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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/PathLengthFingerprints.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,444 @@ +<html> +<head> +<title>MayaChemTools:Documentation:Fingerprints::PathLengthFingerprints.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="./MACCSKeys.html" title="MACCSKeys.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalAtomPairsFingerprints.html" title="TopologicalAtomPairsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>Fingerprints::PathLengthFingerprints.pm</strong></td><td width="33%" align="right"><a href="././code/PathLengthFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/PathLengthFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/PathLengthFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/PathLengthFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/PathLengthFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>PathLengthFingerprints</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>use Fingerprints::PathLengthFingerprints;</p> +<p>use Fingerprints::PathLengthFingerprints qw(:all);</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p><strong>PathLengthFingerprints</strong> 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="#setmaxlength">SetMaxLength</a> +, <a href="#setminlength">SetMinLength</a>, <a href="#setnumofbitstosetperpath">SetNumOfBitsToSetPerPath</a>, <a href="#settype">SetType</a> +, <a href="#stringifypathlengthfingerprints">StringifyPathLengthFingerprints</a> +</p><p><strong>PathLengthFingerprints</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>PathLengthFingerprints</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>AtomTypesFingerpritns</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>Type</strong>, <strong>AtomtomIdentifierTypes</strong>, <strong>MinPathLength</strong> and +<strong>MaxPathLength</strong>, all appropriate atom paths are generated for each atom in the molecule +and collected in a list and the list is filtered to remove any structurally duplicate paths as +indicated by the value of <strong>UseUniquePaths</strong>.</p> +<p>For molecules containing rings, atom paths starting from each atom can be traversed in four +different ways:</p> +<div class="OptionsBox"> + o Atom paths without any rings and sharing of bonds in traversed paths. +<br/> o Atom paths containing rings and without any sharing of bonds in + traversed paths +<br/> o All possible atom paths without any rings and sharing of bonds in + traversed paths +<br/> o All possible atom paths containing rings and with sharing of bonds in + traversed paths.</div> +<p>Atom path traversal is terminated at the last ring atom. For molecules containing no rings, +first two and last two types described above are equivalent.</p> +<p><strong>AllowSharedBonds</strong> and <strong>AllowRings</strong> allow generation of different types of paths +to be used for fingerprints generation.</p> +<p>The combination of <strong>AllowSharedBonds</strong>, <strong>AllowRings</strong>, and <strong>UseBondSymbols</strong> allows generation of +8 different types of path length fingerprints:</p> +<div class="OptionsBox"> + AllowSharedBonds AllowRings UseBondSymbols</div> +<div class="OptionsBox"> + 0 0 1 - AtomPathsNoCyclesWithBondSymbols +<br/> 0 1 1 - AtomPathsWithCyclesWithBondSymbols</div> +<div class="OptionsBox"> + 1 0 1 - AllAtomPathsNoCyclesWithBondSymbols +<br/> 1 1 1 - AllAtomPathsWithCyclesWithBondSymbols + [ DEFAULT ]</div> +<div class="OptionsBox"> + 0 0 0 - AtomPathsNoCyclesNoBondSymbols +<br/> 0 1 0 - AtomPathsWithCyclesNoBondSymbols</div> +<div class="OptionsBox"> + 1 0 0 - AllAtomPathsNoCyclesNoBondSymbols +<br/> 1 1 0 - AllAtomPathsWithCyclesNoWithBondSymbols</div> +<p>Additionally, possible values for option <strong>--AtomIdentifierType</strong> in conjunction with corresponding +specified values for <strong>AtomicInvariantsToUse</strong> and <strong>FunctionalClassesToUse </strong> changes the nature +of atom path length strings and the fingerprints.