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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/ExtendedConnectivityFingerprints.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,745 @@ +<html> +<head> +<title>MayaChemTools:Documentation:ExtendedConnectivityFingerprints.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="./EStateIndiciesFingerprints.html" title="EStateIndiciesFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ExtractFromPDBFiles.html" title="ExtractFromPDBFiles.html">Next</a></td><td width="34%" align="middle"><strong>ExtendedConnectivityFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/ExtendedConnectivityFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/ExtendedConnectivityFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/ExtendedConnectivityFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/ExtendedConnectivityFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/ExtendedConnectivityFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>ExtendedConnectivityFingerprints.pl - Generate extended connectivity fingerprints for SD files</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>ExtendedConnectivityFingerprints.pl SDFile(s)...</p> +<p>ExtendedConnectivityFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>] +[<strong>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes</em>] +[<strong>--AtomicInvariantsToUse</strong> <em>"AtomicInvariant,AtomicInvariant..."</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>] [<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>ExtendedConnectivity | ExtendedConnecticityCount | ExtendedConnecticityBits</em>] +[<strong>-n, --NeighborhoodRadius</strong> <em>number</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>--UsePerlCoreRandom</strong> <em>Yes | No</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 extended connectivity fingerprints [ Ref 48, Ref 52 ] for <em>SDFile(s)</em> and create appropriate +SD, FP or CSV/TSV text file(s) containing fingerprints 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 extended connectivity 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 values specified for <strong>-a, --AtomIdentifierType</strong>, <strong>--AtomicInvariantsToUse</strong> +and <strong>--FunctionalClassesToUse</strong>, initial atom types are assigned to all non-hydrogen atoms in +a molecule and these atom types strings are converted into initial atom identifier integers using +<strong>TextUtil::HashCode</strong> function. The duplicate atom identifiers are removed.</p> +<p>For <strong>-n, --NeighborhoodRadius</strong> value of <em>0</em>, the initial set of unique atom identifiers comprises +the molecule fingerprints. Otherwise, atom neighborhoods are generated for each non-hydrogen +atom up to specified <strong>-n, --NeighborhoodRadius</strong> value. For each non-hydrogen central atom +at a specific radius, its neighbors at next radius level along with their bond orders and previously +calculated atom identifiers are collected which in turn are used to generate a new integer +atom identifier; the bond orders and atom identifier pairs list is first sorted by bond order +followed by atom identifiers to make these values graph invariant.</p> +<p>After integer atom identifiers have been generated for all non-hydrogen atoms at all specified +neighborhood radii, the duplicate integer atom identifiers corresponding to same hash code +value generated using <strong>TextUtil::HashCode</strong> are tracked by keeping the atom identifiers at +lower radius. Additionally, all structurally duplicate integer atom identifiers at each specified +radius are also tracked by identifying equivalent atoms and bonds corresponding to substructures +used for generating atom identifier and keeping integer atom identifier with lowest value.</p> +<p>For <em>ExtendedConnnectivity</em> value of fingerprints <strong>-m, --mode</strong>, the duplicate identifiers are +removed from the list and the unique atom identifiers constitute the extended connectivity +fingerprints of a molecule.</p> +<p>For <em>ExtendedConnnectivityCount</em> value of fingerprints <strong>-m, --mode</strong>, the occurrence of each +unique atom identifiers appears is counted and the unique atom identifiers along with their +count constitute the extended connectivity fingerprints of a molecule.</p> +<p>For <em>ExtendedConnectivityBits</em> value of fingerprints <strong>-m, --mode</strong>, the unique atom identifiers +are used as a random number seed to generate a random integer value between 0 and <strong>--Size</strong> which +in turn is used to set corresponding bits in the fingerprint bit-vector string.</p> +<p>Example of <em>SD</em> file containing extended connectivity fingerprints string data:</p> +<div class="OptionsBox"> + ... ... +<br/> ... ... +<br/> $$$$ +<br/> ... ... +<br/> ... ... +<br/> ... ... +<br/> 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +<br/> ... ... +<br/> 2 3 1 0 0 0 0 +<br/> ... ... +<br/> M END +<br/> > <CmpdID> +<br/> Cmpd1</div> +<div class="OptionsBox"> + > <ExtendedConnectivityFingerprints> +<br/> FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radiu +<br/> s2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391 66 +<br/> 6191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414087 +<br/> 99 49532520 64643108 79385615 96062769 273726379 564565671 855141035 90 +<br/> 6706094 988546669 1018231313 1032696425 1197507444 1331250018 133853...