> <p>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: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</em>. Default value: <em>AtomicInvariantsAtomTypes</em>.</p> </dd> <dt><strong><strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes</em></strong></dt> <dd> <p>Specify atom identifier type to use during generation of atom path strings corresponding to path length fingerprints. Possible values in the current release are: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</em>. Default value: <em>AtomicInvariantsAtomTypes</em>.</p> </dd> <dt><strong><strong>--AtomicInvariantsToUse</strong> <em>"AtomicInvariant1,AtomicInvariant2..."</em></strong></dt> <dd> <p>This value is used during <em>AtomicInvariantsAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong> option. It's a list of comma separated valid atomic invariant atom types.</p> <p>Possible values for atomic invariants are: <em>AS, X, BO, LBO, SB, DB, TB, H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS</em>.</p> <p>The atomic invariants abbreviations correspond to:</p> <div class="OptionsBox"> AS = Atom symbol corresponding to element symbol</div> <div class="OptionsBox"> X<n> = Number of non-hydrogen atom neighbors or heavy atoms <br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms <br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms <br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms <br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms <br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms <br/> H<n> = Number of implicit and explicit hydrogens for atom <br/> Ar = Aromatic annotation indicating whether atom is aromatic <br/> RA = Ring atom annotation indicating whether atom is a ring <br/> FC<+n/-n> = Formal charge assigned to atom <br/> MN<n> = Mass number indicating isotope other than most abundant isotope <br/> SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or 3 (triplet)</div> <p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p> <div class="OptionsBox"> AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></div> <p>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.</p> <p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words are also allowed:</p> <div class="OptionsBox"> X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors <br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms <br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms <br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms <br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms <br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms <br/> H : NumOfImplicitAndExplicitHydrogens <br/> Ar : Aromatic <br/> RA : RingAtom <br/> FC : FormalCharge <br/> MN : MassNumber <br/> SM : SpinMultiplicity</div> <p>Examples:</p> <p><strong>Benzene</strong>: Using value of <em>AS</em> for <strong>--AtomicInvariantsToUse</strong>, <em>Yes</em> for <strong>UseBondSymbols</strong>, and <em> AllAtomPathsWithRings</em> for <strong>-p, --PathMode</strong>, atom path strings generated are:</p> <div class="OptionsBox"> 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</div> <p>And using <em>AS,X,BO</em> for <strong>--AtomicInvariantsToUse</strong> generates following atom path strings:</p> <div class="OptionsBox"> C.X2.BO3 C.X2.BO3:C.X2.BO3 C.X2.BO3:C.X2.BO3:C.X2.BO3 <br/> C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3 <br/> C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3 <br/> C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3 <br/> C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3</div> <p><strong>Urea</strong>: Using value of <em>AS</em> for <strong>--AtomicInvariantsToUse</strong>, <em>Yes</em> for <strong>UseBondSymbols</strong>, and <em> AllAtomPathsWithRings</em> for <strong>-p, --PathMode</strong>, atom path strings are:</p> <div class="OptionsBox"> C N O C=O CN NC=O NCN</div> <p>And using <em>AS,X,BO</em> for <strong>--AtomicInvariantsToUse</strong> generates following atom path strings:</p> <div class="OptionsBox"> C.X3.BO4 N.X1.BO1 O.X1.BO2 C.X3.BO4=O.X1.BO2 <br/> C.X3.BO4N.X1.BO1 N.X1.BO1C.X3.BO4=O.X1.BO2 <br/> N.X1.BO1C.X3.BO4N.X1.BO1</div> </dd> <dt><strong><strong>--FunctionalClassesToUse</strong> <em>"FunctionalClass1,FunctionalClass2..."