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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/ExtendedConnectivityFingerprints.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,415 @@ +<html> +<head> +<title>MayaChemTools:Documentation:Fingerprints::ExtendedConnectivityFingerprints.pm</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="./Fingerprints.html" title="Fingerprints.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::ExtendedConnectivityFingerprints.pm</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</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>use Fingerprints::ExtendedConnectivityFingerprints;</p> +<p>use Fingerprints::ExtendedConnectivityFingerprints qw(:all);</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>ExtendedConnectivityFingerprints [ Ref 48, Ref 52 ] class provides the following methods:</p> +<p> <a href="#new">new</a>, <a href="#generatefingerprints">GenerateFingerprints</a>, <a href="#getdescription">GetDescription</a>, <a href="#setatomidentifiertype">SetAtomIdentifierType</a> +, <a href="#setatomicinvariantstouse">SetAtomicInvariantsToUse</a>, <a href="#setfunctionalclassestouse">SetFunctionalClassesToUse</a>, <a href="#setneighborhoodradius">SetNeighborhoodRadius</a> +, <a href="#stringifyextendedconnectivityfingerprints">StringifyExtendedConnectivityFingerprints</a> +</p><p><strong>ExtendedConnectivityFingerprints</strong> is derived from <strong>Fingerprints</strong> class which in turn +is derived from <strong>ObjectProperty</strong> base class that provides methods not explicitly defined +in <strong>ExtendedConnectivityFingerprints</strong>, <strong>Fingerprints</strong> or <strong>ObjectProperty</strong> classes using Perl's +AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:</p> +<div class="OptionsBox"> + Set<PropertyName>(<PropertyValue>); +<br/> $PropertyValue = Get<PropertyName>(); +<br/> Delete<PropertyName>();</div> +<p>The current release of MayaChemTools supports generation of <strong>ExtendedConnectivityFingerprints</strong> +corresponding to following <strong>AtomtomIdentifierTypes</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>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>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>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 atom 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>Type</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>Type</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>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>METHODS</h2> +<dl> +<dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NewExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + %NamesAndValues);</div> +<p>Using specified <em>ExtendedConnectivityFingerprints</em> property names and values hash, <strong>new</strong> +method creates a new object and returns a reference to newly created <strong>ExtendedConnectivityFingerprints</strong> +object. By default, the following properties are initialized:</p> +<div class="OptionsBox"> + Molecule = '' +<br/> Type = 'ExtendedConnectivity' +<br/> NeighborhoodRadius = 2 +<br/> AtomIdentifierType = '' +<br/> AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC', 'MN'] +<br/> FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']</div> +<p>Examples:</p> +<div class="OptionsBox"> + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes');</div> +<div class="OptionsBox"> + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Type' => 'ExtendedConnectivityCount', + 'Molecule' => $Molecule, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes');</div> +<div class="OptionsBox"> + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Type' => 'ExtendedConnectivityBits', + 'Molecule' => $Molecule, + 'Size' => 1024, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes');</div> +<div class="OptionsBox"> + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Type' => 'ExtendedConnectivity', + 'Molecule' => $Molecule, + 'NeighborhoodRadius' => 2, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes', + 'AtomicInvariantsToUse' => + ['AS', 'X', 'BO', 'H', 'FC', 'MN'] );</div> +<div class="OptionsBox"> + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Type' => 'ExtendedConnectivity', + 'Molecule' => $Molecule, + 'NeighborhoodRadius' => 2, + 'AtomIdentifierType' => + 'FunctionalClassAtomTypes', + 'FunctionalClassesToUse' => + ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] );</div> +<div class="OptionsBox"> + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Type' => 'ExtendedConnectivity', + 'Molecule' => $Molecule,; + 'AtomIdentifierType' => + 'MMFF94AtomTypes');</div> +<div class="OptionsBox"> + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Type' => 'ExtendedConnectivityCount', + 'Molecule' => $Molecule,; + 'AtomIdentifierType' => + 'MMFF94AtomTypes');</div> +<div