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.\" ========================================================================
.\"
.IX Title "CALCULATEPHYSICOCHEMICALPROPERTIES 1"
.TH CALCULATEPHYSICOCHEMICALPROPERTIES 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
CalculatePhysicochemicalProperties.pl \- Calculate physicochemical properties for SD files
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
CalculatePhysicochemicalProperties.pl SDFile(s)...
.PP
PhysicochemicalProperties.pl  [\fB\-\-AromaticityModel\fR \fIAromaticityModelType\fR]
[\fB\-\-CompoundID\fR DataFieldName or LabelPrefixString]
[\fB\-\-CompoundIDLabel\fR text] [\fB\-\-CompoundIDMode\fR] [\fB\-\-DataFields\fR \*(L"FieldLabel1, FieldLabel2,...\*(R"]
[\fB\-d, \-\-DataFieldsMode\fR All | Common | Specify | CompoundID] [\fB\-f, \-\-Filter\fR Yes | No] [\fB\-h, \-\-help\fR]
[\fB\-\-HydrogenBonds\fR HBondsType1 | HBondsType2] [\fB\-k, \-\-KeepLargestComponent\fR Yes | No]
[\fB\-m, \-\-mode\fR All | RuleOf5 | RuleOf3 | \*(L"name1, [name2,...]\*(R"]
[\fB\-\-MolecularComplexity\fR \fIName,Value, [Name,Value,...]\fR]
[\fB\-\-OutDelim\fR comma | tab | semicolon] [\fB\-\-output\fR \s-1SD\s0 | text | both] [\fB\-o, \-\-overwrite\fR]
[\fB\-\-Precision\fR Name,Number,[Name,Number,..]] [\fB\-\-RotatableBonds\fR Name,Value, [Name,Value,...]]
[\fB\-\-RuleOf3Violations\fR Yes | No] [\fB\-\-RuleOf5Violations\fR Yes | No]
[\fB\-q, \-\-quote\fR Yes | No] [\fB\-r, \-\-root\fR RootName]
[\fB\-w, \-\-WorkingDir\fR dirname] SDFile(s)...
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Calculate physicochemical properties for \fISDFile(s)\fR and create appropriate \s-1SD\s0 or \s-1CSV/TSV\s0
text file(s) containing calculated properties.
.PP
The current release of MayaChemTools supports the calculation of these physicochemical
properties:
.PP
.Vb 7
\&    MolecularWeight, ExactMass, HeavyAtoms, Rings, AromaticRings,
\&    van der Waals MolecularVolume [ Ref 93 ], RotatableBonds,
\&    HydrogenBondDonors, HydrogenBondAcceptors, LogP and
\&    Molar Refractivity (SLogP and SMR) [ Ref 89 ], Topological Polar
\&    Surface Area (TPSA) [ Ref 90 ], Fraction of SP3 carbons (Fsp3Carbons)
\&    and SP3 carbons (Sp3Carbons) [ Ref 115\-116, Ref 119 ],
\&    MolecularComplexity [ Ref 117\-119 ]
.Ve
.PP
Multiple SDFile names are separated by spaces. The valid file extensions are \fI.sdf\fR
and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a current directory
can be specified either by \fI*.sdf\fR or the current directory name.
.PP
The calculation of molecular complexity using \fIMolecularComplexityType\fR parameter
corresponds to the number of bits-set or unique keys [ Ref 117\-119 ] in molecular  fingerprints.
Default value for \fIMolecularComplexityType\fR: \fIMACCSKeys\fR of size 166. The calculation
of MACCSKeys is relatively expensive and can take rather substantial amount of time.
.SH "OPTIONS"
.IX Header "OPTIONS"
.IP "\fB\-\-AromaticityModel\fR \fIMDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel\fR" 4
.IX Item "--AromaticityModel MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel"
Specify aromaticity model to use during detection of aromaticity. Possible values in the current
release are: \fIMDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
or MayaChemToolsAromaticityModel\fR. Default value: \fIMayaChemToolsAromaticityModel\fR.