</em></strong></dt> <dd> <p>This value is used during <em>FunctionalClassAtomTypes</em> value of <strong>a, --AtomIdentifierType</strong> option. It's a list of comma separated valid functional classes.</p> <p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>. Default value [ Ref 24 ]: <em>HBD,HBA,PI,NI,Ar,Hal</em>.</p> <p>The functional class abbreviations correspond to:</p> <div class="OptionsBox"> HBD: HydrogenBondDonor <br/> HBA: HydrogenBondAcceptor <br/> PI : PositivelyIonizable <br/> NI : NegativelyIonizable <br/> Ar : Aromatic <br/> Hal : Halogen <br/> H : Hydrophobic <br/> RA : RingAtom <br/> CA : ChainAtom</div> <div class="OptionsBox"> Functional class atom type specification for an atom corresponds to:</div> <div class="OptionsBox"> Ar.CA.H.HBA.HBD.Hal.NI.PI.RA</div> <p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign functional class atom types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:</p> <div class="OptionsBox"> HydrogenBondDonor: NH, NH2, OH <br/> HydrogenBondAcceptor: N[!H], O <br/> PositivelyIonizable: +, NH2 <br/> NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH</div> </dd> <dt><strong><strong>--BitsOrder</strong> <em>Ascending | Descending</em></strong></dt> <dd> <p>Bits order to use during generation of fingerprints bit-vector string for <em>PathLengthBits</em> value of <strong>-m, --mode</strong> option. Possible values: <em>Ascending, Descending</em>. Default: <em>Ascending</em>.</p> <p><em>Ascending</em> bit order which corresponds to first bit in each byte as the lowest bit as opposed to the highest bit.</p> <p>Internally, bits are stored in <em>Ascending</em> 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.</p> </dd> <dt><strong><strong>-b, --BitStringFormat</strong> <em>BinaryString | HexadecimalString</em></strong></dt> <dd> <p>Format of fingerprints bit-vector string data in output SD, FP or CSV/TSV text file(s) specified by <strong>--output</strong> used during <em>PathLengthBits</em> value of <strong>-m, --mode</strong> option. Possible values: <em>BinaryString, HexadecimalString</em>. Default value: <em>HexadecimalString</em>.</p> <p><em>BinaryString</em> corresponds to an ASCII string containing 1s and 0s. <em>HexadecimalString</em> contains bit values in ASCII hexadecimal format.</p> <p>Examples:</p> <div class="OptionsBox"> FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng <br/> th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110 <br/> 0100010101011000101001011100110001000010001001101000001001001001001000 <br/> 0010110100000111001001000001001010100100100000000011000000101001011100 <br/> 0010000001000101010100000100111100110111011011011000000010110111001101 <br/> 0101100011000000010001000011000010100011101100001000001000100000000...</div> <div class="OptionsBox"> FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng <br/> th1:MaxLength8;1024;HexadecimalString;Ascending;48caa1315d82d91122b029 <br/> 42861c9409a4208182d12015509767bd0867653604481a8b1288000056090583603078 <br/> 9cedae54e26596889ab121309800900490515224208421502120a0dd9200509723ae89 <br/> 00024181b86c0122821d4e4880c38620dab280824b455404009f082003d52c212b4e6d <br/> 6ea05280140069c780290c43</div> </dd> <dt><strong><strong>--CompoundID</strong> <em>DataFieldName or LabelPrefixString</em></strong></dt> <dd> <p>This value is <strong>--CompoundIDMode</strong> specific and indicates how compound ID is generated.</p> <p>For <em>DataField</em> value of <strong>--CompoundIDMode</strong> 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, <em>Cmpd</em>, generates compound IDs which look like Cmpd<Number>.