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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/html/CalculatePhysicochemicalProperties.html Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,593 @@ +<html> +<head> +<title>MayaChemTools:Documentation:CalculatePhysicochemicalProperties.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="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./DBSchemaTablesToTextFiles.html" title="DBSchemaTablesToTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>CalculatePhysicochemicalProperties.pl</strong></td><td width="33%" align="right"><a href="././code/CalculatePhysicochemicalProperties.html" title="View source code">Code</a> | <a href="./../pdf/CalculatePhysicochemicalProperties.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/CalculatePhysicochemicalProperties.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/CalculatePhysicochemicalProperties.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/CalculatePhysicochemicalProperties.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>CalculatePhysicochemicalProperties.pl - Calculate physicochemical properties for SD files</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>CalculatePhysicochemicalProperties.pl SDFile(s)...</p> +<p>PhysicochemicalProperties.pl [<strong>--AromaticityModel</strong> <em>AromaticityModelType</em>] +[<strong>--CompoundID</strong> DataFieldName or LabelPrefixString] +[<strong>--CompoundIDLabel</strong> text] [<strong>--CompoundIDMode</strong>] [<strong>--DataFields</strong> "FieldLabel1, FieldLabel2,..."] +[<strong>-d, --DataFieldsMode</strong> All | Common | Specify | CompoundID] [<strong>-f, --Filter</strong> Yes | No] [<strong>-h, --help</strong>] +[<strong>--HydrogenBonds</strong> HBondsType1 | HBondsType2] [<strong>-k, --KeepLargestComponent</strong> Yes | No] +[<strong>-m, --mode</strong> All | RuleOf5 | RuleOf3 | "name1, [name2,...]"] +[<strong>--MolecularComplexity</strong> <em>Name,Value, [Name,Value,...]</em>] +[<strong>--OutDelim</strong> comma | tab | semicolon] [<strong>--output</strong> SD | text | both] [<strong>-o, --overwrite</strong>] +[<strong>--Precision</strong> Name,Number,[Name,Number,..]] [<strong>--RotatableBonds</strong> Name,Value, [Name,Value,...]] +[<strong>--RuleOf3Violations</strong> Yes | No] [<strong>--RuleOf5Violations</strong> Yes | No] +[<strong>-q, --quote</strong> Yes | No] [<strong>-r, --root</strong> RootName] +[<strong>-w, --WorkingDir</strong> dirname] SDFile(s)...</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>Calculate physicochemical properties for <em>SDFile(s)</em> and create appropriate SD or CSV/TSV +text file(s) containing calculated properties.</p> +<p>The current release of MayaChemTools supports the calculation of these physicochemical +properties:</p> +<div class="OptionsBox"> + MolecularWeight, ExactMass, HeavyAtoms, Rings, AromaticRings, +<br/> van der Waals MolecularVolume [ Ref 93 ], RotatableBonds, +<br/> HydrogenBondDonors, HydrogenBondAcceptors, LogP and +<br/> Molar Refractivity (SLogP and SMR) [ Ref 89 ], Topological Polar +<br/> Surface Area (TPSA) [ Ref 90 ], Fraction of SP3 carbons (Fsp3Carbons) +<br/> and SP3 carbons (Sp3Carbons) [ Ref 115-116, Ref 119 ], +<br/> MolecularComplexity [ Ref 117-119 ]</div> +<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 calculation of molecular complexity using <em>MolecularComplexityType</em> parameter +corresponds to the number of bits-set or unique keys [ Ref 117-119 ] in molecular fingerprints. +Default value for <em>MolecularComplexityType</em>: <em>MACCSKeys</em> of size 166. The calculation +of MACCSKeys is relatively expensive and can take rather substantial amount of time.