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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/TopologicalAtomPairsFingerprints.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,602 @@ +<html> +<head> +<title>MayaChemTools:Documentation:TopologicalAtomPairsFingerprints.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="./TextFilesToSDFiles.html" title="TextFilesToSDFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>TopologicalAtomPairsFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/TopologicalAtomPairsFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/TopologicalAtomPairsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/TopologicalAtomPairsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/TopologicalAtomPairsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/TopologicalAtomPairsFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>TopologicalAtomPairsFingerprints.pl - Generate topological atom pairs fingerprints for SD files</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>TopologicalAtomPairsFingerprints.pl SDFile(s)...</p> +<p>TopologicalAtomPairsFingerprints.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>--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>--MinDistance</strong> <em>number</em>] [<strong>--MaxDistance</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>-v, --VectorStringFormat</strong> <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em>] +[<strong>-w, --WorkingDir</strong> dirname] SDFile(s)...</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>Generate topological atom pairs fingerprints [ Ref 57, Ref 59, Ref 72 ] 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 topological atom pairs +corresponding to following <strong>-a, --AtomIdentifierTypes</strong>:</p> +<div class="OptionsBox"> + AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +<br/> FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, +<br/> SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</div> +<p>Based on the values specified for <strong>-a, --AtomIdentifierType</strong> and <strong>--AtomicInvariantsToUse</strong>, +initial atom types are assigned to all non-hydrogen atoms in a molecule. Using the distance +matrix for the molecule and initial atom types assigned to non-hydrogen atoms, all unique atom +pairs within <strong>--MinDistance</strong> and <strong>--MaxDistance</strong> are identified and counted. An atom pair +identifier is generated for each unique atom pair; the format of the atom pair identifier is:</p> +<div class="OptionsBox"> + <AtomType1>-D<n>-<AtomType2></div> +<div class="OptionsBox"> + AtomType1, AtomType2: Atom types assigned to atom1 and atom2 +<br/> D: Distance between atom1 and atom2</div> +<div class="OptionsBox"> + where AtomType1 <= AtomType2</div> +<p>The atom pair identifiers for all unique atom pairs corresponding to non-hydrogen atoms constitute +topological atom pairs fingerprints of the molecule.</p> +<p>Example of <em>SD</em> file containing topological atom pairs fingerprints string data:</p> +<div class="OptionsBox"> + ... ... +<br/> ... ... +<br/> $$$$ +<br/> ... ... +<br/> ... ... +<br/> ... ... +<br/> 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +<br/> ... ... +<br/> 2 3 1 0 0 0 0 +<br/> ... ... +<br/> M END +<br/> > <CmpdID> +<br/> Cmpd1</div> +<div class="OptionsBox"> + > <TopologicalAtomPairsFingerprints> +<br/> FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi +<br/> stance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1.H +<br/> 3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.H1 +<br/> C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-C.X2...; +<br/> 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1 +<br/> 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1 ...</div> +<div class="OptionsBox"> + $$$$ +<br/> ... ... +<br/> ... ...</div> +<p>Example of <em>FP</em> file containing topological atom pairs fingerprints string data:</p> +<div class="OptionsBox"> + # +<br/> # Package = MayaChemTools 7.4 +<br/> # Release Date = Oct 21, 2010 +<br/> # +<br/> # TimeStamp = Fri Mar 11 15:04:36 2011 +<br/> # +<br/> # FingerprintsStringType = FingerprintsVector +<br/> # +<br/> # Description = TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi... +<br/> # VectorStringFormat = IDsAndValuesString +<br/> # VectorValuesType = NumericalValues +<br/> # +<br/> Cmpd1 223;C.X1.BO1.H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2...;1 1... +<br/> Cmpd2 128;C.X1.BO1.H3-D1-C.X2.BO2.H2 C.X1.BO1.H3-D1-C.X3.BO4...;1 1... +<br/> ... ... +<br/> ... ..