</p> <p>Examples for <em>DataField</em> value of <strong>--CompoundIDMode</strong>:</p> <div class="OptionsBox"> MolID <br/> ExtReg</div> <p>Examples for <em>LabelPrefix</em> or <em>MolNameOrLabelPrefix</em> value of <strong>--CompoundIDMode</strong>:</p> <div class="OptionsBox"> Compound</div> <p>The value specified above generates compound IDs which correspond to Compound<Number> instead of default value of Cmpd<Number>.</p> </dd> <dt><strong><strong>--CompoundIDLabel</strong> <em>text</em></strong></dt> <dd> <p>Specify compound ID column label for FP or CSV/TSV text file(s) used during <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option. Default: <em>CompoundID</em>.</p> </dd> <dt><strong><strong>--CompoundIDMode</strong> <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em></strong></dt> <dd> <p>Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated fingerprints for <em>FP | text | all</em> values of <strong>--output</strong> option: use a <em>SDFile(s)</em> datafield value; use molname line from <em>SDFile(s)</em>; generate a sequential ID with specific prefix; use combination of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.</p> <p>Possible values: <em>DataField | MolName | LabelPrefix | MolNameOrLabelPrefix</em>. Default: <em>LabelPrefix</em>.</p> <p>For <em>MolNameAndLabelPrefix</em> value of <strong>--CompoundIDMode</strong>, molname line in <em>SDFile(s)</em> takes precedence over sequential compound IDs generated using <em>LabelPrefix</em> and only empty molname values are replaced with sequential compound IDs.</p> <p>This is only used for <em>CompoundID</em> value of <strong>--DataFieldsMode</strong> option.</p> </dd> <dt><strong><strong>--DataFields</strong> <em>"FieldLabel1,FieldLabel2,... "</em></strong></dt> <dd> <p>Comma delimited list of <em>SDFiles(s)</em> data fields to extract and write to CSV/TSV text file(s) along with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> option.</p> <p>This is only used for <em>Specify</em> value of <strong>--DataFieldsMode</strong> option.</p> <p>Examples:</p> <div class="OptionsBox"> Extreg <br/> MolID,CompoundName</div> </dd> <dt><strong><strong>-d, --DataFieldsMode</strong> <em>All | Common | Specify | CompoundID</em></strong></dt> <dd> <p>Specify how data fields in <em>SDFile(s)</em> are transferred to output CSV/TSV text file(s) along with generated fingerprints for <em>text | all</em> values of <strong>--output</strong> 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: <em>All | Common | specify | CompoundID</em>. Default value: <em>CompoundID</em>.</p> </dd> <dt><strong><strong>--DetectAromaticity</strong> <em>Yes | No</em></strong></dt> <dd> <p>Detect aromaticity before generating fingerprints. Possible values: <em>Yes or No</em>. Default value: <em>Yes</em>.</p> <p><em>No</em> <strong>--DetectAromaticity</strong> forces usage of atom and bond aromaticity values from <em>SDFile(s)</em> and skips the step which detects and assigns aromaticity.</p> <p><em>No</em> <strong>--DetectAromaticity</strong> value is only allowed uring <em>AtomicInvariantsAtomTypes</em> value of <strong>-a, --AtomIdentifierType</strong> options; for all possible values <strong>-a, --AtomIdentifierType</strong> values, it must be <em>Yes</em>.</p> </dd> <dt><strong><strong>-f, --Filter</strong> <em>Yes | No</em></strong></dt> <dd> <p>Specify whether to check and filter compound data in SDFile(s). Possible values: <em>Yes or No</em>. Default value: <em>Yes</em>.</p> <p>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.</p> </dd> <dt><strong><strong>--FingerprintsLabel</strong> <em>text</em></strong></dt> <dd> <p>SD data label or text file column label to use for fingerprints string in output SD or CSV/TSV text file(s) specified by <strong>--output</strong>. Default value: <em>PathLenghFingerprints</em>.</p> </dd> <dt><strong><strong>--fold</strong> <em>Yes | No</em></strong></dt> <dd> <p>Fold fingerprints to increase bit density during <em>PathLengthBits</em> value of <strong>-m, --mode</strong> option. Possible values: <em>Yes or No</em>. Default value: <em>No</em>.