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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/MACCSKeysFingerprints.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,1027 @@ +<html> +<head> +<title>MayaChemTools:Documentation:MACCSKeysFingerprints.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="./JoinTextFiles.html" title="JoinTextFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./MergeTextFiles.html" title="MergeTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>MACCSKeysFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/MACCSKeysFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/MACCSKeysFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/MACCSKeysFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/MACCSKeysFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/MACCSKeysFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>MACCSKeysFingerprints.pl - Generate MACCS key fingerprints for SD files</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>MACCSKeysFingerprints.pl SDFile(s)...</p> +<p>MACCSKeysFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</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>-f, --Filter</strong> <em>Yes | No</em>] [<strong>--FingerprintsLabel</strong> <em>text</em>] [<strong>-h, --help</strong>] [<strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em>] +[<strong>-m, --mode</strong> <em>MACCSKeyBits | MACCSKeyCount</em>] [<strong>--OutDelim</strong> <em>comma | tab | semicolon</em>] +[<strong>--output</strong> <em>SD | FP | text | all</em>] [<strong>-o, --overwrite</strong>] +[<strong>-q, --quote</strong> <em>Yes | No</em>] [<strong>-r, --root</strong> <em>RootName</em>] [<strong>-s, --size</strong> <em>number</em>] +[<strong>-v, --VectorStringFormat</strong> <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em>] +[<strong>-w, --WorkingDir</strong> <em>DirName</em>]</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>Generate MACCS (Molecular ACCess System) keys fingerprints [ Ref 45-47 ] 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>For each MACCS keys definition, atoms are processed to determine their membership to the key +and the appropriate molecular fingerprints strings are generated. An atom can belong to multiple +MACCS keys.</p> +<p>For <em>MACCSKeyBits</em> value of <strong>-m, --mode</strong> option, a fingerprint bit-vector string containing +zeros and ones is generated and for <em>MACCSKeyCount</em> value, a fingerprint vector string +corresponding to number of MACCS keys [ Ref 45-47 ] is generated.</p> +<p><em>MACCSKeyBits | MACCSKeyCount</em> values for <strong>-m, --mode</strong> option along with two possible +<em>166 | 322</em> values of <strong>-s, --size</strong> supports generation of four different types of MACCS +keys fingerprint: <em>MACCS166KeyBits, MACCS166KeyCount, MACCS322KeyBits, MACCS322KeyCount</em>.</p> +<p>Example of <em>SD</em> file containing MAACS keys fingerprints string data:</p> +<div class="OptionsBox"> + ... ... +<br/> ... ... +<br/> $$$$ +<br/> ... ... +<br/> ... ... +<br/> ... ... +<br/> 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +<br/> ... ... +<br/> 2 3 1 0 0 0 0 +<br/> ... ... +<br/> M END +<br/> > <CmpdID> +<br/> Cmpd1</div> +<div class="OptionsBox"> + > <MACCSKeysFingerprints> +<br/> FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;000000000 +<br/> 00000000000000000000000000000000100100001001000000001001000000001110001 +<br/> 00101010111100011011000100110110000011011110100110111111111111011111111 +<br/> 11111111110111000</div> +<div class="OptionsBox"> + $$$$ +<br/> ... ... +<br/> ... ...