.Sp
The supported aromaticity model names along with model specific control parameters
are defined in \fBAromaticityModelsData.csv\fR, which is distributed with the current release
and is available under \fBlib/data\fR directory. \fBMolecule.pm\fR module retrieves data from
this file during class instantiation and makes it available to method \fBDetectAromaticity\fR
for detecting aromaticity corresponding to a specific model.
.IP "\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR" 4
.IX Item "--CompoundID DataFieldName or LabelPrefixString"
This value is \fB\-\-CompoundIDMode\fR specific and indicates how compound \s-1ID\s0 is generated.
.Sp
For \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option, it corresponds to datafield label name
whose value is used as compound \s-1ID\s0; otherwise, it's a prefix string used for generating compound
IDs like LabelPrefixString<Number>. Default value, \fICmpd\fR, generates compound IDs which
look like Cmpd<Number>.
.Sp
Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR:
.Sp
.Vb 2
\&    MolID
\&    ExtReg
.Ve
.Sp
Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR:
.Sp
.Vb 1
\&    Compound
.Ve
.Sp
The value specified above generates compound IDs which correspond to Compound<Number>
instead of default value of Cmpd<Number>.
.IP "\fB\-\-CompoundIDLabel\fR \fItext\fR" 4
.IX Item "--CompoundIDLabel text"
Specify compound \s-1ID\s0 column label for \s-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value
of \fB\-\-DataFieldsMode\fR option. Default value: \fICompoundID\fR.
.IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4
.IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix"
Specify how to generate compound IDs and write to \s-1CSV/TSV\s0 text file(s) along with calculated
physicochemical properties for \fItext | both\fR values of \fB\-\-output\fR option: use a \fISDFile(s)\fR
datafield value; use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0 with specific prefix;
use combination of both MolName and LabelPrefix with usage of LabelPrefix values for empty
molname lines.
.Sp
Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR.
Default value: \fILabelPrefix\fR.
.Sp
For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes
precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname
values are replaced with sequential compound IDs.
.Sp
This is only used for \fICompoundID\fR value of \fB\-\-DataFieldsMode\fR option.
.ie n .IP "\fB\-\-DataFields\fR \fI""FieldLabel1,FieldLabel2,...""\fR" 4
.el .IP "\fB\-\-DataFields\fR \fI``FieldLabel1,FieldLabel2,...''\fR" 4
.IX Item "--DataFields FieldLabel1,FieldLabel2,..."
Comma delimited list of \fISDFiles(s)\fR data fields to extract and write to \s-1CSV/TSV\s0 text file(s) along
with calculated physicochemical properties for \fItext | both\fR values of \fB\-\-output\fR option.
.Sp
This is only used for \fISpecify\fR value of \fB\-\-DataFieldsMode\fR option.
.Sp
Examples:
.Sp
.Vb 2
\&    Extreg
\&    MolID,CompoundName
.Ve
.IP "\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR" 4
.IX Item "-d, --DataFieldsMode All | Common | Specify | CompoundID"
Specify how data fields in \fISDFile(s)\fR are transferred to output \s-1CSV/TSV\s0 text file(s) along
with calculated physicochemical properties for \fItext | both\fR values of \fB\-\-output\fR option:
transfer all \s-1SD\s0 data field; transfer \s-1SD\s0 data files common to all compounds; extract specified
data fields; generate a compound \s-1ID\s0 using molname line, a compound prefix, or a combination
of both. Possible values: \fIAll | Common | specify | CompoundID\fR. Default value: \fICompoundID\fR.
.IP "\fB\-f, \-\-Filter\fR \fIYes | No\fR" 4
.IX Item "-f, --Filter Yes | No"
Specify whether to check and filter compound data in SDFile(s). Possible values: \fIYes or No\fR.
Default value: \fIYes\fR.
.Sp
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.
.IP "\fB\-h, \-\-help\fR" 4
.IX Item "-h, --help"
Print this help message.
.IP "\fB\-\-HydrogenBonds\fR \fIHBondsType1 | HBondsType2\fR" 4
.IX Item "--HydrogenBonds HBondsType1 | HBondsType2"
Parameters to control calculation of hydrogen bond donors and acceptors. Possible values:
\&\fIHBondsType1, HydrogenBondsType1, HBondsType2, HydrogenBondsType2\fR. Default value:
\&\fIHBondsType2\fR which corresponds to \fBRuleOf5\fR definition for number of hydrogen bond
donors and acceptors.
