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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/scripts/html/TopologicalPharmacophoreAtomPairsFingerprints.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,636 @@ +<html> +<head> +<title>MayaChemTools:Documentation:TopologicalPharmacophoreAtomPairsFingerprints.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="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html" title="TopologicalPharmacophoreAtomTripletsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>TopologicalPharmacophoreAtomPairsFingerprints.pl</strong></td><td width="33%" align="right"><a href="././code/TopologicalPharmacophoreAtomPairsFingerprints.html" title="View source code">Code</a> | <a href="./../pdf/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/TopologicalPharmacophoreAtomPairsFingerprints.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>TopologicalPharmacophoreAtomPairsFingerprints.pl - Generate topological pharmacophore atom pairs fingerprints for SD files</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>TopologicalPharmacophoreAtomPairsFingerprints.pl SDFile(s)...</p> +<p>TopologicalPharmacophoreAtomPairsFingerprints.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>] +[<strong>--AtomPairsSetSizeToUse</strong> <em>ArbitrarySize | FixedSize</em>] +[<strong>-a, --AtomTypesToUse</strong> <em>"AtomType1, AtomType2..."</em>] +[<strong>--AtomTypesWeight</strong> <em>"AtomType1, Weight1, AtomType2, Weight2..."</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>--FingerprintsLabelMode</strong> <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em>] [<strong>--FingerprintsLabel</strong> <em>text</em>] +[<strong>--FuzzifyAtomPairsCount</strong> <em>Yes | No</em>] [<strong>--FuzzificationMode</strong> <em>FuzzyBinning | FuzzyBinSmoothing</em>] +[<strong>--FuzzificationMethodology</strong> <em>FuzzyBinning | FuzzyBinSmoothing</em>] [<strong>--FuzzFactor</strong> <em>number</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>-n, --NormalizationMethodology</strong> <em>None | ByHeavyAtomsCount | ByAtomTypesCount</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>--ValuesPrecision</strong> <em>number</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 pharmacophore atom pairs fingerprints [ Ref 60-62, Ref 65, Ref 68 ] 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>Based on the values specified for <strong>--AtomTypesToUse</strong>, pharmacophore atom types are +assigned to all non-hydrogen atoms in a molecule and a distance matrix is generated. +A pharmacophore atom pairs basis set is initialized for all unique possible pairs within +<strong>--MinDistance</strong> and <strong>--MaxDistance</strong> range.</p> +<div class="OptionsBox"> + Let:</div> +<div class="OptionsBox"> + P = Valid pharmacophore atom type</div> +<div class="OptionsBox"> + Px = Pharmacophore atom type x +<br/> Py = Pharmacophore atom type y</div> +<div class="OptionsBox"> + Dmin = Minimum distance corresponding to number of bonds between + two atoms +<br/> Dmax = Maximum distance corresponding to number of bonds between + two atoms +<br/> D = Distance corresponding to number of bonds between two atoms</div> +<div class="OptionsBox"> + Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at + distance Dn</div> +<div class="OptionsBox"> + P = Number of pharmacophore atom types to consider +<br/> PPDn = Number of possible unique pharmacophore atom pairs at a distance Dn</div> +<div class="OptionsBox"> + PPT = Total number of possible pharmacophore atom pairs at all distances + between Dmin and Dmax</div> +<div class="OptionsBox"> + Then:</div> +<div class="OptionsBox"> + PPD = (P * (P - 1))/2 + P</div> +<div class="OptionsBox"> + PPT = ((Dmax - Dmin) + 1) * ((P * (P - 1))/2 + P) +<br/> = ((Dmax - Dmin) + 1) * PPD</div> +<div class="OptionsBox"> + So for default values of Dmin = 1, Dmax = 10 and P = 5,</div> +<div class="OptionsBox"> + PPD = (5 * (5 - 1))/2 + 5 = 15 +<br/> PPT = ((10 - 1) + 1) * 15 = 150</div> +<div class="OptionsBox"> + The pharmacophore atom pairs bais set includes 150 values.