</p> </dd> <dt><strong><strong>--FoldedSize</strong> <em>number</em></strong></dt> <dd> <p>Size of folded fingerprint during <em>PathLengthBits</em> value of <strong>-m, --mode</strong> option. Default value: <em>256</em>. Valid values correspond to any positive integer which is less than <strong>-s, --size</strong> and meets the criteria for its value.</p> <p>Examples:</p> <div class="OptionsBox"> 128 512</div> </dd> <dt><strong><strong>-h, --help</strong></strong></dt> <dd> <p>Print this help message</p> </dd> <dt><strong><strong>-i, --IgnoreHydrogens</strong> <em>Yes | No</em></strong></dt> <dd> <p>Ignore hydrogens during fingerprints generation. Possible values: <em>Yes or No</em>. Default value: <em>Yes</em>.</p> <p>For <em>yes</em> value of <strong>-i, --IgnoreHydrogens</strong>, any explicit hydrogens are also used for generation of atoms path lengths and fingerprints; implicit hydrogens are still ignored.</p> </dd> <dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt> <dd> <p>Generate fingerprints for only the largest component in molecule. Possible values: <em>Yes or No</em>. Default value: <em>Yes</em>.</p> <p>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.</p> </dd> <dt><strong><strong>-m, --mode</strong> <em>PathLengthBits | PathLengthCount</em></strong></dt> <dd> <p>Specify type of path length fingerprints to generate for molecules in <em>SDFile(s)</em>. Possible values: <em>PathLengthBits, PathLengthCount</em>. Default value: <em>PathLengthBits</em>.</p> <p>For <em>PathLengthBits</em> value of <strong>-m, --mode</strong> option, a fingerprint bit-vector string containing zeros and ones is generated and for <em>PathLengthCount</em> value, a fingerprint vector string corresponding to number of atom paths is generated.</p> </dd> <dt><strong><strong>--MinPathLength</strong> <em>number</em></strong></dt> <dd> <p>Minimum atom path length to include in fingerprints. Default value: <em>1</em>. Valid values: positive integers and less than <strong>--MaxPathLength</strong>. Path length of 1 correspond to a path containing only one atom.</p> </dd> <dt><strong><strong>--MaxPathLength</strong> <em>number</em></strong></dt> <dd> <p>Maximum atom path length to include in fingerprints. Default value: <em>8</em>. Valid values: positive integers and greater than <strong>--MinPathLength</strong>.</p> </dd> <dt><strong><strong>-n, --NumOfBitsToSetPerPath</strong> <em>number</em></strong></dt> <dd> <p>Number of bits to set per path during generation of fingerprints bit-vector string for <em>PathLengthBits</em> value of <strong>-m, --mode</strong> option. Default value: <em>1</em>. Valid values: positive integers.</p> </dd> <dt><strong><strong>--OutDelim</strong> <em>comma | tab | semicolon</em></strong></dt> <dd> <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em> Default value: <em>comma</em>.</p> </dd> <dt><strong><strong>--output</strong> <em>SD | FP | text | all</em></strong></dt> <dd> <p>Type of output files to generate. Possible values: <em>SD, FP, text, or all</em>. Default value: <em>text</em>.</p> </dd> <dt><strong><strong>-o, --overwrite</strong></strong></dt> <dd> <p>Overwrite existing files.</p> </dd> <dt><strong><strong>-p, --PathMode</strong> <em>AtomPathsWithoutRings | AtomPathsWithRings | AllAtomPathsWithoutRings | AllAtomPathsWithRings</em></strong></dt> <dd> <p>Specify type of atom paths to use for generating pathlength fingerprints for molecules in <em>SDFile(s)</em>. Possible values:<em>AtomPathsWithoutRings, AtomPathsWithRings, AllAtomPathsWithoutRings, AllAtomPathsWithRings</em>. Default value: <em>AllAtomPathsWithRings</em>.</p> <p>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 <strong>--MinPathLength</strong> and <strong>--MaxPathLength</strong>. However, all these four options can result in the same set of final atom paths for molecules containing fused, bridged or spiro rings.