</p> +<p>For each atom path in the filtered atom paths list, an atom path string is created using value of +<strong>AtomIdentifierType</strong> and specified values to use for a particular atom identifier type. +Value of <strong>UseBondSymbols</strong> controls whether bond order symbols are used during generation +of atom path string. Atom symbol corresponds to element symbol and characters used to represent + bond order are: <em>1 - None; 2 - '='; 3 - '#'; 1.5 or aromatic - ':'; others: bond order value</em>. By default, +bond symbols are included in atom path strings. Exclusion of bond symbols in atom path strings +results in fingerprints which correspond purely to atom paths without considering bonds.</p> +<p><strong>UseUniquePaths</strong> controls the removal of structurally duplicate atom path strings are removed +from the list.</p> +<p>For <em>PathLengthBits</em> value of <strong>Type</strong>, each atom path is hashed to a 32 bit unsigned +integer key using <strong>TextUtil::HashCode</strong> function. Using the hash key as a seed for a random number +generator, a random integer value between 0 and <strong>Size</strong> is used to set corresponding bits +in the fingerprint bit-vector string. Value of <strong>NumOfBitsToSetPerPaths</strong> option controls the number +of time a random number is generated to set corresponding bits.</p> +<p>For <em> PathLengthCount</em> value of <strong>Type</strong>n, the number of times an atom path appears +is tracked and a fingerprints count-string corresponding to count of atom paths is generated.</p> +<p>The current release of MayaChemTools generates the following types of path length +fingerprints bit-vector and vector strings:</p> +<div class="OptionsBox"> + FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng +<br/> th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110 +<br/> 0100010101011000101001011100110001000010001001101000001001001001001000 +<br/> 0010110100000111001001000001001010100100100000000011000000101001011100 +<br/> 0010000001000101010100000100111100110111011011011000000010110111001101 +<br/> 0101100011000000010001000011000010100011101100001000001000100000000...</div> +<div class="OptionsBox"> + FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng +<br/> th1:MaxLength8;1024;HexadecimalString;Ascending;48caa1315d82d91122b029 +<br/> 42861c9409a4208182d12015509767bd0867653604481a8b1288000056090583603078 +<br/> 9cedae54e26596889ab121309800900490515224208421502120a0dd9200509723ae89 +<br/> 00024181b86c0122821d4e4880c38620dab280824b455404009f082003d52c212b4e6d +<br/> 6ea05280140069c780290c43</div> +<div class="OptionsBox"> + FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength +<br/> 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2 +<br/> C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X +<br/> 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1 +<br/> 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO +<br/> 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....</div> +<div class="OptionsBox"> + FingerprintsVector;PathLengthCount:DREIDINGAtomTypes:MinLength1:MaxLen +<br/> gth8;410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_ +<br/> 1 N_3 1 N_R 1 O_2 2 O_3 3 C_2=O_2 2 C_2C_3 1 C_2C_R 1 C_2N_3 1 C_2O_3 +<br/> 1 C_3C_3 7 C_3C_R 1 C_3N_R 1 C_3O_3 2 C_R:C_R 21 C_R:N_R 2 C_RC_R 2 C +<br/> _RF_ 1 C_RN_3 1 C_2C_3C_3 1 C_2C_R:C_R 2 C_2N_3C_R 1 C_3C_2=O_2 1 C_3C +<br/> _2O_3 1 C_3C_3C_3 5 C_3C_3C_R 2 C_3C_3N_R 1 C_3C_3O_3 4 C_3C_R:C_R ...</div> +<div class="OptionsBox"> + FingerprintsVector;PathLengthCount:EStateAtomTypes:MinLength1:MaxLengt +<br/> h8;454;NumericalValues;IDsAndValuesPairsString;aaCH 14 aasC 8 aasN 1 d +<br/> O 2 dssC 2 sCH3 2 sF 1 sOH 3 ssCH2 4 ssNH 1 sssCH 3 aaCH:aaCH 10 aaCH: +<br/> aasC 8 aasC:aasC 3 aasC:aasN 2 aasCaasC 2 aasCdssC 1 aasCsF 1 aasCssNH +<br/> 1 aasCsssCH 1 aasNssCH2 1 dO=dssC 2 dssCsOH 1 dssCssCH2 1 dssCssNH 1 +<br/> sCH3sssCH 2 sOHsssCH 2 ssCH2ssCH2 1 ssCH2sssCH 4 aaCH:aaCH:aaCH 6 a...