</p> +<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>--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 CSV/TSV text file(s) along with calculated +physicochemical properties for <em>text | both</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 calculated physicochemical properties 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 calculated physicochemical properties 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 physiochemical properties and compounds +containing atom data corresponding to non-element symbols or no atom data are ignored.</p> +</dd> +<dt><strong><strong>-h, --help</strong></strong></dt> +<dd> +<p>Print this help message.</p> +</dd> +<dt><strong><strong>--HydrogenBonds</strong> <em>HBondsType1 | HBondsType2</em></strong></dt> +<dd> +<p>Parameters to control calculation of hydrogen bond donors and acceptors. Possible values: +<em>HBondsType1, HydrogenBondsType1, HBondsType2, HydrogenBondsType2</em>. Default value: +<em>HBondsType2</em> which corresponds to <strong>RuleOf5</strong> definition for number of hydrogen bond +donors and acceptors.</p> +<p>The current release of MayaChemTools supports identification of two types of hydrogen bond +donor and acceptor atoms with these names:</p> +<div class="OptionsBox"> + HBondsType1 or HydrogenBondsType1 +<br/> HBondsType2 or HydrogenBondsType2</div> +<p>The names of these hydrogen bond types are rather arbitrary. However, their definitions have +specific meaning and are as follows:</p> +<div class="OptionsBox"> + HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:</div> +<div class="OptionsBox"> + Donor: NH, NH2, OH - Any N and O with available H + Acceptor: N[!H], O - Any N without available H and any O</div> +<div class="OptionsBox"> + HydrogenBondsType2 [ Ref 91 ]:</div> +<div class="OptionsBox"> + Donor: NH, NH2, OH - N and O with available H + Acceptor: N, O - And N and O</div> +</dd> +<dt><strong><strong>-k, --KeepLargestComponent</strong> <em>Yes | No</em></strong></dt> +<dd> +<p>Calculate physicochemical properties 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, physicochemical properties can be +calculated 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 calculation of physicochemical properties.</p> +</dd> +<dt><strong><strong>-m, --mode</strong> <em>All | RuleOf5 | RuleOf3 | "name1, [name2,...]"</em></strong></dt> +<dd> +<p>Specify physicochemical properties to calculate for SDFile(s): calculate all available physical +chemical properties; calculate properties corresponding to Rule of 5; or use a comma delimited +list of supported physicochemical properties. Possible values: <em>All | RuleOf5 | RuleOf3 | +"name1, [name2,...]"</em>.</p> +<p>Default value: <em>MolecularWeight, HeavyAtoms, MolecularVolume, RotatableBonds, HydrogenBondDonors, +HydrogenBondAcceptors, SLogP, TPSA</em>. These properties are calculated by default.</p> +<p><em>RuleOf5</em> [ Ref 91 ] includes these properties: <em>MolecularWeight, HydrogenBondDonors, HydrogenBondAcceptors, +SLogP</em>. <em>RuleOf5</em> states: MolecularWeight <= 500, HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, and +logP <= 5.</p> +<p><em>RuleOf3</em> [ Ref 92 ] includes these properties: <em>MolecularWeight, RotatableBonds, HydrogenBondDonors, +HydrogenBondAcceptors, SLogP, TPSA</em>. <em>RuleOf3</em> states: MolecularWeight <= 300, RotatableBonds <= 3, +HydrogenBondDonors <= 3, HydrogenBondAcceptors <= 3, logP <= 3, and TPSA <= 60.</p> +<p><em>All</em> calculates all supported physicochemical properties: <em>MolecularWeight, ExactMass, +HeavyAtoms, Rings, AromaticRings, MolecularVolume, RotatableBonds, HydrogenBondDonors, +HydrogenBondAcceptors, SLogP, SMR, TPSA, Fsp3Carbons, Sp3Carbons, MolecularComplexity</em>.</p> +</dd> +<dt><strong><strong>--MolecularComplexity</strong> <em>Name,Value, [Name,Value,...]</em></strong></dt> +<dd> +<p>Parameters to control calculation of molecular complexity: it's a comma delimited list of parameter +name and value pairs.