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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/scripts/html/TopologicalAtomTorsionsFingerprints.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,559 @@ +<html> +<head> +<title>MayaChemTools:Documentation:TopologicalAtomTorsionsFingerprints.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="./TopologicalAtomPairsFingerprints.html" title="TopologicalAtomPairsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>TopologicalAtomTorsionsFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/TopologicalAtomTorsionsFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/TopologicalAtomTorsionsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/TopologicalAtomTorsionsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/TopologicalAtomTorsionsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/TopologicalAtomTorsionsFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>TopologicalAtomTorsionsFingerprints.pl - Generate topological atom torsions fingerprints for SD files</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>TopologicalAtomTorsionsFingerprints.pl SDFile(s)...</p> +<p>TopologicalAtomTorsionsFingerprints.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>--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>] +[<strong>-w, --WorkingDir</strong> dirname] SDFile(s)...</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>Generate topological atom torsions fingerprints [ Ref 58, 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 torsions +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 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. All unique atom torsions +are identified and an atom torsion identifier is generated; the format of atom torsion identifier is:</p> +<div class="OptionsBox"> + <AtomType1>-<AtomType2>-<AtomType3>-<AtomType4></div> +<div class="OptionsBox"> + AtomType1, AtomType2, AtomType3, AtomTyp4: Assigned atom types</div> +<div class="OptionsBox"> + where AtomType1 <= AtomType2 <= AtomType3 <= AtomType4</div> +<p>The atom torsion identifiers for all unique atom torsions corresponding to non-hydrogen atoms constitute +topological atom torsions fingerprints of the molecule.</p> +<p>Example of <em>SD</em> file containing topological atom torsions fingerprints string data:</p> +<div class="OptionsBox"> + ... ... +<br/> ... ... +<br/> $$$$ +<br/> ... ... +<br/> ... ... +<br/> ... ... +<br/> 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +<br/> ... ... +<br/> 2 3 1 0 0 0 0 +<br/> ... ... +<br/> M END +<br/> > <CmpdID> +<br/> Cmpd1</div> +<div class="OptionsBox"> + > <TopologicalAtomTorsionsFingerprints> +<br/> FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;33 +<br/> ;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-C. +<br/> X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO2.H +<br/> 2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O.X1....; +<br/> 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1</div> +<div class="OptionsBox"> + $$$$ +<br/> ... ... +<br/> ... ...</div> +<p>Example of <em>FP</em> file containing topological atom torsions fingerprints string data:</p> +<div class="OptionsBox"> + # +<br/> # Package = MayaChemTools 7.4 +<br/> # Release Date = Oct 21, 2010 +<br/> # +<br/> # TimeStamp = Fri Mar 11 15:17:20 2011 +<br/> # +<br/> # FingerprintsStringType = FingerprintsVector +<br/> # +<br/> # Description = TopologicalAtomTorsions:AtomicInvariantsAtomTypes +<br/> # VectorStringFormat = IDsAndValuesString +<br/> # VectorValuesType = NumericalValues +<br/> # +<br/> Cmpd1 33;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-C.X3.BO4...;2 2 1 1 2 2 ... +<br/> Cmpd2 23;C.X1.BO1.H3-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2...;2 2 1 5 ... +<br/> ... ... +<br/> ... ..</div> +<p>Example of CSV <em>Text</em> file containing topological atom torsions fingerprints string data:</p> +<div class="OptionsBox"> + "CompoundID","TopologicalAtomTorsionsFingerprints" +<br/> "Cmpd1","FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAto +<br/> mTypes;33;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C. +<br/> X3.BO4-C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C +<br/> .X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3....; +<br/> 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1 +<br/> ... ... +<br/> ... ...</div> +<p>The current release of MayaChemTools generates the following types of topological atom torsions +fingerprints vector strings:</p> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3 +<br/> 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4- +<br/> C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO +<br/> 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...; +<br/> ;2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3 +<br/> 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3 +<br/> .