.Sp
The current release of MayaChemTools supports identification of two types of hydrogen bond
donor and acceptor atoms with these names:
.Sp
.Vb 2
\&    HBondsType1 or HydrogenBondsType1
\&    HBondsType2 or HydrogenBondsType2
.Ve
.Sp
The names of these hydrogen bond types are rather arbitrary. However, their definitions have
specific meaning and are as follows:
.Sp
.Vb 1
\&    HydrogenBondsType1 [ Ref 60\-61, Ref 65\-66 ]:
\&
\&        Donor: NH, NH2, OH \- Any N and O with available H
\&        Acceptor: N[!H], O \- Any N without available H and any O
\&
\&    HydrogenBondsType2 [ Ref 91 ]:
\&
\&        Donor: NH, NH2, OH \- N and O with available H
\&        Acceptor: N, O \- And N and O
.Ve
.IP "\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR" 4
.IX Item "-k, --KeepLargestComponent Yes | No"
Calculate physicochemical properties for only the largest component in molecule. Possible values:
\&\fIYes or No\fR. Default value: \fIYes\fR.
.Sp
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.
.ie n .IP "\fB\-m, \-\-mode\fR \fIAll | RuleOf5 | RuleOf3 | ""name1, [name2,...]""\fR" 4
.el .IP "\fB\-m, \-\-mode\fR \fIAll | RuleOf5 | RuleOf3 | ``name1, [name2,...]''\fR" 4
.IX Item "-m, --mode All | RuleOf5 | RuleOf3 | name1, [name2,...]"
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: \fIAll | RuleOf5 | RuleOf3 |
\&\*(L"name1, [name2,...]\*(R"\fR.
.Sp
Default value: \fIMolecularWeight, HeavyAtoms, MolecularVolume, RotatableBonds, HydrogenBondDonors,
HydrogenBondAcceptors, SLogP, \s-1TPSA\s0\fR. These properties are calculated by default.
.Sp
\&\fIRuleOf5\fR [ Ref 91 ] includes these properties: \fIMolecularWeight, HydrogenBondDonors, HydrogenBondAcceptors,
SLogP\fR. \fIRuleOf5\fR states: MolecularWeight <= 500, HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, and
logP <= 5.
.Sp
\&\fIRuleOf3\fR [ Ref 92 ] includes these properties: \fIMolecularWeight, RotatableBonds, HydrogenBondDonors,
HydrogenBondAcceptors, SLogP, \s-1TPSA\s0\fR. \fIRuleOf3\fR states: MolecularWeight <= 300, RotatableBonds <= 3,
HydrogenBondDonors <= 3, HydrogenBondAcceptors <= 3, logP <= 3, and \s-1TPSA\s0 <= 60.
.Sp
\&\fIAll\fR calculates all supported physicochemical properties: \fIMolecularWeight, ExactMass,
HeavyAtoms, Rings, AromaticRings, MolecularVolume, RotatableBonds, HydrogenBondDonors,
HydrogenBondAcceptors, SLogP, \s-1SMR\s0, \s-1TPSA\s0, Fsp3Carbons, Sp3Carbons, MolecularComplexity\fR.
.IP "\fB\-\-MolecularComplexity\fR \fIName,Value, [Name,Value,...]\fR" 4
.IX Item "--MolecularComplexity Name,Value, [Name,Value,...]"
Parameters to control calculation of molecular complexity: it's a comma delimited list of parameter
name and value pairs.
.Sp
Possible parameter names: \fIMolecularComplexityType, AtomIdentifierType,
AtomicInvariantsToUse, FunctionalClassesToUse, MACCSKeysSize, NeighborhoodRadius,
MinPathLength, MaxPathLength, UseBondSymbols, MinDistance, MaxDistance,
UseTriangleInequality, DistanceBinSize, NormalizationMethodology\fR.
.Sp
The valid paramater valuse for each parameter name are described in the following sections.