</div> +<div class="OptionsBox"> + The atom pair IDs correspond to:</div> +<div class="OptionsBox"> + Px-Dn-Py = Pharmacophore atom pair ID for atom types Px and Py at + distance Dn</div> +<div class="OptionsBox"> + For example: H-D1-H, H-D2-HBA, PI-D5-PI and so on</div> +<p>Using distance matrix and pharmacohore atom types, occurrence of unique pharmacohore atom +pairs is counted. The contribution of each atom type to atom pair interaction is optionally +weighted by specified <strong>--AtomTypesWeight</strong> before assigning its count to appropriate distance +bin. Based on <strong>--NormalizationMethodology</strong> option, pharmacophore atom pairs count is optionally +normalized. Additionally, pharmacohore atom pairs count is optionally fuzzified before or after +the normalization controlled by values of <strong>--FuzzifyAtomPairsCount</strong>, <strong>--FuzzificationMode</strong>, +<strong>--FuzzificationMethodology</strong> and <strong>--FuzzFactor</strong> options.</p> +<p>The final pharmacophore atom pairs count along with atom pair identifiers involving all non-hydrogen +atoms, with optional normalization and fuzzification, constitute pharmacophore topological atom pairs +fingerprints of the molecule.</p> +<p>For <em>ArbitrarySize</em> value of <strong>--AtomPairsSetSizeToUse</strong> option, the fingerprint vector correspond to +only those topological pharmacophore atom pairs which are present and have non-zero count. However, +for <em>FixedSize</em> value of <strong>--AtomPairsSetSizeToUse</strong> option, the fingerprint vector contains all possible +valid topological pharmacophore atom pairs with both zero and non-zero count values.</p> +<p>Example of <em>SD</em> file containing topological pharmacophore atom pairs fingerprints string data:</p> +<div class="OptionsBox"> + ... ... +<br/> ... ... +<br/> $$$$ +<br/> ... ... +<br/> ... ... +<br/> ... ... +<br/> 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 +<br/> ... ... +<br/> 2 3 1 0 0 0 0 +<br/> ... ... +<br/> M END +<br/> > <CmpdID> +<br/> Cmpd1</div> +<div class="OptionsBox"> + > <TopologicalPharmacophoreAtomPairsFingerprints> +<br/> FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min +<br/> Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H +<br/> -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2- +<br/> HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D...; +<br/> 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 3 +<br/> 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1</div> +<div class="OptionsBox"> + $$$$ +<br/> ... ... +<br/> ... ...</div> +<p>Example of <em>FP</em> file containing topological pharmacophore 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 15:32:48 2011 +<br/> # +<br/> # FingerprintsStringType = FingerprintsVector +<br/> # +<br/> # Description = TopologicalPharmacophoreAtomPairs:ArbitrarySize:MinDistance1:MaxDistance10 +<br/> # VectorStringFormat = IDsAndValuesString +<br/> # VectorValuesType = NumericalValues +<br/> # +<br/> Cmpd1 54;H-D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA...;18 1 2... +<br/> Cmpd2 61;H-D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA...;5 1 2 ... +<br/> ... ... +<br/> ... ..</div> +<p>Example of CSV <em>Text</em> file containing topological pharmacophore atom pairs fingerprints string data:</p> +<div class="OptionsBox"> + "CompoundID","TopologicalPharmacophoreAtomPairsFingerprints" +<br/> "Cmpd1","FingerprintsVector;TopologicalPharmacophoreAtomPairs:Arbitrary +<br/> Size:MinDistance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H +<br/> -D1-H H-D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA H +<br/> BA-D2-HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4...; +<br/> 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 3 +<br/> 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1" +<br/> ... ... +<br/> ... ...</div> +<p>The current release of MayaChemTools generates the following types of topological pharmacophore +atom pairs fingerprints vector strings:</p> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min +<br/> Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H +<br/> -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2- +<br/> HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H +<br/> BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...; +<br/> 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 +<br/> 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist +<br/> ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0 +<br/> 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1 +<br/> 