</div> +<div class="OptionsBox"> + $$$$ +<br/> ... ... +<br/> ... ...</div> +<p>Example of <em>FP</em> file containing extended connectivity fingerprints string data:</p> +<div class="OptionsBox"> + # +<br/> # Package = MayaChemTools 7.4 +<br/> # Release Date = Oct 21, 2010 +<br/> # +<br/> # TimeStamp = Fri Mar 11 14:43:57 2011 +<br/> # +<br/> # FingerprintsStringType = FingerprintsVector +<br/> # +<br/> # Description = ExtendedConnectivity:AtomicInvariantsAtomTypes:Radius2 +<br/> # VectorStringFormat = ValuesString +<br/> # VectorValuesType = AlphaNumericalValues +<br/> # +<br/> Cmpd1 60;73555770 333564680 352413391 666191900 1001270906 137167432... +<br/> Cmpd2 41;73555770 333564680 666191900 1142173602 1363635752 14814699... +<br/> ... ... +<br/> ... ..</div> +<p>Example of CSV <em>Text</em> file containing extended connectivity fingerprints string data:</p> +<div class="OptionsBox"> + "CompoundID","ExtendedConnectivityFingerprints" +<br/> "Cmpd1","FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTy +<br/> pes:Radius2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352 +<br/> 413391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 +<br/> 2141408799 49532520 64643108 79385615 96062769 273726379 564565671 8551 +<br/> 41035 906706094 988546669 1018231313 1032696425 1197507444 13312500..." +<br/> ... ... +<br/> ... ...</div> +<p>The current release of MayaChemTools generates the following types of extended connectivity +fingerprints vector strings:</p> +<div class="OptionsBox"> + FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi +<br/> us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391 +<br/> 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414 +<br/> 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103 +<br/> 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338 +<br/> 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...</div> +<div class="OptionsBox"> + FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes +<br/> :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524 +<br/> 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 +<br/> 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...; +<br/> 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2 +<br/> 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1</div> +<div class="OptionsBox"> + FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp +<br/> es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100 +<br/> 0000000001010000000110000011000000000000100000000000000000000000100001 +<br/> 1000000110000000000000000000000000010011000000000000000000000000010000 +<br/> 0000000000000000000000000010000000000000000001000000000000000000000000 +<br/> 0000000000010000100001000000000000101000000000000000100000000000000...</div> +<div class="OptionsBox"> + FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp +<br/> es:Radius2;1024;HexadecimalString;Ascending;000000010050c0600800000803 +<br/> 0300000091000004000000020000100000000124008200020000000040020000000000 +<br/> 2080000000820040010020000000008040000000000080001000000000400000000000 +<br/> 4040000090000061010000000800200000000000001400000000020080000000000020 +<br/> 00008020200000408000</div> +<div class="OptionsBox"> + FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu +<br/> s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8 +<br/> 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567 +<br/> 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012 +<br/> 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455 +<br/> 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...</div> +<div class="OptionsBox"> + FingerprintsVector;ExtendedConnectivityCount:FunctionalClassAtomTypes: +<br/> Radius2;57;NumericalValues;IDsAndValuesString;24769214 508787397 85039 +<br/> 3286 862102353 981185303 1231636850 1649386610 1941540674 263599683 32 +<br/> 9205671 571109041 639579325 683993318 723853089 810600886 885767127...; +<br/> 1 1 1 10 2 22 3 1 3 3 1 1 1 3 2 2 1 2 2 2 3 1 1 1 1 1 14 1 1 1 1 1 1 2 +<br/> 1 2 1 1 2 2 1 1 2 1 1 1 2 1 1 2 1 1 1 1 1 1 1</div> +<div class="OptionsBox"> + FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType +<br/> s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000 +<br/> 0000000001000100000000001000000000000000000000000000000000101000000010 +<br/> 0000001000000000010000000000000000000000000000000000000000000000000100 +<br/> 0000000000001000000000000001000000000001001000000000000000000000000000 +<br/> 0000000000000000100000000000001000000000000000000000000000000000000...</div> +<div class="OptionsBox"> + FingerprintsVector;ExtendedConnectivity:DREIDINGAtomTypes:Radius2;56;A +<br/> lphaNumericalValues;ValuesString;280305427 357928343 721790579 1151822 +<br/> 898 1207111054 1380963747 1568213839 1603445250 4559268 55012922 18094 +<br/> 0813 335715751 534801009 684609658 829361048 972945982 999881534 10076 +<br/> 55741 1213692591 1222032501 1224517934 1235687794 1244268533 152812070 +<br/> 0 1629595024 1856308891 1978806036 2001865095 2096549435 172675415 ...