.Sp
The current release of MayaChemTools supports calculation of molecular complexity using
\&\fIMolecularComplexityType\fR parameter corresponding to the number of bits-set or unique
keys [ Ref 117\-119 ] in molecular  fingerprints. The valid values for \fIMolecularComplexityType\fR
are:
.Sp
.Vb 9
\&    AtomTypesFingerprints
\&    ExtendedConnectivityFingerprints
\&    MACCSKeys
\&    PathLengthFingerprints
\&    TopologicalAtomPairsFingerprints
\&    TopologicalAtomTripletsFingerprints
\&    TopologicalAtomTorsionsFingerprints
\&    TopologicalPharmacophoreAtomPairsFingerprints
\&    TopologicalPharmacophoreAtomTripletsFingerprints
.Ve
.Sp
Default value for \fIMolecularComplexityType\fR: \fIMACCSKeys\fR.
.Sp
\&\fIAtomIdentifierType\fR parameter name correspods to atom types used during generation of
fingerprints. The valid values for \fIAtomIdentifierType\fR are: \fIAtomicInvariantsAtomTypes,
DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\fR. \fIAtomicInvariantsAtomTypes\fR
is not supported for during the following values of \fIMolecularComplexityType\fR: \fIMACCSKeys,
TopologicalPharmacophoreAtomPairsFingerprints, TopologicalPharmacophoreAtomTripletsFingerprints\fR.
\&\fIFunctionalClassAtomTypes\fR is the only valid value for \fIAtomIdentifierType\fR for topological
pharmacophore fingerprints.
.Sp
Default value for \fIAtomIdentifierType\fR: \fIAtomicInvariantsAtomTypes\fR
for all except topological pharmacophore fingerprints where it is \fIFunctionalClassAtomTypes\fR.
.Sp
\&\fIAtomicInvariantsToUse\fR parameter name and values are used during \fIAtomicInvariantsAtomTypes\fR
value of parameter \fIAtomIdentifierType\fR. It's a list of space separated valid atomic invariant atom types.
.Sp
Possible values for atomic invariants are: \fI\s-1AS\s0, X, \s-1BO\s0,  \s-1LBO\s0, \s-1SB\s0, \s-1DB\s0, \s-1TB\s0, H, Ar, \s-1RA\s0, \s-1FC\s0, \s-1MN\s0, \s-1SM\s0\fR.
Default value for \fIAtomicInvariantsToUse\fR parameter are set differently for different fingerprints
using \fIMolecularComplexityType\fR parameter as shown below:
.Sp
.Vb 1
\&    MolecularComplexityType              AtomicInvariantsToUse
\&
\&    AtomTypesFingerprints                AS X BO H FC
\&    TopologicalAtomPairsFingerprints     AS X BO H FC
\&    TopologicalAtomTripletsFingerprints  AS X BO H FC
\&    TopologicalAtomTorsionsFingerprints  AS X BO H FC
\&
\&    ExtendedConnectivityFingerprints     AS X  BO H FC MN
\&    PathLengthFingerprints               AS
.Ve
.Sp
The atomic invariants abbreviations correspond to:
.Sp
.Vb 1
\&    AS = Atom symbol corresponding to element symbol
\&
\&    X<n>   = Number of non\-hydrogen atom neighbors or heavy atoms
\&    BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
\&    LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
\&    SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
\&    DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
\&    TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
\&    H<n>   = Number of implicit and explicit hydrogens for atom
\&    Ar     = Aromatic annotation indicating whether atom is aromatic
\&    RA     = Ring atom annotation indicating whether atom is a ring
\&    FC<+n/\-n> = Formal charge assigned to atom
\&    MN<n> = Mass number indicating isotope other than most abundant isotope
\&    SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
\&            3 (triplet)
.Ve
.Sp
Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
.Sp
.Vb 1
\&    AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/\-n>.MN<n>.SM<n>
.Ve
.Sp
Except for \s-1AS\s0 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.