</p> <p>For molecules containing rings, atom paths starting from each atom can be traversed in four different ways:</p> <p><em>AtomPathsWithoutRings</em> - Atom paths containing no rings and without sharing of bonds in traversed paths.</p> <p><em>AtomPathsWithRings</em> - Atom paths containing rings and without any sharing of bonds in traversed paths.</p> <p><em>AllAtomPathsWithoutRings</em> - All possible atom paths containing no rings and without any sharing of bonds in traversed paths.</p> <p><em>AllAtomPathsWithRings</em> - All possible atom paths containing rings and with sharing of bonds in traversed paths.</p> <p>Atom path traversal is terminated at the ring atom.</p> <p>Based on values specified for for <strong>-p, --PathMode</strong>, <strong>--MinPathLength</strong> and <strong>--MaxPathLength</strong>, all appropriate atom paths are generated for each atom in the molecule and collected in a list.</p> <p>For each atom path in the filtered atom paths list, an atom path string is created using value of <strong>-a, --AtomIdentifierType</strong> and specified values to use for a particular atom identifier type. Value of <strong>-u, --UseBondSymbols</strong> 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: <em>1 - None; 2 - '='; 3 - '#'; 1.5 or aromatic - ':'; others: bond order value</em>. 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.</p> <p><strong>UseUniquePaths</strong> controls the removal of structurally duplicate atom path strings are removed from the list.</p> <p>For <em>PathLengthBits</em> value of <strong>-m, --mode</strong> option, each atom path is hashed to a 32 bit unsigned integer key using <strong>TextUtil::HashCode</strong> function. Using the hash key as a seed for a random number generator, a random integer value between 0 and <strong>--Size</strong> is used to set corresponding bits in the fingerprint bit-vector string. Value of <strong>--NumOfBitsToSetPerPaths</strong> option controls the number of time a random number is generated to set corresponding bits.</p> <p>For <em> PathLengthCount</em> value of <strong>-m, --mode</strong> option, the number of times an atom path appears is tracked and a fingerprints count-string corresponding to count of atom paths is generated.</p> <p>For molecule containing rings, combination of <strong>-p, --PathMode</strong> and <strong>--UseBondSymbols</strong> allows generation of up to 8 different types of atom path length strings:</p> <div class="OptionsBox"> AllowSharedBonds AllowRings UseBondSymbols</div> <div class="OptionsBox"> 0 0 1 - AtomPathsNoCyclesWithBondSymbols <br/> 0 1 1 - AtomPathsWithCyclesWithBondSymbols</div> <div class="OptionsBox"> 1 0 1 - AllAtomPathsNoCyclesWithBondSymbols <br/> 1 1 1 - AllAtomPathsWithCyclesWithBondSymbols [ DEFAULT ]</div> <div class="OptionsBox"> 0 0 0 - AtomPathsNoCyclesNoBondSymbols <br/> 0 1 0 - AtomPathsWithCyclesNoBondSymbols</div> <div class="OptionsBox"> 1 0 0 - AllAtomPathsNoCyclesNoBondSymbols <br/> 1 1 0 - AllAtomPathsWithCyclesNoWithBondSymbols</div> <p>Default atom path length fingerprints generation for molecules containing rings with <em>AllAtomPathsWithRings</em> value for <strong>-p, --PathMode</strong>, <em>Yes</em> value for <strong>--UseBondSymbols</strong>, <em>2</em> value for <strong>--MinPathLength</strong> and <em>8</em> value for <strong>--MaxPathLength</strong> is the most time consuming. Combinations of other options can substantially speed up fingerprint generation for molecules containing complex ring systems.</p> <p>Additionally, value for option <strong>-a, --AtomIdentifierType</strong> in conjunction with corresponding specified values for atom types changes the nature of atom path length strings and the fingerprints.</p> </dd> <dt><strong><strong>-q, --quote</strong> <em>Yes | No</em></strong></dt> <dd> <p>Put quote around column values in output CSV/TSV text file(s). Possible values: <em>Yes or No</em>. Default value: <em>Yes</em>.