</div> +<div class="OptionsBox"> + FingerprintsVector;PathLengthCount:FunctionalClassAtomTypes:MinLength1 +<br/> :MaxLength8;404;NumericalValues;IDsAndValuesPairsString;Ar 22 Ar.HBA 1 +<br/> HBA 2 HBA.HBD 3 HBD 1 Hal 1 NI 1 None 10 Ar.HBA:Ar 2 Ar.HBANone 1 Ar: +<br/> Ar 21 ArAr 2 ArHBD 1 ArHal 1 ArNone 2 HBA.HBDNI 1 HBA.HBDNone 2 HBA=NI +<br/> 1 HBA=None 1 HBDNone 1 NINone 1 NoneNone 7 Ar.HBA:Ar:Ar 2 Ar.HBA:ArAr +<br/> 1 Ar.HBA:ArNone 1 Ar.HBANoneNone 1 Ar:Ar.HBA:Ar 1 Ar:Ar.HBANone 2 ...</div> +<div class="OptionsBox"> + FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt +<br/> h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1 +<br/> 8 COO 1 CR 9 F 1 N5 1 NC=O 1 O=CN 1 O=CO 1 OC=O 1 OR 2 C5A:C5B 2 C5A:N +<br/> 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1 +<br/> CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR +<br/> OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...</div> +<div class="OptionsBox"> + FingerprintsVector;PathLengthCount:SLogPAtomTypes:MinLength1:MaxLength +<br/> 8;518;NumericalValues;IDsAndValuesPairsString;C1 5 C10 1 C11 1 C14 1 C +<br/> 18 14 C20 4 C21 2 C22 1 C5 2 CS 2 F 1 N11 1 N4 1 O10 1 O2 3 O9 1 C10C1 +<br/> 1 C10N11 1 C11C1 2 C11C21 1 C14:C18 2 C14F 1 C18:C18 10 C18:C20 4 C18 +<br/> :C22 2 C1C5 1 C1CS 4 C20:C20 1 C20:C21 1 C20:N11 1 C20C20 2 C21:C21 1 +<br/> C21:N11 1 C21C5 1 C22N4 1 C5=O10 1 C5=O9 1 C5N4 1 C5O2 1 CSO2 2 C10...</div> +<div class="OptionsBox"> + FingerprintsVector;PathLengthCount:SYBYLAtomTypes:MinLength1:MaxLength +<br/> 8;412;NumericalValues;IDsAndValuesPairsString;C.2 2 C.3 9 C.ar 22 F 1 +<br/> N.am 1 N.ar 1 O.2 1 O.3 2 O.co2 2 C.2=O.2 1 C.2=O.co2 1 C.2C.3 1 C.2C. +<br/> ar 1 C.2N.am 1 C.2O.co2 1 C.3C.3 7 C.3C.ar 1 C.3N.ar 1 C.3O.3 2 C.ar:C +<br/> .ar 21 C.ar:N.ar 2 C.arC.ar 2 C.arF 1 C.arN.am 1 C.2C.3C.3 1 C.2C.ar:C +<br/> .ar 2 C.2N.amC.ar 1 C.3C.2=O.co2 1 C.3C.2O.co2 1 C.3C.3C.3 5 C.3C.3...</div> +<div class="OptionsBox"> + FingerprintsVector;PathLengthCount:TPSAAtomTypes:MinLength1:MaxLength8 +<br/> ;331;NumericalValues;IDsAndValuesPairsString;N21 1 N7 1 None 34 O3 2 O +<br/> 4 3 N21:None 2 N21None 1 N7None 2 None:None 21 None=O3 2 NoneNone 13 N +<br/> oneO4 3 N21:None:None 2 N21:NoneNone 2 N21NoneNone 1 N7None:None 2 N7N +<br/> one=O3 1 N7NoneNone 1 None:N21:None 1 None:N21None 2 None:None:None 20 +<br/> None:NoneNone 12 NoneN7None 1 NoneNone=O3 2 NoneNoneNone 8 NoneNon...</div> +<div class="OptionsBox"> + FingerprintsVector;PathLengthCount:UFFAtomTypes:MinLength1:MaxLength8; +<br/> 410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_ 1 N_ +<br/> 3 1 N_R 1 O_2 2 O_3 3 C_2=O_2 2 C_2C_3 1 C_2C_R 1 C_2N_3 1 C_2O_3 1 C_ +<br/> 3C_3 7 C_3C_R 1 C_3N_R 1 C_3O_3 2 C_R:C_R 21 C_R:N_R 2 C_RC_R 2 C_RF_ +<br/> 1 C_RN_3 1 C_2C_3C_3 1 C_2C_R:C_R 2 C_2N_3C_R 1 C_3C_2=O_2 1 C_3C_2O_3 +<br/> 1 C_3C_3C_3 5 C_3C_3C_R 2 C_3C_3N_R 1 C_3C_3O_3 4 C_3C_R:C_R 1 C_3...</div> +<p> +</p> +<h2>METHODS</h2> +<dl> +<dt><strong><a name="new" class="item"><strong>new</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $NewPathLengthFingerprints = new PathLengthFingerprints( + %NamesAndValues);</div> +<p>Using specified <em>PathLengthFingerprints</em> property names and values hash, <strong>new</strong> method creates a new object +and returns a reference to newly created <strong>PathLengthFingerprints</strong> object. By default, the following properties are +initialized:</p> +<div class="OptionsBox"> + Molecule = ''; +<br/> Type = '' +<br/> Size = 1024 +<br/> MinSize = 32 +<br/> MaxSize = 2**32 +<br/> NumOfBitsToSetPerPath = 1 +<br/> MinLength = 1 +<br/> MaxLength = 8 +<br/> AllowSharedBonds = 1 +<br/> AllowRings = 1 +<br/> UseBondSymbols = 1 +<br/> UseUniquePaths = '' +<br/> AtomIdentifierType = '' +<br/> SetAtomicInvariantsToUse = ['AS'] +<br/> FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']</div> +<p>Examples:</p> +<div class="OptionsBox"> + $PathLengthFingerprints = new PathLengthFingerprints( + 