.Sp
In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
are also allowed:
.Sp
.Vb 12
\&    X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
\&    BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
\&    LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
\&    SB :  NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
\&    DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
\&    TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
\&    H :  NumOfImplicitAndExplicitHydrogens
\&    Ar : Aromatic
\&    RA : RingAtom
\&    FC : FormalCharge
\&    MN : MassNumber
\&    SM : SpinMultiplicity
.Ve
.Sp
\&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
atom types.
.Sp
\&\fIFunctionalClassesToUse\fR parameter name and values are used during \fIFunctionalClassAtomTypes\fR
value of parameter \fIAtomIdentifierType\fR. It's a list of space separated valid atomic invariant atom types.
.Sp
Possible values for atom functional classes are: \fIAr, \s-1CA\s0, H, \s-1HBA\s0, \s-1HBD\s0, Hal, \s-1NI\s0, \s-1PI\s0, \s-1RA\s0\fR.
.Sp
Default value for \fIFunctionalClassesToUse\fR parameter is set to:
.Sp
.Vb 1
\&    HBD HBA PI NI Ar Hal
.Ve
.Sp
for all fingerprints except for the following two \fIMolecularComplexityType\fR fingerints:
.Sp
.Vb 1
\&    MolecularComplexityType                           FunctionalClassesToUse
\&
\&    TopologicalPharmacophoreAtomPairsFingerprints     HBD HBA P, NI H
\&    TopologicalPharmacophoreAtomTripletsFingerprints  HBD HBA PI NI H Ar
.Ve
.Sp
The functional class abbreviations correspond to:
.Sp
.Vb 9
\&    HBD: HydrogenBondDonor
\&    HBA: HydrogenBondAcceptor
\&    PI :  PositivelyIonizable
\&    NI : NegativelyIonizable
\&    Ar : Aromatic
\&    Hal : Halogen
\&    H : Hydrophobic
\&    RA : RingAtom
\&    CA : ChainAtom
\&
\& Functional class atom type specification for an atom corresponds to:
\&
\&    Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
.Ve
.Sp
\&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
.Sp
.Vb 4
\&    HydrogenBondDonor: NH, NH2, OH
\&    HydrogenBondAcceptor: N[!H], O
\&    PositivelyIonizable: +, NH2
\&    NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
.Ve
.Sp
\&\fIMACCSKeysSize\fR parameter name is only used during \fIMACCSKeys\fR value of
\&\fIMolecularComplexityType\fR and corresponds to the size of \s-1MACCS\s0 key set. Possible
values: \fI166 or 322\fR. Default value: \fI166\fR.
.Sp
\&\fINeighborhoodRadius\fR parameter name is only used during \fIExtendedConnectivityFingerprints\fR
value of \fIMolecularComplexityType\fR and corresponds to atomic neighborhoods radius for
generating extended connectivity fingerprints. Possible values: positive integer. Default value:
\&\fI2\fR.
.Sp
\&\fIMinPathLength\fR and \fIMaxPathLength\fR parameters are only used during \fIPathLengthFingerprints\fR
value of \fIMolecularComplexityType\fR and correspond to minimum and maximum path lengths to use
for generating path length fingerprints. Possible values: positive integers. Default value: \fIMinPathLength \- 1\fR;
\&\fIMaxPathLength \- 8\fR.
.Sp
\&\fIUseBondSymbols\fR parameter is only used during \fIPathLengthFingerprints\fR value of
\&\fIMolecularComplexityType\fR and indicates whether bond symbols are included in atom path
strings used to generate path length fingerprints. Possible value: \fIYes or No\fR. Default value:
\&\fIYes\fR.
.Sp
\&\fIMinDistance\fR and \fIMaxDistance\fR parameters are only used during \fITopologicalAtomPairsFingerprints\fR
and \fITopologicalAtomTripletsFingerprints\fR values of \fIMolecularComplexityType\fR and correspond to
minimum and maximum bond distance between atom pairs during topological pharmacophore fingerprints.
Possible values: positive integers. Default value: \fIMinDistance \- 1\fR; \fIMaxDistance \- 10\fR.
.Sp
\&\fIUseTriangleInequality\fR parameter is used during these values for \fIMolecularComplexityType\fR:
\&\fITopologicalAtomTripletsFingerprints\fR and \fITopologicalPharmacophoreAtomTripletsFingerprints\fR.