</div> +<p>Example of <em>FP</em> file containing MAACS keys fingerprints string data:</p> +<div class="OptionsBox"> + # +<br/> # Package = MayaChemTools 7.4 +<br/> # Release Date = Oct 21, 2010 +<br/> # +<br/> # TimeStamp = Fri Mar 11 14:57:24 2011 +<br/> # +<br/> # FingerprintsStringType = FingerprintsBitVector +<br/> # +<br/> # Description = MACCSKeyBits +<br/> # Size = 166 +<br/> # BitStringFormat = BinaryString +<br/> # BitsOrder = Ascending +<br/> # +<br/> Cmpd1 00000000000000000000000000000000000000000100100001001000000001... +<br/> Cmpd2 00000000000000000000000010000000001000000010000000001000000000... +<br/> ... ... +<br/> ... ..</div> +<p>Example of CSV <em>Text</em> file containing MAACS keys fingerprints string data:</p> +<div class="OptionsBox"> + "CompoundID","MACCSKeysFingerprints" +<br/> "Cmpd1","FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending; +<br/> 00000000000000000000000000000000000000000100100001001000000001001000000 +<br/> 00111000100101010111100011011000100110110000011011110100110111111111111 +<br/> 01111111111111111110111000" +<br/> ... ... +<br/> ... ...</div> +<p>The current release of MayaChemTools generates the following types of MACCS keys +fingerprints bit-vector and vector strings:</p> +<div class="OptionsBox"> + FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000 +<br/> 0000000000000000000000000000000001001000010010000000010010000000011100 +<br/> 0100101010111100011011000100110110000011011110100110111111111111011111 +<br/> 11111111111110111000</div> +<div class="OptionsBox"> + FingerprintsBitVector;MACCSKeyBits;166;HexadecimalString;Ascending;000 +<br/> 000000021210210e845f8d8c60b79dffbffffd1</div> +<div class="OptionsBox"> + FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011 +<br/> 1110011111100101111111000111101100110000000000000011100010000000000000 +<br/> 0000000000000000000000000000000000000000000000101000000000000000000000 +<br/> 0000000000000000000000000000000000000000000000000000000000000000000000 +<br/> 0000000000000000000000000000000000000011000000000000000000000000000000 +<br/> 0000000000000000000000000000000000000000</div> +<div class="OptionsBox"> + FingerprintsBitVector;MACCSKeyBits;322;HexadecimalString;Ascending;7d7 +<br/> e7af3edc000c1100000000000000500000000000000000000000000000000300000000 +<br/> 000000000</div> +<div class="OptionsBox"> + FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri +<br/> ng;0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +<br/> 0 0 0 0 0 0 0 1 0 0 3 0 0 0 0 4 0 0 2 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0 +<br/> 0 0 0 0 1 1 8 0 0 0 1 0 0 1 0 1 0 1 0 3 1 3 1 0 0 0 1 2 0 11 1 0 0 0 +<br/> 5 0 0 1 2 0 1 1 0 0 0 0 0 1 1 0 1 1 1 1 0 4 0 0 1 1 0 4 6 1 1 1 2 1 1 +<br/> 3 5 2 2 0 5 3 5 1 1 2 5 1 2 1 2 4 8 3 5 5 2 2 0 3 5 4 1</div> +<div class="OptionsBox"> + FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri +<br/> ng;14 8 2 0 2 0 4 4 2 1 4 0 0 2 5 10 5 2 1 0 0 2 0 5 13 3 28 5 5 3 0 0 +<br/> 0 4 2 1 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 3 0 0 0 1 0 +<br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +<br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 0 0 0 0 0 0 0 0 0 +<br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...