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0 +<br/> 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0 +<br/> 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist +<br/> ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H-D1 +<br/> -H H-D1-HBA H-D1-HBD H-D1-NI H-D1-PI HBA-D1-HBA HBA-D1-HBD HBA-D1-NI H +<br/> BA-D1-PI HBD-D1-HBD HBD-D1-NI HBD-D1-PI NI-D1-NI NI-D1-PI PI-D1-PI H-D +<br/> 2-H H-D2-HBA H-D2-HBD H-D2-NI H-D2-PI HBA-D2-HBA HBA-D2-HBD HBA-D2...; +<br/> 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 +<br/> 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 +<br/> 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0</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>--AtomPairsSetSizeToUse</strong> <em>ArbitrarySize | FixedSize</em></strong></dt> +<dd> +<p>Atom pairs set size to use during generation of topological pharmacophore atom pairs +fingerprints.</p> +<p>Possible values: <em>ArbitrarySize | FixedSize</em>; Default value: <em>ArbitrarySize</em>.</p> +<p>For <em>ArbitrarySize</em> value of <strong>--AtomPairsSetSizeToUse</strong> option, the fingerprint vector +correspond to only those topological pharmacophore atom pairs which are present and +have non-zero count. However, for <em>FixedSize</em> value of <strong>--AtomPairsSetSizeToUse</strong> +option, the fingerprint vector contains all possible valid topological pharmacophore atom +pairs with both zero and non-zero count values.</p> +</dd> +<dt><strong><strong>-a, --AtomTypesToUse</strong> <em>"AtomType1,AtomType2,..."</em></strong></dt> +<dd> +<p>Pharmacophore atom types to use during generation of topological phramacophore +atom pairs. It's a list of comma separated valid pharmacophore atom types.</p> +<p>Possible values for pharmacophore atom types are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>. +Default value [ Ref 60-62 ] : <em>HBD,HBA,PI,NI,H</em>.</p> +<p>The pharmacophore atom types 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> +<p><em>AtomTypes::FunctionalClassAtomTypes</em> module is used to assign pharmacophore 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>--AtomTypesWeight</strong> <em>"AtomType1,Weight1,AtomType2,Weight2..."</em></strong></dt> +<dd> +<p>Weights of specified pharmacophore atom types to use during calculation of their contribution +to atom pair count. Default value: <em>None</em>. Valid values: real numbers greater than 0. In general +it's comma delimited list of valid atom type and its weight.</p> +<p>The weight values allow to increase the importance of specific pharmacophore atom type +in the generated fingerprints. A weight value of 0 for an atom type eliminates its contribution to +atom pair count where as weight value of 2 doubles its contribution.</p> +</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>--FingerprintsLabelMode</strong> <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em></strong></dt> +<dd> +<p>Specify how fingerprints label is generated in conjunction with <strong>--FingerprintsLabel</strong> option value: +use fingerprints label generated only by <strong>--FingerprintsLabel</strong> option value or append topological +atom pair count value IDs to <strong>--FingerprintsLabel</strong> option value.</p> +<p>Possible values: <em>FingerprintsLabelOnly | FingerprintsLabelWithIDs</em>. Default value: +<em>FingerprintsLabelOnly</em>.</p> +<p>Topological atom pairs IDs appended to <strong>--FingerprintsLabel</strong> value during <em>FingerprintsLabelWithIDs</em> +values of <strong>--FingerprintsLabelMode</strong> correspond to atom pair count values in fingerprint vector string.</p> +<p><em>FingerprintsLabelWithIDs</em> value of <strong>--FingerprintsLabelMode</strong> is ignored during <em>ArbitrarySize</em> value +of <strong>--AtomPairsSetSizeToUse</strong> option and topological atom pairs IDs not appended to the label.</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>TopologicalPharmacophoreAtomPairsFingerprints</em>.</p> +</dd> +<dt><strong><strong>--FuzzifyAtomPairsCount</strong> <em>Yes | No</em></strong></dt> +<dd> +<p>To fuzzify or not to fuzzify atom pairs count. Possible values: <em>Yes or No</em>. Default value: +<em>No</em>.</p> +</dd> +<dt><strong><strong>--FuzzificationMode</strong> <em>BeforeNormalization | AfterNormalization</em></strong></dt> +<dd> +<p>When to fuzzify atom pairs count. Possible values: <em>BeforeNormalization | AfterNormalizationYes</em>. +Default value: <em>AfterNormalization</em>.