'Molecule' => $Molecule, + 'Type' => 'PathLengthBits', + 'AtomIdentifierType' = + 'AtomicInvariantsAtomTypes');</div> +<div class="OptionsBox"> + $PathLengthFingerprints = new PathLengthFingerprints( + 'Molecule' => $Molecule, + 'Type' => 'PathLengthBits', + 'Size' => 1024, + 'MinLength' => 1, + 'MaxLength' => 8, + 'AllowRings' => 1, + 'AllowSharedBonds' => 1, + 'UseBondSymbols' => 1, + 'UseUniquePaths' => 1, + 'AtomIdentifierType' = + 'AtomicInvariantsAtomTypes', + 'AtomicInvariantsToUse' => ['AS']);</div> +<div class="OptionsBox"> + $PathLengthFingerprints = new PathLengthFingerprints( + 'Molecule' => $Molecule, + 'Type' => 'PathLengthCount', + 'MinLength' => 1, + 'MaxLength' => 8, + 'AllowRings' => 1, + 'AllowSharedBonds' => 1, + 'UseBondSymbols' => 1, + 'UseUniquePaths' => 1, + 'AtomIdentifierType' => + 'AtomicInvariantsAtomTypes', + 'AtomicInvariantsToUse' => ['AS']);</div> +<div class="OptionsBox"> + $PathLengthFingerprints = new PathLengthFingerprints( + 'Molecule' => $Molecule, + 'Type' => 'PathLengthBits', + 'AtomIdentifierType' = + 'SLogPAtomTypes');</div> +<div class="OptionsBox"> + $PathLengthFingerprints = new PathLengthFingerprints( + 'Molecule' => $Molecule, + 'Type' => 'PathLengthCount', + 'AtomIdentifierType' = + 'SYBYLAtomTypes');</div> +<div class="OptionsBox"> + $PathLengthFingerprints = new PathLengthFingerprints( + 'Molecule' => $Molecule, + 'Type' => 'PathLengthBits', + 'AtomIdentifierType' = + 'FunctionalClassAtomTypes', + 'FunctionalClassesToUse' => ['HBD', 'HBA', 'Ar']);</div> +<div class="OptionsBox"> + $PathLengthFingerprints->GenerateFingerprints(); +<br/> print "$PathLengthFingerprints\n";</div> +</dd> +<dt><strong><a name="getdescription" class="item"><strong>GetDescription</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $Description = $PathLengthFingerprints->GetDescription();</div> +<p>Returns a string containing description of path length fingerprints.</p> +</dd> +<dt><strong><a name="generatefingerprints" class="item"><strong>GenerateFingerprints</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $PathLengthFingerprints->GenerateFingerprints();</div> +<p>Generates path length fingerprints and returns <em>PathLengthFingerprints</em>.</p> +</dd> +<dt><strong><a name="setmaxlength" class="item"><strong>SetMaxLength</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $PathLengthFingerprints->SetMaxLength($Length);</div> +<p>Sets maximum value of atom path length to be used during atom path length fingerprints +generation and returns <em>PathLengthFingerprints</em></p> +</dd> +<dt><strong><a name="setatomidentifiertype" class="item"><strong>SetAtomIdentifierType</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $PathLengthFingerprints->SetAtomIdentifierType();</div> +<p>Sets atom <em>IdentifierType</em> to use during path length fingerprints generation and +returns <em>PathLengthFingerprints</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"> + $PathLengthFingerprints->SetAtomicInvariantsToUse($ValuesRef); +<br/> $PathLengthFingerprints->SetAtomicInvariantsToUse(@Values);</div> +<p>Sets atomic invariants to use during <em>AtomicInvariantsAtomTypes</em> value of <em>AtomIdentifierType</em> +for path length fingerprints generation and returns <em>PathLengthFingerprints</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: <em>AS</em>.</p> +<p>The atomic invariants abbreviations correspond to:</p> +<div class="OptionsBox"> + AS = Atom symbol corresponding to element symbol</div> +<div class="OptionsBox"> + X<n> = Number of non-hydrogen atom neighbors or heavy atoms +<br/> BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms +<br/> LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms +<br/> SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms +<br/> DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms +<br/> TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms +<br/> H<n> = Number of implicit and explicit hydrogens for atom +<br/> Ar = Aromatic annotation indicating whether