</p> +<p>Possible parameter names: <em>MolecularComplexityType, AtomIdentifierType, +AtomicInvariantsToUse, FunctionalClassesToUse, MACCSKeysSize, NeighborhoodRadius, +MinPathLength, MaxPathLength, UseBondSymbols, MinDistance, MaxDistance, +UseTriangleInequality, DistanceBinSize, NormalizationMethodology</em>.</p> +<p>The valid paramater valuse for each parameter name are described in the following sections.</p> +<p>The current release of MayaChemTools supports calculation of molecular complexity using +<em>MolecularComplexityType</em> parameter corresponding to the number of bits-set or unique +keys [ Ref 117-119 ] in molecular fingerprints. The valid values for <em>MolecularComplexityType</em> +are:</p> +<div class="OptionsBox"> + AtomTypesFingerprints +<br/> ExtendedConnectivityFingerprints +<br/> MACCSKeys +<br/> PathLengthFingerprints +<br/> TopologicalAtomPairsFingerprints +<br/> TopologicalAtomTripletsFingerprints +<br/> TopologicalAtomTorsionsFingerprints +<br/> TopologicalPharmacophoreAtomPairsFingerprints +<br/> TopologicalPharmacophoreAtomTripletsFingerprints</div> +<p>Default value for <em>MolecularComplexityType</em>: <em>MACCSKeys</em>.</p> +<p><em>AtomIdentifierType</em> parameter name correspods to atom types used during generation of +fingerprints. The valid values for <em>AtomIdentifierType</em> are: <em>AtomicInvariantsAtomTypes, +DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, +SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes</em>. <em>AtomicInvariantsAtomTypes</em> +is not supported for during the following values of <em>MolecularComplexityType</em>: <em>MACCSKeys, +TopologicalPharmacophoreAtomPairsFingerprints, TopologicalPharmacophoreAtomTripletsFingerprints</em>. +<em>FunctionalClassAtomTypes</em> is the only valid value for <em>AtomIdentifierType</em> for topological +pharmacophore fingerprints.</p> +<p>Default value for <em>AtomIdentifierType</em>: <em>AtomicInvariantsAtomTypes</em> +for all except topological pharmacophore fingerprints where it is <em>FunctionalClassAtomTypes</em>.</p> +<p><em>AtomicInvariantsToUse</em> parameter name and values are used during <em>AtomicInvariantsAtomTypes</em> +value of parameter <em>AtomIdentifierType</em>. It's a list of space 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 for <em>AtomicInvariantsToUse</em> parameter are set differently for different fingerprints +using <em>MolecularComplexityType</em> parameter as shown below:</p> +<div class="OptionsBox"> + MolecularComplexityType AtomicInvariantsToUse</div> +<div class="OptionsBox"> + AtomTypesFingerprints AS X BO H FC +<br/> TopologicalAtomPairsFingerprints AS X BO H FC +<br/> TopologicalAtomTripletsFingerprints AS X BO H FC +<br/> TopologicalAtomTorsionsFingerprints AS X BO H FC</div> +<div class="OptionsBox"> + ExtendedConnectivityFingerprints AS X BO H FC MN +<br/> PathLengthFingerprints AS</div> +<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> +<p><em>FunctionalClassesToUse</em> parameter name and values are used during <em>FunctionalClassAtomTypes</em> +value of parameter <em>AtomIdentifierType</em>. It's a list of space separated valid atomic invariant atom types.</p> +<p>Possible values for atom functional classes are: <em>Ar, CA, H, HBA, HBD, Hal, NI, PI, RA</em>.</p> +<p>Default value for <em>FunctionalClassesToUse</em> parameter is set to:</p> +<div class="OptionsBox"> + HBD HBA PI NI Ar Hal</div> +<p>for all fingerprints except for the following two <em>MolecularComplexityType</em> fingerints:</p> +<div class="OptionsBox"> + MolecularComplexityType FunctionalClassesToUse</div> +<div class="OptionsBox"> + TopologicalPharmacophoreAtomPairsFingerprints HBD HBA P, NI H +<br/> TopologicalPharmacophoreAtomTripletsFingerprints HBD HBA PI NI H Ar</div> +<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> +<p><em>MACCSKeysSize</em> parameter name is only used during <em>MACCSKeys</em> value of +<em>MolecularComplexityType</em> and corresponds to the size of MACCS key set. Possible +values: <em>166 or 322</em>. Default value: <em>166</em>.