</div> +<div class="OptionsBox"> + FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp +<br/> haNumericalValues;ValuesString;25189973 528584866 662581668 671034184 +<br/> 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450 +<br/> 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430 +<br/> 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134 +<br/> 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...</div> +<div class="OptionsBox"> + FingerprintsVector;ExtendedConnectivity:MMFF94AtomTypes:Radius2;64;Alp +<br/> haNumericalValues;ValuesString;224051550 746527773 998750766 103704190 +<br/> 2 1239701709 1248384926 1259447756 1521678386 1631549126 1909437580 20 +<br/> 37095052 2104274756 2117729376 8770364 31445800 81450228 314289324 344 +<br/> 041929 581773587 638555787 692022098 811840536 929651561 936421792 988 +<br/> 636432 1048624296 1054288509 1369487579 1454058929 1519352190 17271...</div> +<div class="OptionsBox"> + FingerprintsVector;ExtendedConnectivity:SLogPAtomTypes:Radius2;71;Alph +<br/> aNumericalValues;ValuesString;78989290 116507218 489454042 888737940 1 +<br/> 162561799 1241797255 1251494264 1263717127 1471206899 1538061784 17654 +<br/> 07295 1795036542 1809833874 2020454493 2055310842 2117729376 11868981 +<br/> 56731842 149505242 184525155 196984339 288181334 481409282 556716568 6 +<br/> 41915747 679881756 721736571 794256218 908276640 992898760 10987549...</div> +<div class="OptionsBox"> + FingerprintsVector;ExtendedConnectivity:SYBYLAtomTypes:Radius2;58;Alph +<br/> aNumericalValues;ValuesString;199957044 313356892 455463968 465982819 +<br/> 1225318176 1678585943 1883366064 1963811677 2117729376 113784599 19153 +<br/> 8837 196629033 263865277 416380653 477036669 681527491 730724924 90906 +<br/> 5537 1021959189 1133014972 1174311016 1359441203 1573452838 1661585138 +<br/> 1668649038 1684198062 1812312554 1859266290 1891651106 2072549404 ...</div> +<div class="OptionsBox"> + FingerprintsVector;ExtendedConnectivity:TPSAAtomTypes:Radius2;47;Alpha +<br/> NumericalValues;ValuesString;20818206 259344053 862102353 1331904542 1 +<br/> 700688206 265614156 363161397 681332588 810600886 885767127 950172500 +<br/> 951454814 1059668746 1247054493 1382302230 1399502637 1805025917 19189 +<br/> 39561 2114677228 2126402271 8130483 17645742 32278373 149975755 160327 +<br/> 654 256360355 279492740 291251259 317592700 333763396 972105960 101...</div> +<div class="OptionsBox"> + FingerprintsVector;ExtendedConnectivity:UFFAtomTypes:Radius2;56;AlphaN +<br/> umericalValues;ValuesString;280305427 357928343 721790579 1151822898 1 +<br/> 207111054 1380963747 1568213839 1603445250 4559268 55012922 180940813 +<br/> 335715751 534801009 684609658 829361048 972945982 999881534 1007655741 +<br/> 1213692591 1222032501 1224517934 1235687794 1244268533 1528120700 162 +<br/> 9595024 1856308891 1978806036 2001865095 2096549435 172675415 18344...</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>-a, --AtomIdentifierType</strong> <em>AtomicInvariantsAtomTypes | FunctionalClassAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes</em></strong></dt> +<dd> +<p>Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen +atoms during calculation of extended connectivity fingerprints [ Ref 48, Ref 52]. Possible values +in the current release are: <em>AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, +DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, +TPSAAtomTypes, UFFAtomTypes</em>. Default value: <em>AtomicInvariantsAtomTypes</em>.</p> +</dd> +<dt><strong><strong>--AtomicInvariantsToUse</strong> <em>"AtomicInvariant,AtomicInvariant..."</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 invarians are: <em>AS, X, BO, LBO, SB, DB, TB, +H, Ar, RA, FC, MN, SM</em>. Default value [ Ref 24 ]: <em>AS,X,BO,H,FC,MN</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><em>AtomTypes::AtomicInvariantsAtomTypes</em> module is used to assign atomic invariant +atom types.</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>ExtendedConnectivityBits</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>ExtendedConnectivityBits</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;ExtendedConnectivityBits:AtomicInvariantsAtomTyp +<br/> es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100 +<br/> 0000000001010000000110000011000000000000100000000000000000000000100001 +<br/> 1000000110000000000000000000000000010011000000000000000000000000010000 +<br/> 0000000000000000000000000010000000000000000001000000000000000000000000 +<br/> 0000000000010000100001000000000000101000000000000000100000000000000...</div> +<div class="OptionsBox"> + FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType +<br/> s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000 +<br/> 0000000001000100000000001000000000000000000000000000000000101000000010 +<br/> 0000001000000000010000000000000000000000000000000000000000000000000100 +<br/> 0000000000001000000000000001000000000001001000000000000000000000000000 +<br/> 0000000000000000100000000000001000000000000000000000000000000000000...</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>--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>ExtendedConnectivityFingerprints</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>ExtendedConnectivity | ExtendedConnectivityCount | ExtendedConnectivityBits</em></strong></dt> +<dd> +<p>Specify type of extended connectivity fingerprints to generate for molecules in <em>SDFile(s)</em>. +Possible values: <em>ExtendedConnectivity, ExtendedConnecticityCount or +ExtendedConnectivityBits</em>. Default value: <em>ExtendedConnectivity</em>.