</p> +</dd> +<dt><strong><strong>--FuzzificationMethodology</strong> <em>FuzzyBinning | FuzzyBinSmoothing</em></strong></dt> +<dd> +<p>How to fuzzify atom pairs count. Possible values: <em>FuzzyBinning | FuzzyBinSmoothing</em>. +Default value: <em>FuzzyBinning</em>.</p> +<p>In conjunction with values for options <strong>--FuzzifyAtomPairsCount</strong>, <strong>--FuzzificationMode</strong> and +<strong>--FuzzFactor</strong>, <strong>--FuzzificationMethodology</strong> option is used to fuzzify pharmacophore atom +pairs count.</p> +<p>Let:</p> +<div class="OptionsBox"> + Px = Pharmacophore atom type x +<br/> Py = Pharmacophore atom type y +<br/> PPxy = Pharmacophore atom pair between atom type Px and Py</div> +<div class="OptionsBox"> + PPxyDn = Pharmacophore atom pairs count between atom type Px and Py + at distance Dn +<br/> PPxyDn-1 = Pharmacophore atom pairs count between atom type Px and Py + at distance Dn - 1 +<br/> PPxyDn+1 = Pharmacophore atom pairs count between atom type Px and Py + at distance Dn + 1</div> +<div class="OptionsBox"> + FF = FuzzFactor for FuzzyBinning and FuzzyBinSmoothing</div> +<p>Then:</p> +<p>For <em>FuzzyBinning</em>:</p> +<div class="OptionsBox"> + PPxyDn = PPxyDn (Unchanged)</div> +<div class="OptionsBox"> + PPxyDn-1 = PPxyDn-1 + PPxyDn * FF +<br/> PPxyDn+1 = PPxyDn+1 + PPxyDn * FF</div> +<p>For <em>FuzzyBinSmoothing</em>:</p> +<div class="OptionsBox"> + PPxyDn = PPxyDn - PPxyDn * 2FF for Dmin < Dn < Dmax +<br/> PPxyDn = PPxyDn - PPxyDn * FF for Dn = Dmin or Dmax</div> +<div class="OptionsBox"> + PPxyDn-1 = PPxyDn-1 + PPxyDn * FF +<br/> PPxyDn+1 = PPxyDn+1 + PPxyDn * FF</div> +<p>In both fuzzification schemes, a value of 0 for FF implies no fuzzification of occurrence counts. +A value of 1 during <em>FuzzyBinning</em> corresponds to maximum fuzzification of occurrence counts; +however, a value of 1 during <em>FuzzyBinSmoothing</em> ends up completely distributing the value over +the previous and next distance bins.</p> +<p>So for default value of <strong>--FuzzFactor</strong> (FF) 0.15, the occurrence count of pharmacohore atom pairs +at distance Dn during FuzzyBinning is left unchanged and the counts at distances Dn -1 and Dn + 1 +are incremented by PPxyDn * 0.15.</p> +<p>And during <em>FuzzyBinSmoothing</em> the occurrence counts at Distance Dn is scaled back using multiplicative +factor of (1 - 2*0.15) and the occurrence counts at distances Dn -1 and Dn + 1 are incremented by +PPxyDn * 0.15. In otherwords, occurrence bin count is smoothed out by distributing it over the +previous and next distance value.</p> +</dd> +<dt><strong><strong>--FuzzFactor</strong> <em>number</em></strong></dt> +<dd> +<p>Specify by how much to fuzzify atom pairs count. Default value: <em>0.15</em>. Valid values: For +<em>FuzzyBinning</em> value of <strong>--FuzzificationMethodology</strong> option: <em>between 0 and 1.0</em>; For +<em>FuzzyBinSmoothing</em> value of <strong>--FuzzificationMethodology</strong> option: <em>between 0 and 0.5</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 pharmacophore atom +pairs. Default value: <em>1</em>. Valid values: positive integers including 0 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 pharmacophore atom + pairs. Default value: <em>10</em>. Valid values: positive integers and greater than <strong>--MinDistance</strong>.</p> +</dd> +<dt><strong><strong>-n, --NormalizationMethodology</strong> <em>None | ByHeavyAtomsCount | ByAtomTypesCount</em></strong></dt> +<dd> +<p>Normalization methodology to use for scaling the occurrence count of pharmacophore atom +pairs within specified distance range. Possible values: <em>None, ByHeavyAtomsCount or +ByAtomTypesCount</em>. Default value: <em>None</em>.</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><TopologicalPharmacophoreAtomPairsFP>.<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>--ValuesPrecision</strong> <em>number</em></strong></dt> +<dd> +<p>Precision of atom pairs count real values which might be generated after normalization +or fuzzification. Default value: up to <em>2</em> decimal places. Valid values: positive integers.