</div> +<p>Example of CSV <em>Text</em> file containing topological atom pairs fingerprints string data:</p> +<div class="OptionsBox"> + "CompoundID","TopologicalAtomPairsFingerprints" +<br/> "Cmpd1","FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTy +<br/> pes:MinDistance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C +<br/> .X1.BO1.H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X +<br/> 3.BO3.H1C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1...; +<br/> 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1 +<br/> 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1 ... +<br/> ... ... +<br/> ... ...</div> +<p>The current release of MayaChemTools generates the following types of topological atom pairs +fingerprints vector strings:</p> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD +<br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1 +<br/> .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3. +<br/> H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...; +<br/> 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1 +<br/> 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD +<br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X +<br/> 1.BO1.H3-D1-C.X3.BO3.H1 2 C.X2.BO2.H2-D1-C.X2.BO2.H2 1 C.X2.BO2.H2-D1- +<br/> C.X3.BO3.H1 4 C.X2.BO2.H2-D1-C.X3.BO4 1 C.X2.BO2.H2-D1-N.X3.BO3 1 C.X2 +<br/> .BO3.H1-D1-C.X2.BO3.H1 10 C.X2.BO3.H1-D1-C.X3.BO4 8 C.X3.BO3.H1-D1-C.X +<br/> 3.BO4 1 C.X3.BO3.H1-D1-O.X1.BO1.H1 2 C.X3.BO4-D1-C.X3.BO4 6 C.X3.BO...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomPairs:DREIDINGAtomTypes:MinDistance1 +<br/> :MaxDistance10;157;NumericalValues;IDsAndValuesString;C_2-D1-C_3 C_2-D +<br/> 1-C_R C_2-D1-N_3 C_2-D1-O_2 C_2-D1-O_3 C_3-D1-C_3 C_3-D1-C_R C_3-D1-N_ +<br/> R C_3-D1-O_3 C_R-D1-C_R C_R-D1-F_ C_R-D1-N_3 C_R-D1-N_R C_2-D2-C_3 C_2 +<br/> 1 1 1 2 1 7 1 1 2 23 1 1 2 1 3 5 5 2 1 5 28 2 3 3 1 1 1 2 4 1 1 4 9 3 +<br/> 1 4 24 2 4 3 3 4 5 5 14 1 1 2 3 22 1 3 4 4 1 1 1 1 2 2 5 1 4 21 3 1...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomPairs:EStateAtomTypes:MinDistance1:M +<br/> axDistance10;251;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH aaCH- +<br/> D1-aasC aasC-D1-aasC aasC-D1-aasN aasC-D1-dssC aasC-D1-sF aasC-D1-ssNH +<br/> aasC-D1-sssCH aasN-D1-ssCH2 dO-D1-dssC dssC-D1-sOH dssC-D1-ssCH2 d...; +<br/> 10 8 5 2 1 1 1 1 1 2 1 1 1 2 2 1 4 10 12 2 2 6 3 1 3 2 2 1 1 1 1 1 1 1 +<br/> 1 1 5 2 1 1 6 12 2 2 2 2 6 1 3 2 2 5 2 2 1 2 1 1 1 1 1 1 3 1 3 19 2...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi +<br/> stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar +<br/> Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H +<br/> BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...; +<br/> 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4 +<br/> 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomPairs:MMFF94AtomTypes:MinDistance1:M +<br/> axDistance10;227;NumericalValues;IDsAndValuesPairsString;C5A-D1-C5B 2 +<br/> C5A-D1-CB 1 C5A-D1-CR 1 C5A-D1-N5 2 C5B-D1-C5B 1 C5B-D1-C=ON 1 C5B-D1- +<br/> CB 1 C=ON-D1-NC=O 1 C=ON-D1-O=CN 1 CB-D1-CB 18 CB-D1-F 1 CB-D1-NC=O 1 +<br/> COO-D1-CR 1 COO-D1-O=CO 1 COO-D1-OC=O 1 CR-D1-CR 7 CR-D1-N5 1 CR-D1-OR +<br/> 2 C5A-D2-C5A 1 C5A-D2-C5B 2 C5A-D2-C=ON 1 C5A-D2-CB 3 C5A-D2-CR 4 ...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomPairs:SLogPAtomTypes:MinDistance1:Ma +<br/> xDistance10;329;NumericalValues;IDsAndValuesPairsString;C1-D1-C10 1 C1 +<br/> -D1-C11 2 C1-D1-C5 1 C1-D1-CS 4 C10-D1-N11 1 C11-D1-C21 1 C14-D1-C18 2 +<br/> C14-D1-F 1 C18-D1-C18 10 C18-D1-C20 4 C18-D1-C22 2 C20-D1-C20 3 C20-D +<br/> 1-C21 1 C20-D1-N11 1 C21-D1-C21 1 C21-D1-C5 1 C21-D1-N11 1 C22-D1-N4 1 +<br/> C5-D1-N4 1 C5-D1-O10 1 C5-D1-O2 1 C5-D1-O9 1 CS-D1-O2 2 C1-D2-C1 3...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomPairs:SYBYLAtomTypes:MinDistance1:Ma +<br/> xDistance10;159;NumericalValues;IDsAndValuesPairsString;C.2-D1-C.3 1 C +<br/> .2-D1-C.ar 1 C.2-D1-N.am 1 C.2-D1-O.2 1 C.2-D1-O.co2 2 C.3-D1-C.3 7 C. +<br/> 3-D1-C.ar 1 C.3-D1-N.ar 1 C.3-D1-O.3 2 C.ar-D1-C.ar 23 C.ar-D1-F 1 C.a +<br/> r-D1-N.am 1 C.ar-D1-N.ar 2 C.2-D2-C.3 1 C.2-D2-C.ar 3 C.3-D2-C.3 5 C.3 +<br/> -D2-C.ar 5 C.3-D2-N.ar 2 C.3-D2-O.3 4 C.3-D2-O.co2 2 C.ar-D2-C.ar 2...