</p> +<p>For <em>ExtendedConnnectivity</em> value of fingerprints <strong>-m, --mode</strong>, a fingerprint vector +containing unique atom identifiers constitute the extended connectivity fingerprints +of a molecule.</p> +<p>For <em>ExtendedConnnectivityCount</em> value of fingerprints <strong>-m, --mode</strong>, a fingerprint vector +containing unique atom identifiers along with their count constitute the extended connectivity +fingerprints of a molecule.</p> +<p>For <em>ExtendedConnnectivityBits</em> value of fingerprints <strong>-m, --mode</strong>, a fingerprint bit vector +indicating presence/absence of structurally unique atom identifiers constitute the extended +connectivity fingerprints of a molecule.</p> +</dd> +<dt><strong><strong>-n, --NeighborhoodRadius</strong> <em>number</em></strong></dt> +<dd> +<p>Atomic neighborhood radius for generating extended connectivity neighborhoods. Default +value: <em>2</em>. Valid values: >= 0. Neighborhood radius of zero correspond to just the list +of non-hydrogen atoms.</p> +<p>Default value of <em>2</em> for atomic neighborhood radius generates extended connectivity +fingerprints corresponding to path length or diameter value of <em>4</em> [ Ref 52b ].</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>-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><ExtendedConnectivityFP>.<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 bit-vector to use during generation of fingerprints bit-vector string for +<em>ExtendedConnectivityBits</em> value of <strong>-m, --mode</strong>. 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"> + 512 + 1024 + 2048</div> +</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>-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 <ExtendedConnectivityCount> value of <strong>-m, --mode</strong> option. Possible +values: <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | +ValuesAndIDsPairsString</em>.</p> +<p>Default value during <ExtendedConnectivityCount> value of <strong>-m, --mode</strong> option: +<em>IDsAndValuesString</em>.</p> +<p>Default value during <ExtendedConnectivity> value of <strong>-m, --mode</strong> option: <em>ValuesString</em>.</p> +<p>Examples:</p> +<div class="OptionsBox"> + FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi +<br/> us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391 +<br/> 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414 +<br/> 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103 +<br/> 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338 +<br/> 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...</div> +<div class="OptionsBox"> + FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes +<br/> :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524 +<br/> 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 +<br/> 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...; +<br/> 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2 +<br/> 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1</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 extended connectivity fingerprints corresponding to neighborhood radius up to +2 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -r SampleECAIFP -o Sample.sdf</div> +<p>To generate extended connectivity count fingerprints corresponding to neighborhood radius up to +2 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityCount + -r SampleECAIFP -o Sample.sdf</div> +<p>To generate extended connectivity bits fingerprints as hexadecimal bit-string corresponding to +neighborhood radius up to 2 using atomic invariants atom types in vector string format and +create a SampleECAIFP.csv file containing sequential compound IDs along with fingerprints +vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityBits + -r SampleECAIFP -o Sample.sdf</div> +<p>To generate extended connectivity bits fingerprints as binary bit-string corresponding to +neighborhood radius up to 2 using atomic invariants atom types in vector string format and +create a SampleECAIFP.csv file containing sequential compound IDs along with fingerprints +vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityBits + --BitStringFormat BinaryString -r SampleECAIFP -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using atomic invariants atom types in vector string format and create SampleECAIFP.sdf, SampleECAIFP.fpf +and SampleECAIFP.csv files containing sequential compound IDs in CSV file along with fingerprints +vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl --output all -r SampleECAIFP + -o Sample.sdf</div> +<p>To generate extended connectivity count fingerprints corresponding to neighborhood radius up to +2 using atomic invariants atom types in vector string format and create SampleECAIFP.sdf, SampleECAIFP.fpf +and SampleECAIFP.csv files containing sequential compound IDs in CSV file along with fingerprints +vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityCount + --output all -r SampleECAIFP -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using