Possible values: \fIYes or No\fR. It determines wheter to apply triangle inequality to distance triplets.
Default value: \fITopologicalAtomTripletsFingerprints \- No\fR;
\&\fITopologicalPharmacophoreAtomTripletsFingerprints \- Yes\fR.
.Sp
\&\fIDistanceBinSize\fR parameter is used during \fITopologicalPharmacophoreAtomTripletsFingerprints\fR
value of \fIMolecularComplexityType\fR and correspons to distance bin size used for binning
distances during generation of topological pharmacophore atom triplets fingerprints. Possible
value: positive integer. Default value: \fI2\fR.
.Sp
\&\fINormalizationMethodology\fR is only used for these values for \fIMolecularComplexityType\fR:
\&\fIExtendedConnectivityFingerprints\fR, \fITopologicalPharmacophoreAtomPairsFingerprints\fR
and \fITopologicalPharmacophoreAtomTripletsFingerprints\fR. It corresponds to normalization
methodology to use for scaling the number of bits-set or unique keys during generation of
fingerprints. Possible values during \fIExtendedConnectivityFingerprints\fR: \fINone or
ByHeavyAtomsCount\fR; Default value: \fINone\fR. Possible values during topological
pharmacophore atom pairs and tripletes fingerprints: \fINone or ByPossibleKeysCount\fR;
Default value: \fINone\fR. \fIByPossibleKeysCount\fR corresponds to total number of
possible topological pharmacophore atom pairs or triplets in a molecule.
.Sp
Examples of \fIMolecularComplexity\fR name and value parameters:
.Sp
.Vb 2
\&    MolecularComplexityType,AtomTypesFingerprints,AtomIdentifierType,
\&    AtomicInvariantsAtomTypes,AtomicInvariantsToUse,AS X BO H FC
\&
\&    MolecularComplexityType,ExtendedConnectivityFingerprints,
\&    AtomIdentifierType,AtomicInvariantsAtomTypes,
\&    AtomicInvariantsToUse,AS X BO H FC MN,NeighborhoodRadius,2,
\&    NormalizationMethodology,None
\&
\&    MolecularComplexityType,MACCSKeys,MACCSKeysSize,166
\&
\&    MolecularComplexityType,PathLengthFingerprints,AtomIdentifierType,
\&    AtomicInvariantsAtomTypes,AtomicInvariantsToUse,AS,MinPathLength,
\&    1,MaxPathLength,8,UseBondSymbols,Yes
\&
\&    MolecularComplexityType,TopologicalAtomPairsFingerprints,
\&    AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse,
\&    AS X BO H FC,MinDistance,1,MaxDistance,10
\&
\&    MolecularComplexityType,TopologicalAtomTripletsFingerprints,
\&    AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse,
\&    AS X BO H FC,MinDistance,1,MaxDistance,10,UseTriangleInequality,No
\&
\&    MolecularComplexityType,TopologicalAtomTorsionsFingerprints,
\&    AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse,
\&    AS X BO H FC
\&
\&    MolecularComplexityType,TopologicalPharmacophoreAtomPairsFingerprints,
\&    AtomIdentifierType,FunctionalClassAtomTypes,FunctionalClassesToUse,
\&    HBD HBA PI NI H,MinDistance,1,MaxDistance,10,NormalizationMethodology,
\&    None
\&
\&    MolecularComplexityType,TopologicalPharmacophoreAtomTripletsFingerprints,
\&    AtomIdentifierType,FunctionalClassAtomTypes,FunctionalClassesToUse,
\&    HBD HBA PI NI H Ar,MinDistance,1,MaxDistance,10,NormalizationMethodology,
\&    None,UseTriangleInequality,Yes,NormalizationMethodology,None,
\&    DistanceBinSize,2
.Ve
.IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4
.IX Item "--OutDelim comma | tab | semicolon"
Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR
Default value: \fIcomma\fR.
.IP "\fB\-\-output\fR \fI\s-1SD\s0 | text | both\fR" 4
.IX Item "--output SD | text | both"
Type of output files to generate. Possible values: \fI\s-1SD\s0, text, or both\fR. Default value: \fItext\fR.