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomPairs:TPSAAtomTypes:MinDistance1:Max +<br/> Distance10;64;NumericalValues;IDsAndValuesPairsString;N21-D1-None 3 N7 +<br/> -D1-None 2 None-D1-None 34 None-D1-O3 2 None-D1-O4 3 N21-D2-None 5 N7- +<br/> D2-None 3 N7-D2-O3 1 None-D2-None 44 None-D2-O3 2 None-D2-O4 5 O3-D2-O +<br/> 4 1 N21-D3-None 7 N7-D3-None 4 None-D3-None 45 None-D3-O3 4 None-D3-O4 +<br/> 5 N21-D4-N7 1 N21-D4-None 5 N21-D4-O3 1 N21-D4-O4 1 N7-D4-None 4 N...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomPairs:UFFAtomTypes:MinDistance1:MaxD +<br/> istance10;157;NumericalValues;IDsAndValuesPairsString;C_2-D1-C_3 1 C_2 +<br/> -D1-C_R 1 C_2-D1-N_3 1 C_2-D1-O_2 2 C_2-D1-O_3 1 C_3-D1-C_3 7 C_3-D1-C +<br/> _R 1 C_3-D1-N_R 1 C_3-D1-O_3 2 C_R-D1-C_R 23 C_R-D1-F_ 1 C_R-D1-N_3 1 +<br/> C_R-D1-N_R 2 C_2-D2-C_3 1 C_2-D2-C_R 3 C_3-D2-C_3 5 C_3-D2-C_R 5 C_3-D +<br/> 2-N_R 2 C_3-D2-O_2 1 C_3-D2-O_3 5 C_R-D2-C_R 28 C_R-D2-F_ 2 C_R-D2-...</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 | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | 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 topological atom pairs fingerprints. Possible values in the current +release are: <em>AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, +FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, +TPSAAtomTypes, UFFAtomTypes</em>. Default value: <em>AtomicInvariantsAtomTypes</em>.</p> +</dd> +<dt><strong><strong>--AtomicInvariantsToUse</strong> <em>"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 invariants are: <em>AS, X, BO, LBO, SB, DB, TB, +H, Ar, RA, FC, MN, SM</em>. Default value: <em>AS,X,BO,H,FC</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>--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 CSV/TSV text file(s) used during <em>CompoundID</em> value +of <strong>--DataFieldsMode</strong> option. Default value: <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 value: <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 | both</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 | both</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>TopologicalAtomPairsFingerprints</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>--MinDistance</strong> <em>number</em></strong></dt> +<dd> +<p>Minimum bond distance between atom pairs for generating topological atom pairs. Default value: +<em>1</em>. Valid values: positive integers and less than <strong>--MaxDistance</strong>.</p> +</dd> +<dt><strong><strong>--MaxDistance</strong> <em>number</em></strong></dt> +<dd> +<p>Maximum bond distance between atom pairs for generating topological atom pairs. Default value: +<em>10</em>. Valid values: positive integers and greater than <strong>--MinDistance</strong>.</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><TopologicalAtomPairsFP>.<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>-v, --VectorStringFormat</strong> <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt> +<dd> +<p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by +<strong>--output</strong> option. Possible values: <em>IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | +ValuesAndIDsPairsString</em>. Default value: <em>IDsAndValuesString</em>.</p> +<p>Examples:</p> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD +<br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1 +<br/> .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3. +<br/> H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...; +<br/> 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1 +<br/> 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD +<br/> istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X +<br/> 1.BO1.H3-D1-C.X3.BO3.H1 2 C.X2.BO2.H2-D1-C.X2.BO2.H2 1 C.X2.BO2.H2-D1- +<br/> C.X3.BO3.H1 4 C.X2.BO2.H2-D1-C.X3.BO4 1 C.X2.BO2.H2-D1-N.X3.BO3 1 C.X2 +<br/> .BO3.H1-D1-C.X2.BO3.H1 10 C.X2.BO3.H1-D1-C.X3.BO4 8 C.X3.BO3.H1-D1-C.X +<br/> 3.BO4 1 C.X3.BO3.H1-D1-O.X1.BO1.H1 2 C.X3.BO4-D1-C.X3.BO4 6 C.X3.BO...</div> +</dd> +<dt><strong><strong>-w, --WorkingDir</strong> <em>DirName</em></strong></dt> +<dd> +<p>Location of working directory. Default value: current directory.