</p> +<p><em>NeighborhoodRadius</em> parameter name is only used during <em>ExtendedConnectivityFingerprints</em> +value of <em>MolecularComplexityType</em> and corresponds to atomic neighborhoods radius for +generating extended connectivity fingerprints. Possible values: positive integer. Default value: +<em>2</em>.</p> +<p><em>MinPathLength</em> and <em>MaxPathLength</em> parameters are only used during <em>PathLengthFingerprints</em> +value of <em>MolecularComplexityType</em> and correspond to minimum and maximum path lengths to use +for generating path length fingerprints. Possible values: positive integers. Default value: <em>MinPathLength - 1</em>; +<em>MaxPathLength - 8</em>.</p> +<p><em>UseBondSymbols</em> parameter is only used during <em>PathLengthFingerprints</em> value of +<em>MolecularComplexityType</em> and indicates whether bond symbols are included in atom path +strings used to generate path length fingerprints. Possible value: <em>Yes or No</em>. Default value: +<em>Yes</em>.</p> +<p><em>MinDistance</em> and <em>MaxDistance</em> parameters are only used during <em>TopologicalAtomPairsFingerprints</em> +and <em>TopologicalAtomTripletsFingerprints</em> values of <em>MolecularComplexityType</em> and correspond to +minimum and maximum bond distance between atom pairs during topological pharmacophore fingerprints. +Possible values: positive integers. Default value: <em>MinDistance - 1</em>; <em>MaxDistance - 10</em>.</p> +<p><em>UseTriangleInequality</em> parameter is used during these values for <em>MolecularComplexityType</em>: +<em>TopologicalAtomTripletsFingerprints</em> and <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>. +Possible values: <em>Yes or No</em>. It determines wheter to apply triangle inequality to distance triplets. +Default value: <em>TopologicalAtomTripletsFingerprints - No</em>; +<em>TopologicalPharmacophoreAtomTripletsFingerprints - Yes</em>.</p> +<p><em>DistanceBinSize</em> parameter is used during <em>TopologicalPharmacophoreAtomTripletsFingerprints</em> +value of <em>MolecularComplexityType</em> and correspons to distance bin size used for binning +distances during generation of topological pharmacophore atom triplets fingerprints. Possible +value: positive integer. Default value: <em>2</em>.</p> +<p><em>NormalizationMethodology</em> is only used for these values for <em>MolecularComplexityType</em>: +<em>ExtendedConnectivityFingerprints</em>, <em>TopologicalPharmacophoreAtomPairsFingerprints</em> +and <em>TopologicalPharmacophoreAtomTripletsFingerprints</em>. It corresponds to normalization +methodology to use for scaling the number of bits-set or unique keys during generation of +fingerprints. Possible values during <em>ExtendedConnectivityFingerprints</em>: <em>None or +ByHeavyAtomsCount</em>; Default value: <em>None</em>. Possible values during topological +pharmacophore atom pairs and tripletes fingerprints: <em>None or ByPossibleKeysCount</em>; +Default value: <em>None</em>. <em>ByPossibleKeysCount</em> corresponds to total number of +possible topological pharmacophore atom pairs or triplets in a molecule.