</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> +</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>MACCSKeyBits</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>MACCSKeyBits</em> value of <strong>-m, --mode</strong> option. Possible +values: <em>BinaryString, HexadecimalString</em>. Default value: <em>BinaryString</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;MACCSKeyBits;166;BinaryString;Ascending;00000000 +<br/> 0000000000000000000000000000000001001000010010000000010010000000011100 +<br/> 0100101010111100011011000100110110000011011110100110111111111111011111 +<br/> 11111111111110111000</div> +<div class="OptionsBox"> + FingerprintsBitVector;MACCSKeyBits;166;HexadecimalString;Ascending;000 +<br/> 000000021210210e845f8d8c60b79dffbffffd1</div> +<div class="OptionsBox"> + FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011 +<br/> 1110011111100101111111000111101100110000000000000011100010000000000000 +<br/> 0000000000000000000000000000000000000000000000101000000000000000000000 +<br/> 0000000000000000000000000000000000000000000000000000000000000000000000 +<br/> 0000000000000000000000000000000000000011000000000000000000000000000000 +<br/> 0000000000000000000000000000000000000000</div> +<div class="OptionsBox"> + FingerprintsBitVector;MACCSKeyBits;322;HexadecimalString;Ascending;7d7 +<br/> e7af3edc000c1100000000000000500000000000000000000000000000000300000000 +<br/> 000000000</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>-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>MACCSKeyFingerprints</em>.</p> +</dd> +<dt><strong><strong>-h, --help</strong></strong></dt> +<dd> +<p>Print this help message.</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>MACCSKeyBits | MACCSKeyCount</em></strong></dt> +<dd> +<p>Specify type of MACCS keys [ Ref 45-47 ] fingerprints to generate for molecules in <em>SDFile(s)</em>. +Possible values: <em>MACCSKeyBits, MACCSKeyCount</em>. Default value: <em>MACCSKeyBits</em>.</p> +<p>For <em>MACCSKeyBits</em> value of <strong>-m, --mode</strong> option, a fingerprint bit-vector string containing +zeros and ones is generated and for <em>MACCSKeyCount</em> value, a fingerprint vector string +corresponding to number of MACCS keys is generated.</p> +<p><em>MACCSKeyBits | MACCSKeyCount</em> values for <strong>-m, --mode</strong> option along with two possible +<em>166 | 322</em> values of <strong>-s, --size</strong> supports generation of four different types of MACCS +keys fingerprint: <em>MACCS166KeyBits, MACCS166KeyCount, MACCS322KeyBits, MACCS322KeyCount</em>.</p> +<p>Definition of MACCS keys uses the following atom and bond symbols to define atom and +bond environments:</p> +<div class="OptionsBox"> + Atom symbols for 166 keys [ Ref 47 ]:</div> +<div class="OptionsBox"> + A : Any valid periodic table element symbol +<br/> Q : Hetro atoms; any non-C or non-H atom +<br/> X : Halogens; F, Cl, Br, I +<br/> Z : Others; other than H, C, N, O, Si, P, S, F, Cl, Br, I</div> +<div class="OptionsBox"> + Atom symbols for 322 keys [ Ref 46 ]:</div> +<div class="OptionsBox"> + A : Any valid periodic table element symbol +<br/> Q : Hetro atoms; any non-C or non-H atom +<br/> X : Others; other than H, C, N, O, Si, P, S, F, Cl, Br, I +<br/> Z is neither defined nor used</div> +<div class="OptionsBox"> + Bond types:</div> +<div class="OptionsBox"> + - : Single +<br/> = : Double +<br/> T : Triple +<br/> # : Triple +<br/> ~ : Single or double query bond +<br/> % : An aromatic query bond</div> +<div class="OptionsBox"> + None : Any bond type; no explicit bond specified</div> +<div class="OptionsBox"> + $ : Ring bond; $ before a bond type specifies ring bond +<br/> ! : Chain or non-ring bond; ! before a bond type specifies chain bond</div> +<div class="OptionsBox"> + @ : A ring linkage and the number following it specifies the + atoms position in the line, thus @1 means linked back to the first + atom in the list.