</p> </dd> <dt><strong><strong>-r, --root</strong> <em>RootName</em></strong></dt> <dd> <p>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.</p> </dd> <dt><strong><strong>-s, --size</strong> <em>number</em></strong></dt> <dd> <p>Size of fingerprints. Default value: <em>1024</em>. Valid values correspond to any positive integer which satisfies the following criteria: power of 2, >= 32 and <= 2 ** 32.</p> <p>Examples:</p> <div class="OptionsBox"> 256 512 2048</div> </dd> <dt><strong><strong>-u, --UseBondSymbols</strong> <em>Yes | No</em></strong></dt> <dd> <p>Specify whether to use bond symbols for atom paths during generation of atom path strings. Possible values: <em>Yes or No</em>. Default value: <em>Yes</em>.</p> <p><em>No</em> value option for <strong>-u, --UseBondSymbols</strong> allows the generation of fingerprints corresponding purely to atoms disregarding all bonds.</p> </dd> <dt><strong><strong>--UsePerlCoreRandom</strong> <em>Yes | No</em></strong></dt> <dd> <p>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: <em>Yes or No</em>. Default value: <em>Yes</em>.</p> <p><em>No</em> value option for <strong>--UsePerlCoreRandom</strong> allows the generation of fingerprints bit-vector strings which are same across different platforms.</p> <p>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.</p> <p>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.</p> </dd> <dt><strong><strong>--UseUniquePaths</strong> <em>Yes | No</em></strong></dt> <dd> <p>Specify whether to use structurally unique atom paths during generation of atom path strings. Possible values: <em>Yes or No</em>. Default value: <em>Yes</em>.</p> <p><em>No</em> value option for <strong>--UseUniquePaths</strong> allows usage of all atom paths generated by <strong>-p, --PathMode</strong> option value for generation of atom path strings leading to duplicate path count during <em>PathLengthCount</em> value of <strong>-m, --mode</strong> option. It doesn't change fingerprint string generated during <em>PathLengthBits</em> value of <strong>-m, --mode</strong>.</p> <p>For example, during <em>AllAtomPathsWithRings</em> value of <strong>-p, --PathMode</strong> 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.</p> </dd> <dt><strong><strong>-v, --VectorStringFormat</strong> <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt> <dd> <p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by <strong>--output</strong> used during <em>PathLengthCount</em> value of <strong>-m, --mode</strong> option. Possible values: <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em>. Defaultvalue: <em>IDsAndValuesString</em>.</p> <p>Examples:</p> <div class="OptionsBox"> FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength <br/> 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 <br/> 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1 <br/> 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO <br/> 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....</div> <div class="OptionsBox"> FingerprintsVector;PathLengthCount:EStateAtomTypes:MinLength1:MaxLengt <br/> h8;454;NumericalValues;IDsAndValuesPairsString;aaCH 14 aasC 8 aasN 1 d <br/> O 2 dssC 2 sCH3 2 sF 1 sOH 3 ssCH2 4 ssNH 1 sssCH 3 aaCH:aaCH 10 aaCH: <br/> aasC 8 aasC:aasC 3 aasC:aasN 2 aasCaasC 2 aasCdssC 1 aasCsF 1 aasCssNH <br/> 1 aasCsssCH 1 aasNssCH2 1 dO=dssC 2 dssCsOH 1 dssCssCH2 1 dssCssNH 1 <br/> sCH3sssCH 2 sOHsssCH 2 ssCH2ssCH2 1 ssCH2sssCH 4 aaCH:aaCH:aaCH 6 a...</div> </dd> <dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt> <dd> <p>Location of working directory. Default: current directory.