.IP "\fB\-o, \-\-overwrite\fR" 4
.IX Item "-o, --overwrite"
Overwrite existing files.
.IP "\fB\-\-Precision\fR \fIName,Number,[Name,Number,..]\fR" 4
.IX Item "--Precision Name,Number,[Name,Number,..]"
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: \fIMolecularWeight,
ExactMass\fR. Possible values: positive intergers. Default value: \fIMolecularWeight,2,
ExactMass,4\fR.
.Sp
Examples:
.Sp
.Vb 2
\&    ExactMass,3
\&    MolecularWeight,1,ExactMass,2
.Ve
.IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4
.IX Item "-q, --quote Yes | No"
Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values:
\&\fIYes or No\fR. Default value: \fIYes\fR.
.IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4
.IX Item "-r, --root RootName"
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 \s-1SD\s0, comma/semicolon, and tab
delimited text files, respectively.This option is ignored for multiple input files.
.IP "\fB\-\-RotatableBonds\fR \fIName,Value, [Name,Value,...]\fR" 4
.IX Item "--RotatableBonds Name,Value, [Name,Value,...]"
Parameters to control calculation of rotatable bonds [ Ref 92 ]: it's a comma delimited list of parameter
name and value pairs. Possible parameter names: \fIIgnoreTerminalBonds, IgnoreBondsToTripleBonds,
IgnoreAmideBonds, IgnoreThioamideBonds, IgnoreSulfonamideBonds\fR. Possible parameter values:
\&\fIYes or No\fR. By default, value of all parameters is set to \fIYes\fR.
.IP "\fB\-\-RuleOf3Violations\fR \fIYes | No\fR" 4
.IX Item "--RuleOf3Violations Yes | No"
Specify whether to calculate \fBRuleOf3Violations\fR for SDFile(s). Possible values: \fIYes or No\fR.
Default value: \fINo\fR.
.Sp
For \fIYes\fR value of \fBRuleOf3Violations\fR, in addition to calculating total number of \fBRuleOf3\fR violations,
individual violations for compounds are also written to output files.
.Sp
\&\fBRuleOf3\fR [ Ref 92 ] states: MolecularWeight <= 300, RotatableBonds <= 3, HydrogenBondDonors <= 3,
HydrogenBondAcceptors <= 3, logP <= 3, and \s-1TPSA\s0 <= 60.
.IP "\fB\-\-RuleOf5Violations\fR \fIYes | No\fR" 4
.IX Item "--RuleOf5Violations Yes | No"
Specify whether to calculate \fBRuleOf5Violations\fR for SDFile(s). Possible values: \fIYes or No\fR.
Default value: \fINo\fR.
.Sp
For \fIYes\fR value of \fBRuleOf5Violations\fR, in addition to calculating total number of \fBRuleOf5\fR violations,
individual violations for compounds are also written to output files.
.Sp
\&\fBRuleOf5\fR [ Ref 91 ] states: MolecularWeight <= 500, HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10,
and logP <= 5.
.IP "\fB\-\-TPSA\fR \fIName,Value, [Name,Value,...]\fR" 4
.IX Item "--TPSA Name,Value, [Name,Value,...]"
Parameters to control calculation of \s-1TPSA:\s0 it's a comma delimited list of parameter name and value
pairs. Possible parameter names: \fIIgnorePhosphorus, IgnoreSulfur\fR. Possible parameter values:
\&\fIYes or No\fR. By default, value of all parameters is set to \fIYes\fR.
.Sp
By default, \s-1TPSA\s0 atom contributions from Phosphorus and Sulfur atoms are not included during
\&\s-1TPSA\s0 calculations. [ Ref 91 ]
.IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4
.IX Item "-w, --WorkingDir DirName"
Location of working directory. Default value: current directory.