</div> +<div class="OptionsBox"> + Aromatic: Kekule or Arom5</div> +<div class="OptionsBox"> + Kekule: Bonds in 6-membered rings with alternate single/double bonds + or perimeter bonds +<br/> Arom5: Bonds in 5-membered rings with two double bonds and a hetro + atom at the apex of the ring.</div> +<p>MACCS 166 keys [ Ref 45-47 ] are defined as follows:</p> +<div class="OptionsBox"> + Key Description</div> +<div class="OptionsBox"> + 1 ISOTOPE +<br/> 2 103 < ATOMIC NO. < 256 +<br/> 3 GROUP IVA,VA,VIA PERIODS 4-6 (Ge...) +<br/> 4 ACTINIDE +<br/> 5 GROUP IIIB,IVB (Sc...) +<br/> 6 LANTHANIDE +<br/> 7 GROUP VB,VIB,VIIB (V...) +<br/> 8 QAAA@1 +<br/> 9 GROUP VIII (Fe...) +<br/> 10 GROUP IIA (ALKALINE EARTH) +<br/> 11 4M RING +<br/> 12 GROUP IB,IIB (Cu...) +<br/> 13 ON(C)C +<br/> 14 S-S +<br/> 15 OC(O)O +<br/> 16 QAA@1 +<br/> 17 CTC +<br/> 18 GROUP IIIA (B...) +<br/> 19 7M RING +<br/> 20 SI +<br/> 21 C=C(Q)Q +<br/> 22 3M RING +<br/> 23 NC(O)O +<br/> 24 N-O +<br/> 25 NC(N)N +<br/> 26 C$=C($A)$A +<br/> 27 I +<br/> 28 QCH2Q +<br/> 29 P +<br/> 30 CQ(C)(C)A +<br/> 31 QX +<br/> 32 CSN +<br/> 33 NS +<br/> 34 CH2=A +<br/> 35 GROUP IA (ALKALI METAL) +<br/> 36 S HETEROCYCLE +<br/> 37 NC(O)N +<br/> 38 NC(C)N +<br/> 39 OS(O)O +<br/> 40 S-O +<br/> 41 CTN +<br/> 42 F +<br/> 43 QHAQH +<br/> 44 OTHER +<br/> 45 C=CN +<br/> 46 BR +<br/> 47 SAN +<br/> 48 OQ(O)O +<br/> 49 CHARGE +<br/> 50 C=C(C)C +<br/> 51 CSO +<br/> 52 NN +<br/> 53 QHAAAQH +<br/> 54 QHAAQH +<br/> 55 OSO +<br/> 56 ON(O)C +<br/> 57 O HETEROCYCLE +<br/> 58 QSQ +<br/> 59 Snot%A%A +<br/> 60 S=O +<br/> 61 AS(A)A +<br/> 62 A$A!A$A +<br/> 63 N=O +<br/> 64 A$A!S +<br/> 65 C%N +<br/> 66 CC(C)(C)A +<br/> 67 QS +<br/> 68 QHQH (&...) +<br/> 69 QQH +<br/> 70 QNQ +<br/> 71 NO +<br/> 72 OAAO +<br/> 73 S=A +<br/> 74 CH3ACH3 +<br/> 75 A!N$A +<br/> 76 C=C(A)A +<br/> 77 NAN +<br/> 78 C=N +<br/> 79 NAAN +<br/> 80 NAAAN +<br/> 81 SA(A)A +<br/> 82 ACH2QH +<br/> 83 QAAAA@1 +<br/> 84 NH2 +<br/> 85 CN(C)C +<br/> 86 CH2QCH2 +<br/> 87 X!A$A +<br/> 88 S +<br/> 89 OAAAO +<br/> 90 QHAACH2A +<br/> 91 QHAAACH2A +<br/> 92 OC(N)C +<br/> 93 QCH3 +<br/> 94 QN +<br/> 95 NAAO +<br/> 96 5M RING +<br/> 97 NAAAO +<br/> 98 QAAAAA@1 +<br/> 99 C=C +<br/> 100 ACH2N +<br/> 101 8M RING +<br/> 102 QO +<br/> 103 CL +<br/> 104 QHACH2A +<br/> 105 A$A($A)$A +<br/> 106 QA(Q)Q +<br/> 107 XA(A)A +<br/> 108 CH3AAACH2A +<br/> 109 ACH2O +<br/> 110 NCO +<br/> 111 NACH2A +<br/> 112 AA(A)(A)A +<br/> 113 Onot%A%A +<br/> 114 CH3CH2A +<br/> 115 CH3ACH2A +<br/> 116 CH3AACH2A +<br/> 117 NAO +<br/> 118 ACH2CH2A > 1 +<br/> 119 N=A +<br/> 120 HETEROCYCLIC ATOM > 1 (&...) +<br/> 121 N HETEROCYCLE +<br/> 122 AN(A)A +<br/> 123 OCO +<br/> 124 QQ +<br/> 125 AROMATIC RING > 1 +<br/> 126 A!O!A +<br/> 127 A$A!O > 1 (&...) +<br/> 128 ACH2AAACH2A +<br/> 129 ACH2AACH2A +<br/> 130 QQ > 1 (&...) +<br/> 131 QH > 1 +<br/> 132 OACH2A +<br/> 133 A$A!N +<br/> 134 X (HALOGEN) +<br/> 135 Nnot%A%A +<br/> 136 O=A > 1 +<br/> 137 HETEROCYCLE +<br/> 138 QCH2A > 1 (&...) +<br/> 139 OH +<br/> 140 O > 3 (&...) +<br/> 141 CH3 > 2 (&...) +<br/> 142 N > 1 +<br/> 143 A$A!O +<br/> 144 Anot%A%Anot%A +<br/> 145 6M RING > 1 +<br/> 146 O > 2 +<br/> 147 ACH2CH2A +<br/> 148 AQ(A)A +<br/> 149 CH3 > 1 +<br/> 150 A!A$A!A +<br/> 151 NH +<br/> 152 OC(C)C +<br/> 153 QCH2A +<br/> 154 C=O +<br/> 155 A!CH2!A +<br/> 156 NA(A)A +<br/> 157 C-O +<br/> 158 C-N +<br/> 159 O > 1 +<br/> 160 CH3 +<br/> 161 N +<br/> 162 AROMATIC +<br/> 163 6M RING +<br/> 164 O +<br/> 165 RING +<br/> 166 FRAGMENTS</div> +<p>MACCS 322 keys set as defined in tables 1, 2 and 3 [ Ref 46 ] include:</p> +<div class="OptionsBox"> + . 26 atom properties of type P, as listed in Table 1 +<br/> . 32 one-atom environments, as listed in Table 3 +<br/> . 