</p> +<p>Examples of <em>MolecularComplexity</em> name and value parameters:</p> +<div class="OptionsBox"> + MolecularComplexityType,AtomTypesFingerprints,AtomIdentifierType, +<br/> AtomicInvariantsAtomTypes,AtomicInvariantsToUse,AS X BO H FC</div> +<div class="OptionsBox"> + MolecularComplexityType,ExtendedConnectivityFingerprints, +<br/> AtomIdentifierType,AtomicInvariantsAtomTypes, +<br/> AtomicInvariantsToUse,AS X BO H FC MN,NeighborhoodRadius,2, +<br/> NormalizationMethodology,None</div> +<div class="OptionsBox"> + MolecularComplexityType,MACCSKeys,MACCSKeysSize,166</div> +<div class="OptionsBox"> + MolecularComplexityType,PathLengthFingerprints,AtomIdentifierType, +<br/> AtomicInvariantsAtomTypes,AtomicInvariantsToUse,AS,MinPathLength, +<br/> 1,MaxPathLength,8,UseBondSymbols,Yes</div> +<div class="OptionsBox"> + MolecularComplexityType,TopologicalAtomPairsFingerprints, +<br/> AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse, +<br/> AS X BO H FC,MinDistance,1,MaxDistance,10</div> +<div class="OptionsBox"> + MolecularComplexityType,TopologicalAtomTripletsFingerprints, +<br/> AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse, +<br/> AS X BO H FC,MinDistance,1,MaxDistance,10,UseTriangleInequality,No</div> +<div class="OptionsBox"> + MolecularComplexityType,TopologicalAtomTorsionsFingerprints, +<br/> AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse, +<br/> AS X BO H FC</div> +<div class="OptionsBox"> + MolecularComplexityType,TopologicalPharmacophoreAtomPairsFingerprints, +<br/> AtomIdentifierType,FunctionalClassAtomTypes,FunctionalClassesToUse, +<br/> HBD HBA PI NI H,MinDistance,1,MaxDistance,10,NormalizationMethodology, +<br/> None</div> +<div class="OptionsBox"> + MolecularComplexityType,TopologicalPharmacophoreAtomTripletsFingerprints, +<br/> AtomIdentifierType,FunctionalClassAtomTypes,FunctionalClassesToUse, +<br/> HBD HBA PI NI H Ar,MinDistance,1,MaxDistance,10,NormalizationMethodology, +<br/> None,UseTriangleInequality,Yes,NormalizationMethodology,None, +<br/> DistanceBinSize,2</div> +</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 | text | both</em></strong></dt> +<dd> +<p>Type of output files to generate. Possible values: <em>SD, text, or both</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>--Precision</strong> <em>Name,Number,[Name,Number,..]</em></strong></dt> +<dd> +<p>Precision of calculated property values in the output file: it's a comma delimited list of +property name and precision value pairs. Possible property names: <em>MolecularWeight, +ExactMass</em>. Possible values: positive intergers. Default value: <em>MolecularWeight,2, +ExactMass,4</em>.</p> +<p>Examples:</p> +<div class="OptionsBox"> + ExactMass,3 +<br/> MolecularWeight,1,ExactMass,2</div> +</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><PhysicochemicalProperties>.<Ext>. The file type determines <Ext> value. +The sdf, csv, and tsv <Ext> values are used for SD, comma/semicolon, and tab +delimited text files, respectively.This option is ignored for multiple input files.</p> +</dd> +<dt><strong><strong>--RotatableBonds</strong> <em>Name,Value, [Name,Value,...]</em></strong></dt> +<dd> +<p>Parameters to control calculation of rotatable bonds [ Ref 92 ]: it's a comma delimited list of parameter +name and value pairs. Possible parameter names: <em>IgnoreTerminalBonds, IgnoreBondsToTripleBonds, +IgnoreAmideBonds, IgnoreThioamideBonds, IgnoreSulfonamideBonds</em>. Possible parameter values: +<em>Yes or No</em>. By default, value of all parameters is set to <em>Yes</em>.</p> +</dd> +<dt><strong><strong>--RuleOf3Violations</strong> <em>Yes | No</em></strong></dt> +<dd> +<p>Specify whether to calculate <strong>RuleOf3Violations</strong> for SDFile(s). Possible values: <em>Yes or No</em>. +Default value: <em>No</em>.</p> +<p>For <em>Yes</em> value of <strong>RuleOf3Violations</strong>, in addition to calculating total number of <strong>RuleOf3</strong> violations, +individual violations for compounds are also written to output files.</p> +<p><strong>RuleOf3</strong> [ Ref 92 ] states: MolecularWeight <= 300, RotatableBonds <= 3, HydrogenBondDonors <= 3, +HydrogenBondAcceptors <= 3, logP <= 3, and TPSA <= 60.</p> +</dd> +<dt><strong><strong>--RuleOf5Violations</strong> <em>Yes | No</em></strong></dt> +<dd> +<p>Specify whether to calculate <strong>RuleOf5Violations</strong> for SDFile(s). Possible values: <em>Yes or No</em>. +Default value: <em>No</em>.