</p> +</dd> +</dl> +<p> +</p> +<h2>EXAMPLES</h2> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl -r SampleTAPFP -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create SampleTAPFP.sdf, +SampleTAPFP.fpf and SampleTAPFP.csv files containing sequential compound IDs in CSV file along +with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl --output all -r SampleTAPFP + -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using DREIDING atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl -a DREIDINGAtomTypes + -r SampleTAPFP -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using E-state types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl -a EStateAtomTypes + -r SampleTAPFP -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using DREIDING atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl -a DREIDINGAtomTypes + -r SampleTAPFP -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using functional class atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl -a FunctionalClassAtomTypes + -r SampleTAPFP -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using MMFF94 atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl -a MMFF94AtomTypes + -r SampleTAPFP -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using SLogP atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl -a SLogPAtomTypes + -r SampleTAPFP -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using SYBYL atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl -a SYBYLAtomTypes + -r SampleTAPFP -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using TPSA atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl -a TPSAAtomTypes + -r SampleTAPFP -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using UFF atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl -a UFFAtomTypes + -r SampleTAPFP -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesPairsString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl --VectorStringFormat + IDsAndValuesPairsString -r SampleTAPFP -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +6 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing sequential compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes + --MinDistance 1 --MaxDistance 6 -r SampleTAPFP -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using only AS,X atomic invariants atom types in IDsAndValuesString format and create a +SampleTAPFP.csv file containing sequential compound IDs along with fingerprints vector strings +data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes + --AtomicInvariantsToUse "AS,X" --MinDistance 1 --MaxDistance 6 + -r SampleTAPFP -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing compound ID from molecule name line along with fingerprints vector strings +data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode MolName + -r SampleTAPFP -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing compound IDs using specified data field along with fingerprints vector strings +data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID + Mol_ID -r SampleTAPFP -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv +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"> + % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTAPFP -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing specific data fields columns along with fingerprints vector strings +data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode Specify --DataFields Mol_ID -r SampleTAPFP + -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv +file containing common data fields columns along with fingerprints vector strings +data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode Common -r SampleTAPFP -o Sample.sdf</div> +<p>To generate topological atom pairs fingerprints corresponding to bond distances from 1 through +10 using atomic invariants atom types in IDsAndValuesString format and create SampleTAPFP.sdf, +SampleTAPFP.fpf and SampleTAPFP.csv files containing all data fields columns in CSV file along +with fingerprints data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode All --output all -r SampleTAPFP + -o Sample.sdf</div> +<p> +</p> +<h2>AUTHOR</h2> +<p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> +<p> +</p> +<h2>SEE ALSO</h2> +<p><a href="./InfoFingerprintsFiles.html">InfoFingerprintsFiles.pl</a>, <a href="./SimilarityMatricesFingerprints.html">SimilarityMatricesFingerprints.pl</a>, <a href="./AtomNeighborhoodsFingerprints.html">AtomNeighborhoodsFingerprints.pl</a>,  +<a href="./ExtendedConnectivityFingerprints.html">ExtendedConnectivityFingerprints.pl</a>, <a href="./MACCSKeysFingerprints.html">MACCSKeysFingerprints.pl</a>,  +<a href="./PathLengthFingerprints.html">PathLengthFingerprints.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="./TextFilesToSDFiles.html" title="TextFilesToSDFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalAtomTorsionsFingerprints.html" title="TopologicalAtomTorsionsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>TopologicalAtomPairsFingerprints.pl</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>