264 atom-bond-atom combinations listed in Table 4</div> +<p>Total number of keys in three tables is : 322</p> +<p>Atom symbol, X, used for 322 keys [ Ref 46 ] doesn't refer to Halogens as it does for 166 keys. In +order to keep the definition of 322 keys consistent with the published definitions, the symbol X is +used to imply "others" atoms, but it's internally mapped to symbol X as defined for 166 keys +during the generation of key values.</p> +<p>Atom properties-based keys (26):</p> +<div class="OptionsBox"> + Key Description +<br/> 1 A(AAA) or AA(A)A - atom with at least three neighbors +<br/> 2 Q - heteroatom +<br/> 3 Anot%not-A - atom involved in one or more multiple bonds, not aromatic +<br/> 4 A(AAAA) or AA(A)(A)A - atom with at least four neighbors +<br/> 5 A(QQ) or QA(Q) - atom with at least two heteroatom neighbors +<br/> 6 A(QQQ) or QA(Q)Q - atom with at least three heteroatom neighbors +<br/> 7 QH - heteroatom with at least one hydrogen attached +<br/> 8 CH2(AA) or ACH2A - carbon with at least two single bonds and at least + two hydrogens attached +<br/> 9 CH3(A) or ACH3 - carbon with at least one single bond and at least three + hydrogens attached +<br/> 10 Halogen +<br/> 11 A(-A-A-A) or A-A(-A)-A - atom has at least three single bonds +<br/> 12 AAAAAA@1 > 2 - atom is in at least two different six-membered rings +<br/> 13 A($A$A$A) or A$A($A)$A - atom has more than two ring bonds +<br/> 14 A$A!A$A - atom is at a ring/chain boundary. When a comparison is done + with another atom the path passes through the chain bond. +<br/> 15 Anot%A%Anot%A - atom is at an aromatic/nonaromatic boundary. When a + comparison is done with another atom the path + passes through the aromatic bond. +<br/> 16 A!A!A - atom with more than one chain bond +<br/> 17 A!A$A!A - atom is at a ring/chain boundary. When a comparison is done + with another atom the path passes through the ring bond. +<br/> 18 A%Anot%A%A - atom is at an aromatic/nonaromatic boundary. When a + comparison is done with another atom the + path passes through the nonaromatic bond. +<br/> 19 HETEROCYCLE - atom is a heteroatom in a ring. +<br/> 20 rare properties: atom with five or more neighbors, atom in + four or more rings, or atom types other than + H, C, N, O, S, F, Cl, Br, or I +<br/> 21 rare properties: atom has a charge, is an isotope, has two or + more multiple bonds, or has a triple bond. +<br/> 22 N - nitrogen +<br/> 23 S - sulfur +<br/> 24 O - oxygen +<br/> 25 A(AA)A(A)A(AA) - atom has two neighbors, each with three or + more neighbors (including the central atom). +<br/> 26 CHACH2 - atom has two hydrocarbon (CH2) neighbors</div> +<p>Atomic environments properties-based keys (32):</p> +<div class="OptionsBox"> + Key Description +<br/> 27 C(CC) +<br/> 28 C(CCC) +<br/> 29 C(CN) +<br/> 30 C(CCN) +<br/> 31 C(NN) +<br/> 32 C(NNC) +<br/> 33 C(NNN) +<br/> 34 C(CO) +<br/> 35 C(CCO) +<br/> 36 C(NO) +<br/> 37 C(NCO) +<br/> 38 C(NNO) +<br/> 39 C(OO) +<br/> 40 C(COO) +<br/> 41 C(NOO) +<br/> 42 C(OOO) +<br/> 43 Q(CC) +<br/> 44 Q(CCC) +<br/> 45 Q(CN) +<br/> 46 Q(CCN) +<br/> 47 Q(NN) +<br/> 48 Q(CNN) +<br/> 49 Q(NNN) +<br/> 50 Q(CO) +<br/> 51 Q(CCO) +<br/> 52 Q(NO) +<br/> 53 Q(CNO) +<br/> 54 Q(NNO) +<br/> 55 Q(OO) +<br/> 56 Q(COO) +<br/> 57 Q(NOO) +<br/> 58 Q(OOO)</div> +<p>Note: The first symbol is the central atom, with atoms bonded to the central atom listed in +parentheses. Q is any non-C, non-H atom. If only two atoms are in parentheses, there is +no implication concerning the other atoms bonded to the central atom.