</p> +<p>For <em>Yes</em> value of <strong>RuleOf5Violations</strong>, in addition to calculating total number of <strong>RuleOf5</strong> violations, +individual violations for compounds are also written to output files.</p> +<p><strong>RuleOf5</strong> [ Ref 91 ] states: MolecularWeight <= 500, HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, +and logP <= 5.</p> +</dd> +<dt><strong><strong>--TPSA</strong> <em>Name,Value, [Name,Value,...]</em></strong></dt> +<dd> +<p>Parameters to control calculation of TPSA: it's a comma delimited list of parameter name and value +pairs. Possible parameter names: <em>IgnorePhosphorus, IgnoreSulfur</em>. Possible parameter values: +<em>Yes or No</em>. By default, value of all parameters is set to <em>Yes</em>.</p> +<p>By default, TPSA atom contributions from Phosphorus and Sulfur atoms are not included during +TPSA calculations. [ Ref 91 ]</p> +</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 calculate default set of physicochemical properties - MolecularWeight, HeavyAtoms, +MolecularVolume, RotatableBonds, HydrogenBondDonor, HydrogenBondAcceptors, SLogP, +TPSA - and generate a SamplePhysicochemicalProperties.csv file containing sequential +compound IDs along with properties data, type:</p> +<div class="ExampleBox"> + % CalculatePhysicochemicalProperties.pl -o Sample.sdf</div> +<p>To calculate all available physicochemical properties and generate both SampleAllProperties.csv +and SampleAllProperties.sdf files containing sequential compound IDs in CSV file along with +properties data, type:</p> +<div class="ExampleBox"> + % CalculatePhysicochemicalProperties.pl -m All --output both + -r SampleAllProperties -o Sample.sdf</div> +<p>To calculate RuleOf5 physicochemical properties and generate a SampleRuleOf5Properties.csv file +containing sequential compound IDs along with properties data, type:</p> +<div class="ExampleBox"> + % CalculatePhysicochemicalProperties.pl -m RuleOf5 + -r SampleRuleOf5Properties -o Sample.sdf</div> +<p>To calculate RuleOf5 physicochemical properties along with counting RuleOf5 violations and generate +a SampleRuleOf5Properties.csv file containing sequential compound IDs along with properties data, type:</p> +<div class="ExampleBox"> + % CalculatePhysicochemicalProperties.pl -m RuleOf5 --RuleOf5Violations Yes + -r SampleRuleOf5Properties -o Sample.sdf</div> +<p>To calculate RuleOf3 physicochemical properties and generate a SampleRuleOf3Properties.csv file +containing sequential compound IDs along with properties data, type:</p> +<div class="ExampleBox"> + % CalculatePhysicochemicalProperties.pl -m RuleOf3 + -r SampleRuleOf3Properties -o Sample.sdf</div> +<p>To calculate RuleOf3 physicochemical properties along with counting RuleOf3 violations and generate +a SampleRuleOf3Properties.csv file containing sequential compound IDs along with properties data, type:</p> +<div class="ExampleBox"> + % CalculatePhysicochemicalProperties.pl -m RuleOf3 --RuleOf3Violations Yes + -r SampleRuleOf3Properties -o Sample.sdf</div> +<p>To calculate a specific set of physicochemical properties and generate a SampleProperties.csv file +containing sequential compound IDs along with properties data, type:</p> +<div class="ExampleBox"> + % CalculatePhysicochemicalProperties.pl -m "Rings,AromaticRings" + -r SampleProperties -o Sample.sdf</div> +<p>To calculate HydrogenBondDonors and HydrogenBondAcceptors using HydrogenBondsType1 definition +and generate a SampleProperties.csv file containing sequential compound IDs along with properties +data, type:</p> +<div class="ExampleBox"> + % CalculatePhysicochemicalProperties.pl -m "HydrogenBondDonors,HydrogenBondAcceptors" + --HydrogenBonds HBondsType1 -r SampleProperties -o Sample.sdf</div> +<p>To calculate TPSA using sulfur and phosphorus atoms along with nitrogen