Mercurial > repos > deepakjadmin > mayatool3_test3
diff mayachemtools/docs/scripts/html/PathLengthFingerprints.html @ 0:73ae111cf86f draft
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 11:55:01 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/scripts/html/PathLengthFingerprints.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,800 @@ +<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>