</p> +</dd> +<dt><strong><strong>-v, --VectorStringFormat</strong> <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString</em></strong></dt> +<dd> +<p>Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by +<strong>--output</strong> option. Possible values: <em>ValuesString, IDsAndValuesString | IDsAndValuesPairsString +| ValuesAndIDsString | ValuesAndIDsPairsString</em>.</p> +<p>Default value during <em>FixedSize</em> value of <strong>--AtomPairsSetSizeToUse</strong> option: <em>ValuesString</em>. Default +value during <em>ArbitrarySize</em> value of <strong>--AtomPairsSetSizeToUse</strong> option: <em>IDsAndValuesString</em>.</p> +<p><em>ValuesString</em> option value is not allowed for <em>ArbitrarySize</em> value of <strong>--AtomPairsSetSizeToUse</strong> +option.</p> +<p>Examples:</p> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomPairs:ArbitrarySize:Min +<br/> Distance1:MaxDistance10;54;NumericalValues;IDsAndValuesString;H-D1-H H +<br/> -D1-NI HBA-D1-NI HBD-D1-NI H-D2-H H-D2-HBA H-D2-HBD HBA-D2-HBA HBA-D2- +<br/> HBD H-D3-H H-D3-HBA H-D3-HBD H-D3-NI HBA-D3-NI HBD-D3-NI H-D4-H H-D4-H +<br/> BA H-D4-HBD HBA-D4-HBA HBA-D4-HBD HBD-D4-HBD H-D5-H H-D5-HBA H-D5-...; +<br/> 18 1 2 1 22 12 8 1 2 18 6 3 1 1 1 22 13 6 5 7 2 28 9 5 1 1 1 36 16 10 +<br/> 3 4 1 37 10 8 1 35 10 9 3 3 1 28 7 7 4 18 16 12 5 1 2 1</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist +<br/> ance1:MaxDistance10;150;OrderedNumericalValues;ValuesString;18 0 0 1 0 +<br/> 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 1 0 0 0 1 +<br/> 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 1 0 0 1 0 +<br/> 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0 0 37 10 8 0 0 0 0 1 0 0 0 0 0 0 +<br/> 0 35 10 9 0 0 3 3 0 0 1 0 0 0 0 0 28 7 7 4 0 0 0 0 0 0 0 0 0 0 0 18...</div> +<div class="OptionsBox"> + FingerprintsVector;TopologicalPharmacophoreAtomPairs:FixedSize:MinDist +<br/> ance1:MaxDistance10;150;OrderedNumericalValues;IDsAndValuesString;H-D1 +<br/> -H H-D1-HBA H-D1-HBD H-D1-NI H-D1-PI HBA-D1-HBA HBA-D1-HBD HBA-D1-NI H +<br/> BA-D1-PI HBD-D1-HBD HBD-D1-NI HBD-D1-PI NI-D1-NI NI-D1-PI PI-D1-PI H-D +<br/> 2-H H-D2-HBA H-D2-HBD H-D2-NI H-D2-PI HBA-D2-HBA HBA-D2-HBD HBA-D2...; +<br/> 18 0 0 1 0 0 0 2 0 0 1 0 0 0 0 22 12 8 0 0 1 2 0 0 0 0 0 0 0 0 18 6 3 +<br/> 1 0 0 0 1 0 0 1 0 0 0 0 22 13 6 0 0 5 7 0 0 2 0 0 0 0 0 28 9 5 1 0 0 0 +<br/> 1 0 0 1 0 0 0 0 36 16 10 0 0 3 4 0 0 1 0 0 0 0</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 pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances +from 1 through 10 using default atom types with no weighting, normalization, and fuzzification +of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomPairsFingerprints.pl -r SampleTPAPFP + -o Sample.sdf</div> +<p>To generate topological pharmacophore atom pairs fingerprints of fixed size corresponding to distances +from 1 through 10 using default atom types with no weighting, normalization, and fuzzification +of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomPairsFingerprints.pl + --AtomPairsSetSizeToUse FixedSize -r SampleTPAPFP-o Sample.sdf</div> +<p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances +from 1 through 10 using default atom types with no weighting, normalization, and fuzzification +of atom pairs count and create SampleTPAPFP.sdf, SampleTPAPFP.fpf and SampleTPAPFP.csv files containing +sequential compound IDs in CSV file along with fingerprints vector strings data in ValuesString +format, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomPairsFingerprints.pl --output all + -r SampleTPAPFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances +from 1 through 10 using default atom types with no weighting, normalization, and fuzzification +of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in IDsAndValuesPairsString format, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomPairsFingerprints.pl --VectorStringFormat + IDsAndValuesPairsString -r SampleTPAPFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances +from 1 through 6 using default atom types with no weighting, normalization, and fuzzification +of atom pairs count and create a SampleTPAPFP.csv file containing sequential compound IDs along +with fingerprints vector strings data in ValuesString format, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1 + -MaxDistance 6 -r SampleTPAPFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances +from 1 through 10 using "HBD,HBA,PI,NI" atom types with