class="OptionsBox"> + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Type' => 'ExtendedConnectivityCount', + 'Molecule' => $Molecule,; + 'AtomIdentifierType' => + 'SLogPAtomTypes');</div> +<div class="OptionsBox"> + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Type' => 'ExtendedConnectivity', + 'Molecule' => $Molecule,; + 'AtomIdentifierType' => + 'SLogPAtomTypes');</div> +<div class="OptionsBox"> + $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints( + 'Type' => 'ExtendedConnectivity', + 'Molecule' => $Molecule,; + 'AtomIdentifierType' => + 'SYBYLAtomTypes');</div> +<div class="OptionsBox"> + $ExtendedConnectivityFingerprints->GenerateFingerprints(); +<br/> print "$ExtendedConnectivityFingerprints\n";</div> +</dd> +<dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $ExtendedConnectivityFingerprints->GenerateFingerprints();</div> +<p>Generates extended connectivity fingerprints and returns <em>ExtendedConnectivityFingerprints</em>.</p> +</dd> +<dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Description = $ExtendedConnectivityFingerprints->GetDescription();</div> +<p>Returns a string containing description of extended connectivity fingerprints +fingerprints.</p> +</dd> +<dt><strong><a name="setatomidentifiertype" class="item"><strong>SetAtomIdentifierType</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $ExtendedConnectivityFingerprints->SetAtomIdentifierType($IdentifierType);</div> +<p>Sets atom <em>IdentifierType</em> to use during extended connectivity fingerprints generation and +returns <em>ExtendedConnectivityFingerprints</em>.</p> +<p>Possible values: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, +TPSAAtomTypes, UFFAtomTypes</em>.</p> +</dd> +<dt><strong><a name="setatomicinvariantstouse" class="item"><strong>SetAtomicInvariantsToUse</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $ExtendedConnectivityFingerprints->SetAtomicInvariantsToUse($ValuesRef); +<br/> $ExtendedConnectivityFingerprints->SetAtomicInvariantsToUse(@Values);</div> +<p>Sets atomic invariants to use during <em>AtomicInvariantsAtomTypes</em> value of <em>AtomIdentifierType</em> +for extended connectivity fingerprints generation and returns <em>ExtendedConnectivityFingerprints</em>.</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 [ 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><a name="setfunctionalclassestouse" class="item"><strong>SetFunctionalClassesToUse</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $ExtendedConnectivityFingerprints->SetFunctionalClassesToUse($ValuesRef); +<br/> $ExtendedConnectivityFingerprints->SetFunctionalClassesToUse(@Values);</div> +<p>Sets functional classes invariants to use during <em>FunctionalClassAtomTypes</em> value of <em>AtomIdentifierType</em> +for extended connectivity fingerprints generation and returns <em>ExtendedConnectivityFingerprints</em>.</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 or None</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><a name="setneighborhoodradius" class="item"><strong>SetNeighborhoodRadius</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $ExtendedConnectivityFingerprints->SetNeighborhoodRadius($Radius);</div> +<p>Sets neighborhood radius to use during extended connectivity fingerprints generation and +returns <em>ExtendedConnectivityFingerprints</em>.</p> +</dd> +<dt><strong><a name="stringifyextendedconnectivityfingerprints" class="item"><strong>StringifyExtendedConnectivityFingerprints</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $String = $Fingerprints->StringifyExtendedConnectivityFingerprints();</div> +<p>Returns a string containing information about <em>ExtendedConnectivityFingerprints</em> object.</p> +</dd> +</dl> +<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="./Fingerprints.html">Fingerprints.pm</a>, <a href="./FingerprintsStringUtil.html">FingerprintsStringUtil.pm</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pm</a>,  +<a href="./AtomTypesFingerprints.html">AtomTypesFingerprints.pm</a>, <a href="./EStateIndiciesFingerprints.html">EStateIndiciesFingerprints.pm</a>, <a href="./MACCSKeys.html">MACCSKeys.pm</a>,  +<a href="./PathLengthFingerprints.html">PathLengthFingerprints.pm</a>, <a href="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.pm</a>,  +<a href="./TopologicalAtomTripletsFingerprints.html">TopologicalAtomTripletsFingerprints.pm</a>, <a href="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.pm</a>,  +<a href="./TopologicalPharmacophoreAtomPairsFingerprints.html">TopologicalPharmacophoreAtomPairsFingerprints.pm</a>,  +<a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html">TopologicalPharmacophoreAtomTripletsFingerprints.pm</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="./Fingerprints.html" title="Fingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::ExtendedConnectivityFingerprints.pm</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>