and oxygen atoms and +generate a SampleProperties.csv file containing sequential compound IDs along with properties +data, type:</p> +<div class="ExampleBox"> + % CalculatePhysicochemicalProperties.pl -m "TPSA" --TPSA "IgnorePhosphorus,No, + IgnoreSulfur,No" -r SampleProperties -o Sample.sdf</div> +<p>To calculate MolecularComplexity using extendend connectivity fingerprints corresponding +to atom neighborhood radius of 2 with atomic invariant atom types without any scaling and +generate a SampleProperties.csv file containing sequential compound IDs along with properties +data, type:</p> +<div class="ExampleBox"> + % CalculatePhysicochemicalProperties.pl -m MolecularComplexity --MolecularComplexity + "MolecularComplexityType,ExtendedConnectivityFingerprints,NeighborhoodRadius,2, + AtomIdentifierType, AtomicInvariantsAtomTypes, + AtomicInvariantsToUse,AS X BO H FC MN,NormalizationMethodology,None" + -r SampleProperties -o Sample.sdf</div> +<p>To calculate RuleOf5 physicochemical properties along with counting RuleOf5 violations and generate +a SampleRuleOf5Properties.csv file containing compound IDs from molecule name line along with +properties data, type:</p> +<div class="ExampleBox"> + % CalculatePhysicochemicalProperties.pl -m RuleOf5 --RuleOf5Violations Yes + --DataFieldsMode CompoundID --CompoundIDMode MolName + -r SampleRuleOf5Properties -o Sample.sdf</div> +<p>To calculate all available physicochemical properties and generate a SampleAllProperties.csv +file containing compound ID using specified data field along with along with properties data, +type:</p> +<div class="ExampleBox"> + % CalculatePhysicochemicalProperties.pl -m All + --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID Mol_ID + -r SampleAllProperties -o Sample.sdf</div> +<p>To calculate all available physicochemical properties and generate a SampleAllProperties.csv +file containing compound ID using combination of molecule name line and an explicit compound +prefix along with properties data, type:</p> +<div class="ExampleBox"> + % CalculatePhysicochemicalProperties.pl -m All + --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleAllProperties + -o Sample.sdf</div> +<p>To calculate all available physicochemical properties and generate a SampleAllProperties.csv +file containing specific data fields columns along with with properties data, type:</p> +<div class="ExampleBox"> + % CalculatePhysicochemicalProperties.pl -m All + --DataFieldsMode Specify --DataFields Mol_ID -r SampleAllProperties + -o Sample.sdf</div> +<p>To calculate all available physicochemical properties and generate a SampleAllProperties.csv +file containing common data fields columns along with with properties data, type:</p> +<div class="ExampleBox"> + % CalculatePhysicochemicalProperties.pl -m All + --DataFieldsMode Common -r SampleAllProperties -o Sample.sdf</div> +<p>To calculate all available physicochemical properties and generate both SampleAllProperties.csv +and CSV files containing all data fields columns in CSV files along with with properties data, type:</p> +<div class="ExampleBox"> + % CalculatePhysicochemicalProperties.pl -m All + --DataFieldsMode All --output both -r SampleAllProperties + -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="./ExtractFromSDtFiles.html">ExtractFromSDtFiles.pl</a>, <a href="./ExtractFromTextFiles.html">ExtractFromTextFiles.pl</a>, <a href="./InfoSDFiles.html">InfoSDFiles.pl</a>, <a href="./InfoTextFiles.html">InfoTextFiles.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="./AtomTypesFingerprints.html" title="AtomTypesFingerprints.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./DBSchemaTablesToTextFiles.html" title="DBSchemaTablesToTextFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>CalculatePhysicochemicalProperties.pl</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>