</p> </dd> </dl> <p> </p> <h2>EXAMPLES</h2> <p>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:</p> <div class="ExampleBox"> % PathLengthFingerprints.pl -o -r SamplePLFPHex Sample.sdf</div> <p>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:</p> <div class="ExampleBox"> % PathLengthFingerprints.pl --output all -o -r SamplePLFPHex Sample.sdf</div> <p>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:</p> <div class="ExampleBox"> % PathLengthFingerprints.pl --BitStringFormat BinaryString --size 2048 -o -r SamplePLFPBin Sample.sdf</div> <p>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:</p> <div class="ExampleBox"> % PathLengthFingerprints.pl -m PathLengthCount -o -r SamplePLFPCount Sample.sdf</div> <p>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:</p> <div class="ExampleBox"> % PathLengthFingerprints.pl -m PathLengthCount --AtomIdentifierType EStateAtomTypes -o -r SamplePLFPCount Sample.sdf</div> <p>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:</p> <div class="ExampleBox"> % PathLengthFingerprints.pl -m PathLengthCount --AtomIdentifierType SLogPAtomTypes -o -r SamplePLFPCount Sample.sdf</div> <p>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:</p> <div class="ExampleBox"> % PathLengthFingerprints.pl -m PathLengthCount --VectorStringFormat ValuesAndIDsPairsString -o -r SamplePLFPCount Sample.sdf</div> <p>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:</p> <div class="ExampleBox"> % PathLengthFingerprints.pl -m PathLengthCount --AtomIdentifierType AtomicInvariantsAtomTypes --AtomicInvariantsToUse "AS,X,BO" -o -r SamplePLFPCount Sample.sdf</div> <p>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:</p> <div class="ExampleBox"> % PathLengthFingerprints.pl -m PathLengthCount --UseUniquePaths No -o --CompoundIDMode MolName -r SamplePLFPCount --UseUniquePaths No Sample.sdf</div> <p>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:</p> <div class="ExampleBox"> % PathLengthFingerprints.pl --output all --Fold Yes --FoldedSize 512 -o -r SamplePLFPHex Sample.sdf</div> <p>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:</p> <div class="ExampleBox"> % PathLengthFingerprints.pl -p AtomPathsWithoutRings --DataFieldsMode All -o -r SamplePLFPHex Sample.sdf</div> <p>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:</p> <div class="ExampleBox"> % PathLengthFingerprints.pl -p AtomPathsWithRings --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix --CompoundID Cmpd --CompoundIDLabel MolID --FingerprintsLabel PathLengthFP --OutDelim Tab -r SamplePLFPHex -o Sample.sdf</div> <p>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:</p> <div class="ExampleBox"> % PathLengthFingerprints.pl -m PathLengthCount --DetectAromaticity No -o -r SamplePLFPCount Sample.sdf</div> <p>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:</p> <div class="ExampleBox"> % PathLengthFingerprints.pl --MinPathLength 2 --MaxPathLength 6 -o -r SamplePLFPHex Sample.sdf</div> <p> </p> <h2>AUTHOR</h2> <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> <p> </p> <h2>SEE ALSO</h2> <p><a href="./InfoFingerprintsFiles.html">InfoFingerprintsFiles.pl</a>, <a href="./SimilarityMatricesFingerprints.html">SimilarityMatricesFingerprints.pl</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pl</a>,  <a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>, <a href="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>,  <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pl</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pl</a>,  <a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pl</a>, <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pl</a> </p> <p> </p> <h2>COPYRIGHT</h2> <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> <p>This file is part of MayaChemTools.</p> <p>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.</p> <p> </p><p> </p><div class="DocNav"> <table width="100%" border=0 cellpadding=0 cellspacing=2> <tr align="left" valign="top"><td width="33%" align="left"><a href="./MolFilesToSD.html" title="MolFilesToSD.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./SDFilesToHTML.html" title="SDFilesToHTML.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>PathLengthFingerprints.pl</strong></td></tr> </table> </div> <br /> <center> <img src="../../images/h2o2.png"> </center> </body> </html>