atom is aromatic +<br/> RA = Ring atom annotation indicating whether atom is a ring +<br/> FC<+n/-n> = Formal charge assigned to atom +<br/> MN<n> = Mass number indicating isotope other than most abundant isotope +<br/> SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or + 3 (triplet)</div> +<p>Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:</p> +<div class="OptionsBox"> + AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n></div> +<p>Except for AS which is a required atomic invariant in atom types, all other atomic invariants are +optional. Atom type specification doesn't include atomic invariants with zero or undefined values.</p> +<p>In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words +are also allowed:</p> +<div class="OptionsBox"> + X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors +<br/> BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms +<br/> LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms +<br/> SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms +<br/> DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms +<br/> TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms +<br/> H : NumOfImplicitAndExplicitHydrogens +<br/> Ar : Aromatic +<br/> RA : RingAtom +<br/> FC : FormalCharge +<br/> MN : MassNumber +<br/> SM : SpinMultiplicity</div> +<p><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"> + $PathLengthFingerprints->SetFunctionalClassesToUse($ValuesRef); +<br/> $PathLengthFingerprints->SetFunctionalClassesToUse(@Values);</div> +<p>Sets functional classes invariants to use during <em>FunctionalClassAtomTypes</em> value of <em>AtomIdentifierType</em> +for path length fingerprints generation and returns <em>PathLengthFingerprints</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="setminlength" class="item"><strong>SetMinLength</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $PathLengthFingerprints->SetMinLength($Length);</div> +<p>Sets minimum value of atom path length to be used during atom path length fingerprints +generation and returns <em>PathLengthFingerprints</em>.</p> +</dd> +<dt><strong><a name="setmaxlength2" class="item"><strong>SetMaxLength</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $PathLengthFingerprints->SetMaxLength($Length);</div> +<p>Sets maximum value of atom path length to be used during atom path length fingerprints +generation and returns <em>PathLengthFingerprints</em>.</p> +</dd> +<dt><strong><a name="setnumofbitstosetperpath" class="item"><strong>SetNumOfBitsToSetPerPath</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $PathLengthFingerprints->SetNumOfBitsToSetPerPath($NumOfBits);</div> +<p>Sets number of bits to set for each path during <em>PathLengthBits</em> <strong>Type </strong> during path length fingerprints +generation and returns <em>PathLengthFingerprints</em>.</p> +</dd> +<dt><strong><a name="settype" class="item"><strong>SetType</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $PathLengthFingerprints->SetType($Type);</div> +<p>Sets type of path length fingerprints and returns <em>PathLengthFingerprints</em>. Possible values: +<em>PathLengthBits or PathLengthCount</em>.</p> +</dd> +<dt><strong><a name="stringifypathlengthfingerprints" class="item"><strong>StringifyPathLengthFingerprints</strong></a></strong></dt> +<dd> +<div class="OptionsBox"> + $String = $PathLengthFingerprints->StringifyPathLengthFingerprints();</div> +<p>Returns a string containing information about <em>PathLengthFingerprints</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="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pm</a>,  +<a href="./MACCSKeys.html">MACCSKeys.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="./MACCSKeys.html" title="MACCSKeys.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalAtomPairsFingerprints.html" title="TopologicalAtomPairsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>Fingerprints::PathLengthFingerprints.pm</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>