</p> +<p>Atom-Bond-Atom properties-based keys: (264)</p> +<div class="OptionsBox"> + Key Description +<br/> 59 C-C +<br/> 60 C-N +<br/> 61 C-O +<br/> 62 C-S +<br/> 63 C-Cl +<br/> 64 C-P +<br/> 65 C-F +<br/> 66 C-Br +<br/> 67 C-Si +<br/> 68 C-I +<br/> 69 C-X +<br/> 70 N-N +<br/> 71 N-O +<br/> 72 N-S +<br/> 73 N-Cl +<br/> 74 N-P +<br/> 75 N-F +<br/> 76 N-Br +<br/> 77 N-Si +<br/> 78 N-I +<br/> 79 N-X +<br/> 80 O-O +<br/> 81 O-S +<br/> 82 O-Cl +<br/> 83 O-P +<br/> 84 O-F +<br/> 85 O-Br +<br/> 86 O-Si +<br/> 87 O-I +<br/> 88 O-X +<br/> 89 S-S +<br/> 90 S-Cl +<br/> 91 S-P +<br/> 92 S-F +<br/> 93 S-Br +<br/> 94 S-Si +<br/> 95 S-I +<br/> 96 S-X +<br/> 97 Cl-Cl +<br/> 98 Cl-P +<br/> 99 Cl-F +<br/> 100 Cl-Br +<br/> 101 Cl-Si +<br/> 102 Cl-I +<br/> 103 Cl-X +<br/> 104 P-P +<br/> 105 P-F +<br/> 106 P-Br +<br/> 107 P-Si +<br/> 108 P-I +<br/> 109 P-X +<br/> 110 F-F +<br/> 111 F-Br +<br/> 112 F-Si +<br/> 113 F-I +<br/> 114 F-X +<br/> 115 Br-Br +<br/> 116 Br-Si +<br/> 117 Br-I +<br/> 118 Br-X +<br/> 119 Si-Si +<br/> 120 Si-I +<br/> 121 Si-X +<br/> 122 I-I +<br/> 123 I-X +<br/> 124 X-X +<br/> 125 C=C +<br/> 126 C=N +<br/> 127 C=O +<br/> 128 C=S +<br/> 129 C=Cl +<br/> 130 C=P +<br/> 131 C=F +<br/> 132 C=Br +<br/> 133 C=Si +<br/> 134 C=I +<br/> 135 C=X +<br/> 136 N=N +<br/> 137 N=O +<br/> 138 N=S +<br/> 139 N=Cl +<br/> 140 N=P +<br/> 141 N=F +<br/> 142 N=Br +<br/> 143 N=Si +<br/> 144 N=I +<br/> 145 N=X +<br/> 146 O=O +<br/> 147 O=S +<br/> 148 O=Cl +<br/> 149 O=P +<br/> 150 O=F +<br/> 151 O=Br +<br/> 152 O=Si +<br/> 153 O=I +<br/> 154 O=X +<br/> 155 S=S +<br/> 156 S=Cl +<br/> 157 S=P +<br/> 158 S=F +<br/> 159 S=Br +<br/> 160 S=Si +<br/> 161 S=I +<br/> 162 S=X +<br/> 163 Cl=Cl +<br/> 164 Cl=P +<br/> 165 Cl=F +<br/> 166 Cl=Br +<br/> 167 Cl=Si +<br/> 168 Cl=I +<br/> 169 Cl=X +<br/> 170 P=P +<br/> 171 P=F +<br/> 172 P=Br +<br/> 173 P=Si +<br/> 174 P=I +<br/> 175 P=X +<br/> 176 F=F +<br/> 177 F=Br +<br/> 178 F=Si +<br/> 179 F=I +<br/> 180 F=X +<br/> 181 Br=Br +<br/> 182 Br=Si +<br/> 183 Br=I +<br/> 184 Br=X +<br/> 185 Si=Si +<br/> 186 Si=I +<br/> 187 Si=X +<br/> 188 I=I +<br/> 189 I=X +<br/> 190 X=X +<br/> 191 C#C +<br/> 192 C#N +<br/> 193 C#O +<br/> 194 C#S +<br/> 195 C#Cl +<br/> 196 C#P +<br/> 197 C#F +<br/> 198 C#Br +<br/> 199 C#Si +<br/> 200 C#I +<br/> 201 C#X +<br/> 202 N#N +<br/> 203 N#O +<br/> 204 N#S +<br/> 205 N#Cl +<br/> 206 N#P +<br/> 207 N#F +<br/> 208 N#Br +<br/> 209 N#Si +<br/> 210 N#I +<br/> 211 N#X +<br/> 212 O#O +<br/> 213 O#S +<br/> 214 O#Cl +<br/> 215 O#P +<br/> 216 O#F +<br/> 217 O#Br +<br/> 218 O#Si +<br/> 219 O#I +<br/> 220 O#X +<br/> 221 S#S +<br/> 222 S#Cl +<br/> 223 S#P +<br/> 224 S#F +<br/> 225 S#Br +<br/> 226 S#Si +<br/> 227 S#I +<br/> 228 S#X +<br/> 229 Cl#Cl +<br/> 230 Cl#P +<br/> 231 Cl#F +<br/> 232 Cl#Br +<br/> 233 Cl#Si +<br/> 234 Cl#I +<br/> 235 Cl#X +<br/> 236 P#P +<br/> 237 P#F +<br/> 238 P#Br +<br/> 239 P#Si +<br/> 240 P#I +<br/> 241 P#X +<br/> 242 F#F +<br/> 243 F#Br +<br/> 244 F#Si +<br/> 245 F#I +<br/> 246 F#X +<br/> 247 Br#Br +<br/> 248 Br#Si +<br/> 249 Br#I +<br/> 250 Br#X +<br/> 251 Si#Si +<br/> 252 Si#I +<br/> 253 Si#X +<br/> 254 I#I +<br/> 255 I#X +<br/> 256 X#X +<br/> 257 C$C +<br/> 258 C$N +<br/> 259 C$O +<br/> 260 C$S +<br/> 261 C$Cl +<br/> 262 C$P +<br/> 263 C$F +<br/> 264 C$Br +<br/> 265 C$Si +<br/> 266 C$I +<br/> 267 C$X +<br/> 268 N$N +<br/> 269 N$O +<br/> 270 N$S +<br/> 271 N$Cl +<br/> 272 N$P +<br/> 273 N$F +<br/> 274 N$Br +<br/> 275 N$Si +<br/> 276 N$I +<br/> 277 N$X +<br/> 278 O$O +<br/> 279 O$S +<br/> 280 O$Cl +<br/> 281 O$P +<br/> 282 O$F +<br/> 283 O$Br +<br/> 284 O$Si +<br/> 285 O$I +<br/> 286 O$X +<br/> 287 S$S +<br/> 288 S$Cl +<br/> 289 S$P +<br/> 290 S$F +<br/> 291 S$Br +<br/> 292 S$Si +<br/> 293 S$I +<br/> 294 S$X +<br/> 295 Cl$Cl +<br/> 296 Cl$P +<br/> 297 Cl$F +<br/> 298 Cl$Br +<br/> 299 Cl$Si +<br/> 300 Cl$I +<br/> 301 Cl$X +<br/> 302 P$P +<br/> 303 P$F +<br/> 304 P$Br +<br/> 305 P$Si +<br/> 306 P$I +<br/> 307 P$X +<br/> 308 F$F +<br/> 309 F$Br +<br/> 310 F$Si +<br/> 311 F$I +<br/> 312 F$X +<br/> 313 Br$Br +<br/> 314 Br$Si +<br/> 315 Br$I +<br/> 316 Br$X +<br/> 317 Si$Si +<br/> 318 Si$I +<br/> 319 Si$X +<br/> 320 I$I +<br/> 321 I$X +<br/> 322 X$X</div> +</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>-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><MACCSKeysFP>.