functional class atom types in vector string format and create a SampleECFCFP.csv file +containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes + -r SampleECFCFP -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using DREIDING atom types in vector string format and create a SampleECFP.csv file +containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -a DREIDINGAtomTypes + -r SampleECFP -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using E-state atom types in vector string format and create a SampleECFP.csv file +containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -a EStateAtomTypes + -r SampleECFP -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using MMFF94 atom types in vector string format and create a SampleECFP.csv file +containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -a MMFF94AtomTypes + -r SampleECFP -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using SLogP atom types in vector string format and create a SampleECFP.csv file +containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -a SLogPAtomTypes + -r SampleECFP -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using SYBYL atom types in vector string format and create a SampleECFP.csv file +containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -a SYBYLAtomTypes + -r SampleECFP -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using TPSA atom types in vector string format and create a SampleECFP.csv file +containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -a TPSAAtomTypes + -r SampleECFP -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using UFF atom types in vector string format and create a SampleECFP.csv file +containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -a UFFAtomTypes + -r SampleECFP -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +3 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes -n 3 + -r SampleECAIFP -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +3 using functional class atom types in vector string format and create a SampleECFCFP.csv file +containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes -n 3 + -r SampleECFCFP -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using only AS,X atomic invariants atom types in vector string format and create a +SampleECAIFP.csv file containing sequential compound IDs along with fingerprints vector +strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes + --AtomicInvariantsToUse "AS,X" -r SampleECAIFP -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using only HBD,HBA functional class atom types in vector string format and create a +SampleECFCFP.csv file containing sequential compound IDs along with fingerprints vector +strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes + --FunctionalClassesToUse "HBD,HBA" -r SampleECFCFP -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv +file containing compound ID from molecule name line along with fingerprints vector strings +data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode MolName + -r SampleECAIFP -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using functional class atom types in vector string format and create a SampleECFCFP.csv +file containing compound IDs using specified data field along with fingerprints vector strings +data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID Mol_ID + -r SampleECFCFP -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using atomic invariants atom types in vector string format and create a SampleECAIFP.tsv +file containing compound ID using combination of molecule name line and an explicit compound +prefix along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleECAIFP -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using functional class atom types in vector string format and create a SampleECFCFP.csv +file containing specific data fields columns along with fingerprints vector strings +data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes + --DataFieldsMode Specify --DataFields Mol_ID -r SampleECFCFP + -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using atomic invariants atom types in vector string format and create a SampleECAIFP.tsv +file containing common data fields columns along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode Common -r SampleECAIFP -o Sample.sdf</div> +<p>To generate extended connectivity fingerprints corresponding to neighborhood radius up to +2 using functional class atom types in vector string format and create SampleECFCFP.sdf, SampleECFCFP.fpf +and SampleECFCFP.csv files containing all data fields columns in CSV file along with fingerprints +vector strings data, type:</p> +<div class="ExampleBox"> + % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes + --DataFieldsMode All --output all -r SampleECFCFP + -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="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.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="./EStateIndiciesFingerprints.html" title="EStateIndiciesFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ExtractFromPDBFiles.html" title="ExtractFromPDBFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>ExtendedConnectivityFingerprints.pl</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>