double the weighting for "HBD,HBA" and +normalization by HeavyAtomCount but no fuzzification of atom pairs count and create a +SampleTPAPFP.csv file containing sequential compound IDs along with fingerprints vector strings +data in ValuesString format, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1 + -MaxDistance 10 --AtomTypesToUse "HBD,HBA,PI, NI" --AtomTypesWeight + "HBD,2,HBA,2,PI,1,NI,1" --NormalizationMethodology ByHeavyAtomsCount + --FuzzifyAtomPairsCount No -r SampleTPAPFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to +distances from 1 through 10 using "HBD,HBA,PI,NI,H" atom types with no weighting of atom types and +normalization but with fuzzification of atom pairs count using FuzzyBinning methodology +with FuzzFactor value 0.15 and create a SampleTPAPFP.csv file containing sequential compound +IDs along with fingerprints vector strings data in ValuesString format, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomPairsFingerprints.pl --MinDistance 1 + --MaxDistance 10 --AtomTypesToUse "HBD,HBA,PI, NI,H" --AtomTypesWeight + "HBD,1,HBA,1,PI,1,NI,1,H,1" --NormalizationMethodology None + --FuzzifyAtomPairsCount Yes --FuzzificationMethodology FuzzyBinning + --FuzzFactor 0.5 -r SampleTPAPFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding to distances +distances from 1 through 10 using default atom types with no weighting, +normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv +file containing compound ID from molecule name line along with fingerprints vector strings +data, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode + CompoundID -CompoundIDMode MolName -r SampleTPAPFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding +to distances from 1 through 10 using default atom types with no weighting, +normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv +file containing compound IDs using specified data field along with fingerprints vector strings +data, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode + CompoundID -CompoundIDMode DataField --CompoundID Mol_ID + -r SampleTPAPFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding +to distances from 1 through 10 using default atom types with no weighting, +normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.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"> + % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode + CompoundID -CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTPAPFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding +to distances from 1 through 10 using default atom types with no weighting, +normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv +file containing specific data fields columns along with fingerprints vector strings +data, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode + Specify --DataFields Mol_ID -r SampleTPAPFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding +to distances from 1 through 10 using default atom types with no weighting, +normalization, and fuzzification of atom pairs count and create a SampleTPAPFP.csv +file containing common data fields columns along with fingerprints vector strings +data, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode + Common -r SampleTPAPFP -o Sample.sdf</div> +<p>To generate topological pharmacophore atom pairs fingerprints of arbitrary size corresponding +to distances from 1 through 10 using default atom types with no weighting, +normalization, and fuzzification of atom pairs count and create SampleTPAPFP.sdf, SampleTPAPFP.fpf, +and SampleTPAPFP.csv files containing all data fields columns in CSV file along with fingerprints +data, type:</p> +<div class="ExampleBox"> + % TopologicalPharmacophoreAtomPairsFingerprints.pl --DataFieldsMode + All --output all -r SampleTPAPFP -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="./TopologicalAtomTorsionsFingerprints.html">TopologicalAtomTorsionsFingerprints.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="./TopologicalAtomTripletsFingerprints.html" title="TopologicalAtomTripletsFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./TopologicalPharmacophoreAtomTripletsFingerprints.html" title="TopologicalPharmacophoreAtomTripletsFingerprints.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>TopologicalPharmacophoreAtomPairsFingerprints.pl</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>