<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 MACCS keys [ Ref 45-47 ] set to use during fingerprints generation. Possible values: <em>166 or 322</em>. +Default value: <em>166</em>.</p> +</dd> +<dt><strong><strong>-v, --VectorStringFormat</strong> <em>ValuesString | 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>MACCSKeyCount</em> value of <strong>-m, --mode</strong> option. Possible +values: <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | +ValuesAndIDsPairsString</em>. Defaultvalue: <em>ValuesString</em>.</p> +<p>Examples:</p> +<div class="OptionsBox"> + FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri +<br/> ng;0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +<br/> 0 0 0 0 0 0 0 1 0 0 3 0 0 0 0 4 0 0 2 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0 +<br/> 0 0 0 0 1 1 8 0 0 0 1 0 0 1 0 1 0 1 0 3 1 3 1 0 0 0 1 2 0 11 1 0 0 0 +<br/> 5 0 0 1 2 0 1 1 0 0 0 0 0 1 1 0 1 1 1 1 0 4 0 0 1 1 0 4 6 1 1 1 2 1 1 +<br/> 3 5 2 2 0 5 3 5 1 1 2 5 1 2 1 2 4 8 3 5 5 2 2 0 3 5 4 1</div> +<div class="OptionsBox"> + FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri +<br/> ng;14 8 2 0 2 0 4 4 2 1 4 0 0 2 5 10 5 2 1 0 0 2 0 5 13 3 28 5 5 3 0 0 +<br/> 0 4 2 1 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 3 0 0 0 1 0 +<br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +<br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 0 0 0 0 0 0 0 0 0 +<br/> 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...</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 MACCS keys fingerprints of size 166 in binary bit-vector string format +and create a SampleMACCS166FPBin.csv file containing sequential compound IDs along with +fingerprints bit-vector strings data, type:</p> +<div class="ExampleBox"> + % MACCSKeysFingerprints.pl -r SampleMACCS166FPBin -o Sample.sdf</div> +<p>To generate MACCS keys fingerprints of size 166 in binary bit-vector string format +and create SampleMACCS166FPBin.sdf, SampleMACCS166FPBin.csv and SampleMACCS166FPBin.csv +files containing sequential compound IDs in CSV file along with fingerprints bit-vector strings data, type:</p> +<div class="ExampleBox"> + % MACCSKeysFingerprints.pl --output all -r SampleMACCS166FPBin + -o Sample.sdf</div> +<p>To generate MACCS keys fingerprints of size 322 in binary bit-vector string format +and create a SampleMACCS322FPBin.csv file containing sequential compound IDs along with +fingerprints bit-vector strings data, type:</p> +<div class="ExampleBox"> + % MACCSKeysFingerprints.pl -size 322 -r SampleMACCS322FPBin -o Sample.sdf</div> +<p>To generate MACCS keys fingerprints of size 166 corresponding to count of keys in +ValuesString format and create a SampleMACCS166FPCount.csv file containing sequential +compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % MACCSKeysFingerprints.pl -m MACCSKeyCount -r SampleMACCS166FPCount + -o Sample.sdf</div> +<p>To generate MACCS keys fingerprints of size 322 corresponding to count of keys in +ValuesString format and create a SampleMACCS322FPCount.csv file containing sequential +compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % MACCSKeysFingerprints.pl -m MACCSKeyCount -size 322 + -r SampleMACCS322FPCount -o Sample.sdf</div> +<p>To generate MACCS keys fingerprints of size 166 in hexadecimal bit-vector string format with +ascending bits order and create a SampleMACCS166FPHex.csv file containing compound IDs +from MolName along with fingerprints bit-vector strings data, type:</p> +<div class="ExampleBox"> + % MACCSKeysFingerprints.pl -m MACCSKeyBits --size 166 --BitStringFormat + HexadecimalString --BitsOrder Ascending --DataFieldsMode CompoundID + --CompoundIDMode MolName -r SampleMACCS166FPBin -o Sample.sdf</div> +<p>To generate MACCS keys fingerprints of size 166 corresponding to count of keys in +IDsAndValuesString format and create a SampleMACCS166FPCount.csv file containing +compound IDs from MolName line along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166 + --VectorStringFormat IDsAndValuesString --DataFieldsMode CompoundID + --CompoundIDMode MolName -r SampleMACCS166FPCount -o Sample.sdf</div> +<p>To generate MACCS keys fingerprints of size 166 corresponding to count of keys in +IDsAndValuesString format and create a SampleMACCS166FPCount.csv file containing +compound IDs using specified data field along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166 + --VectorStringFormat IDsAndValuesString --DataFieldsMode CompoundID + --CompoundIDMode DataField --CompoundID Mol_ID -r + SampleMACCS166FPCount -o Sample.sdf</div> +<p>To generate MACCS keys fingerprints of size 322 corresponding to count of keys in +ValuesString format and create a SampleMACCS322FPCount.tsv file containing compound +IDs derived from combination of molecule name line and an explicit compound prefix +along with fingerprints vector strings data in a column labels MACCSKeyCountFP, type:</p> +<div class="ExampleBox"> + % MACCSKeysFingerprints.pl -m MACCSKeyCount -size 322 --DataFieldsMode + CompoundID --CompoundIDMode MolnameOrLabelPrefix --CompoundID Cmpd + --CompoundIDLabel MolID --FingerprintsLabel MACCSKeyCountFP --OutDelim + Tab -r SampleMACCS322FPCount -o Sample.sdf</div> +<p>To generate MACCS keys fingerprints of size 166 corresponding to count of keys in +ValuesString format and create a SampleMACCS166FPCount.csv file containing +specific data fields columns along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166 + --VectorStringFormat ValuesString --DataFieldsMode Specify --DataFields + Mol_ID -r SampleMACCS166FPCount -o Sample.sdf</div> +<p>To generate MACCS keys fingerprints of size 322 corresponding to count of keys in +ValuesString format and create a SampleMACCS322FPCount.csv file containing +common data fields columns along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 322 + --VectorStringFormat ValuesString --DataFieldsMode Common -r + SampleMACCS322FPCount -o Sample.sdf</div> +<p>To generate MACCS keys fingerprints of size 166 corresponding to count of keys in +ValuesString format and create SampleMACCS166FPCount.sdf, SampleMACCS166FPCount.fpf and +SampleMACCS166FPCount.csv files containing all data fields columns in CSV file +along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166 --output all + --VectorStringFormat ValuesString --DataFieldsMode All -r + SampleMACCS166FPCount -o 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="./PathLengthFingerprints.html">PathLengthFingerprints.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="./JoinTextFiles.html" title="JoinTextFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./MergeTextFiles.html" title="MergeTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>MACCSKeysFingerprints.pl</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>