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H +<br/> 2-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 1 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.B +<br/> O3.H1-O.X1.BO1.H1 1 C.X2.BO2.H2-C.X2.BO2.H2-N.X3.BO3-C.X3.BO4 2 C.X2.B +<br/> O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTorsions:DREIDINGAtomTypes;27;Numeri +<br/> calValues;IDsAndValuesString;C_2-C_3-C_3-C_3 C_2-C_3-C_3-O_3 C_2-C_R-C +<br/> _R-C_3 C_2-C_R-C_R-C_R C_2-C_R-C_R-N_R C_2-N_3-C_R-C_R C_3-C_3-C_2-O_2 +<br/> C_3-C_3-C_2-O_3 C_3-C_3-C_3-C_3 C_3-C_3-C_3-N_R C_3-C_3-C_3-O_3 C_...; +<br/> 1 1 1 2 1 2 1 1 3 1 3 2 2 2 1 1 1 3 1 2 2 32 2 2 5 3 1</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica +<br/> lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC +<br/> H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC- +<br/> ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...; +<br/> 4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTorsions:FunctionalClassAtomTypes;26 +<br/> ;NumericalValues;IDsAndValuesString;Ar-Ar-Ar-Ar Ar-Ar-Ar-Ar.HBA Ar-Ar- +<br/> Ar-HBD Ar-Ar-Ar-Hal Ar-Ar-Ar-None Ar-Ar-Ar.HBA-Ar Ar-Ar-Ar.HBA-None Ar +<br/> -Ar-HBD-None Ar-Ar-None-HBA Ar-Ar-None-HBD Ar-Ar-None-None Ar-Ar.H...; +<br/> 32 5 2 2 3 3 3 2 2 2 2 1 2 1 1 1 2 1 1 1 1 3 1 1 1 3</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTorsions:MMFF94AtomTypes;43;Numerica +<br/> lValues;IDsAndValuesString;C5A-C5B-C5B-C5A C5A-C5B-C5B-C=ON C5A-C5B-C5 +<br/> B-CB C5A-C5B-C=ON-NC=O C5A-C5B-C=ON-O=CN C5A-C5B-CB-CB C5A-CB-CB-CB C5 +<br/> A-N5-C5A-C5B C5A-N5-C5A-CB C5A-N5-C5A-CR C5A-N5-CR-CR C5B-C5A-CB-C...; +<br/> 1 1 1 1 1 2 2 2 1 1 2 2 2 2 1 1 2 1 1 2 1 2 1 1 1 2 1 1 1 2 18 2 2 1 1 +<br/> 1 1 2 1 1 3 1 3</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTorsions:SLogPAtomTypes;49;Numerical +<br/> Values;IDsAndValuesPairsString;C1-C10-N11-C20 1 C1-C10-N11-C21 1 C1-C1 +<br/> 1-C21-C21 2 C1-C11-C21-N11 2 C1-CS-C1-C10 1 C1-CS-C1-C5 1 C1-CS-C1-CS +<br/> 2 C10-C1-CS-O2 1 C10-N11-C20-C20 2 C10-N11-C21-C11 1 C10-N11-C21-C21 1 +<br/> C11-C21-C21-C20 1 C11-C21-C21-C5 1 C11-C21-N11-C20 1 C14-C18-C18-C20 +<br/> 2 C18-C14-C18-C18 2 C18-C18-C14-F 2 C18-C18-C18-C18 4 C18-C18-C18-C...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTorsions:SYBYLAtomTypes;26;Numerical +<br/> Values;IDsAndValuesPairsString;C.2-C.3-C.3-C.3 1 C.2-C.3-C.3-O.3 1 C.2 +<br/> -C.ar-C.ar-C.3 1 C.2-C.ar-C.ar-C.ar 2 C.2-C.ar-C.ar-N.ar 1 C.2-N.am-C. +<br/> ar-C.ar 2 C.3-C.3-C.2-O.co2 2 C.3-C.3-C.3-C.3 3 C.3-C.3-C.3-N.ar 1 C.3 +<br/> -C.3-C.3-O.3 3 C.3-C.3-C.ar-C.ar 2 C.3-C.3-C.ar-N.ar 2 C.3-C.3-N.ar-C. +<br/> ar 2 C.3-C.ar-C.ar-C.ar 1 C.3-C.ar-N.ar-C.3 1 C.3-C.ar-N.ar-C.ar 1 ...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTorsions:TPSAAtomTypes;8;NumericalVa +<br/> lues;IDsAndValuesPairsString;N21-None-None-None 9 N7-None-None-None 4 +<br/> None-N21-None-None 10 None-N7-None-None 3 None-N7-None-O3 1 None-None- +<br/> None-None 44 None-None-None-O3 3 None-None-None-O4 5</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTorsions:UFFAtomTypes;27;NumericalVa +<br/> lues;IDsAndValuesPairsString;C_2-C_3-C_3-C_3 1 C_2-C_3-C_3-O_3 1 C_2-C +<br/> _R-C_R-C_3 1 C_2-C_R-C_R-C_R 2 C_2-C_R-C_R-N_R 1 C_2-N_3-C_R-C_R 2 C_3 +<br/> -C_3-C_2-O_2 1 C_3-C_3-C_2-O_3 1 C_3-C_3-C_3-C_3 3 C_3-C_3-C_3-N_R 1 C +<br/> _3-C_3-C_3-O_3 3 C_3-C_3-C_R-C_R 2 C_3-C_3-C_R-N_R 2 C_3-C_3-N_R-C_R 2 + C_3-C_R-C_R-C_R 1 C_3-C_R-N_R-C_3 1 C_3-C_R-N_R-C_R 1 C_3-N_R-C_R-...</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 torsions 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 | 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>TopologicalAtomTorsionsFingerprints</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>--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><TopologicalAtomTorsionsFP>.<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>. Defaultvalue: <em>IDsAndValuesString</em>.</p> +<p>Examples:</p> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3 +<br/> 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4- +<br/> C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO +<br/> 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...; +<br/> 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3 +<br/> 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3 +<br/> .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H +<br/> 2-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 1 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.B +<br/> O3.H1-O.X1.BO1.H1 1 C.X2.BO2.H2-C.X2.BO2.H2-N.X3.BO3-C.X3.BO4 2 C.X2.B +<br/> O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1...</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 torsions fingerprints using atomic invariants atom types in +IDsAndValuesString format and create a SampleTATFP.csv file containing sequential +compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTorsionsFingerprints.pl -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom torsions fingerprints using atomic invariants atom types in +IDsAndValuesString format and create SampleTATFP.sdf, SampleTATFP.fpf and SampleTATFP.csv +files containing sequential compound IDs in CSV file along with fingerprints vector strings +data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTorsionsFingerprints.pl --output all -r SampleTATFP + -o Sample.sdf</div> +<p>To generate topological atom torsions fingerprints using atomic invariants atom types in +IDsAndValuesPairsString format and create a SampleTATFP.csv file containing sequential +compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTorsionsFingerprints.pl --VectorStringFormat + IDsAndValuesPairsString -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom torsions fingerprints using DREIDING atom types in +IDsAndValuesString format and create a SampleTATFP.csv file containing sequential +compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTorsionsFingerprints.pl -a DREIDINGAtomTypes + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom torsions fingerprints using E-state atom types in +IDsAndValuesString format and create a SampleTATFP.csv file containing sequential +compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTorsionsFingerprints.pl -a EStateAtomTypes + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom torsions fingerprints using functional class atom types in +IDsAndValuesString format and create a SampleTATFP.csv file containing sequential +compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTorsionsFingerprints.pl -a FunctionalClassAtomTypes + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom torsions fingerprints using MMFF94 atom types in +IDsAndValuesString format and create a SampleTATFP.csv file containing sequential +compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTorsionsFingerprints.pl -a MMFF94AtomTypes + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom torsions fingerprints using SLogP atom types in +IDsAndValuesString format and create a SampleTATFP.csv file containing sequential +compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTorsionsFingerprints.pl -a SLogPAtomTypes + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom torsions fingerprints using SYBYL atom types in +IDsAndValuesString format and create a SampleTATFP.csv file containing sequential +compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTorsionsFingerprints.pl -a SYBYLAtomTypes + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom torsions fingerprints using TPSA atom types in +IDsAndValuesString format and create a SampleTATFP.csv file containing sequential +compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTorsionsFingerprints.pl -a TPSAAtomTypes + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom torsions fingerprints using UFF atom types in +IDsAndValuesString format and create a SampleTATFP.csv file containing sequential +compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTorsionsFingerprints.pl -a UFFAtomTypes + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom torsions fingerprints using only AS,X atomic invariants atom +types in IDsAndValuesString format and create a SampleTATFP.csv file containing sequential +compound IDs along with fingerprints vector strings data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes + --AtomicInvariantsToUse "AS,X" -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom torsions fingerprints using atomic invariants atom types in +IDsAndValuesString format and create a SampleTATFP.csv file containing compoundID +from molecule name line along with fingerprints vector strings, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode MolName + -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom torsions fingerprints using atomic invariants atom types in +IDsAndValuesString format and create a SampleTATFP.csv file containing compound IDs +using specified data field along with fingerprints vector strings, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID + Mol_ID -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom torsions fingerprints using atomic invariants atom types in +IDsAndValuesString format and create a SampleTATFP.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"> + % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom torsions fingerprints using atomic invariants atom types in +IDsAndValuesString format and create a SampleTATFP.csv file containing specific data +fields columns along with fingerprints vector strings, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode Specify --DataFields Mol_ID -r SampleTATFP + -o Sample.sdf</div> +<p>To generate topological atom torsions fingerprints using atomic invariants atom types in +IDsAndValuesString format and create a SampleTATFP.csv file containing common +data fields columns along with fingerprints vector strings, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode Common -r SampleTATFP -o Sample.sdf</div> +<p>To generate topological atom torsions fingerprints using atomic invariants atom types in +IDsAndValuesString format and create SampleTATFP.sdf, SampleTATFP.fpf and SampleTATFP.csv +files containing all data fields columns in CSV file along with fingerprints data, type:</p> +<div class="ExampleBox"> + % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode All --output all -r SampleTATFP + -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="./TopologicalAtomPairsFingerprints.html">TopologicalAtomPairsFingerprints.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="./TopologicalAtomPairsFingerprints.html" title="TopologicalAtomPairsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>TopologicalAtomTorsionsFingerprints.pl</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>