.SH "EXAMPLES"
.IX Header "EXAMPLES"
To calculate default set of physicochemical properties \- MolecularWeight, HeavyAtoms,
MolecularVolume, RotatableBonds, HydrogenBondDonor, HydrogenBondAcceptors, SLogP,
\&\s-1TPSA\s0 \- and generate a SamplePhysicochemicalProperties.csv file containing sequential
compound IDs along with properties data, type:
.PP
.Vb 1
\&    % CalculatePhysicochemicalProperties.pl \-o Sample.sdf
.Ve
.PP
To calculate all available physicochemical properties and generate both SampleAllProperties.csv
and SampleAllProperties.sdf files containing sequential compound IDs in \s-1CSV\s0 file along with
properties data, type:
.PP
.Vb 2
\&    % CalculatePhysicochemicalProperties.pl \-m All \-\-output both
\&      \-r SampleAllProperties \-o Sample.sdf
.Ve
.PP
To calculate RuleOf5 physicochemical properties and generate a SampleRuleOf5Properties.csv file
containing sequential compound IDs along with properties data, type:
.PP
.Vb 2
\&    % CalculatePhysicochemicalProperties.pl \-m RuleOf5
\&      \-r SampleRuleOf5Properties \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 2
\&    % CalculatePhysicochemicalProperties.pl \-m RuleOf5 \-\-RuleOf5Violations Yes
\&      \-r SampleRuleOf5Properties \-o Sample.sdf
.Ve
.PP
To calculate RuleOf3 physicochemical properties and generate a SampleRuleOf3Properties.csv file
containing sequential compound IDs along with properties data, type:
.PP
.Vb 2
\&    % CalculatePhysicochemicalProperties.pl \-m RuleOf3
\&      \-r SampleRuleOf3Properties \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 2
\&    % CalculatePhysicochemicalProperties.pl \-m RuleOf3 \-\-RuleOf3Violations Yes
\&      \-r SampleRuleOf3Properties \-o Sample.sdf
.Ve
.PP
To calculate a specific set of physicochemical properties and generate a SampleProperties.csv file
containing sequential compound IDs along with properties data, type:
.PP
.Vb 2
\&    % CalculatePhysicochemicalProperties.pl \-m "Rings,AromaticRings"
\&      \-r SampleProperties \-o Sample.sdf
.Ve
.PP
To calculate HydrogenBondDonors and HydrogenBondAcceptors using HydrogenBondsType1 definition
and generate a SampleProperties.csv file containing sequential compound IDs along with properties
data, type:
.PP
.Vb 2
\&    % CalculatePhysicochemicalProperties.pl \-m "HydrogenBondDonors,HydrogenBondAcceptors"
\&      \-\-HydrogenBonds HBondsType1 \-r SampleProperties \-o Sample.sdf
.Ve
.PP
To calculate \s-1TPSA\s0 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:
.PP
.Vb 2
\&    % CalculatePhysicochemicalProperties.pl \-m "TPSA" \-\-TPSA "IgnorePhosphorus,No,
\&      IgnoreSulfur,No" \-r SampleProperties \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 5
\&    % 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
.Ve
.PP
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:
.PP
.Vb 3
\&    % CalculatePhysicochemicalProperties.pl \-m RuleOf5 \-\-RuleOf5Violations Yes
\&      \-\-DataFieldsMode CompoundID \-\-CompoundIDMode MolName
\&      \-r SampleRuleOf5Properties \-o Sample.sdf
.Ve
.PP
To calculate all available physicochemical properties and generate a SampleAllProperties.csv
file containing compound \s-1ID\s0 using specified data field along with along with properties data,
type:
.PP
.Vb 3
\&    % CalculatePhysicochemicalProperties.pl \-m All
\&      \-\-DataFieldsMode CompoundID \-\-CompoundIDMode DataField \-\-CompoundID Mol_ID
\&      \-r SampleAllProperties \-o Sample.sdf
.Ve
.PP
To calculate all available physicochemical properties and generate a SampleAllProperties.csv
file containing compound \s-1ID\s0 using combination of molecule name line and an explicit compound
prefix along with properties data, type:
.PP
.Vb 4
\&    % CalculatePhysicochemicalProperties.pl \-m All
\&      \-\-DataFieldsMode CompoundID \-\-CompoundIDMode MolnameOrLabelPrefix
\&      \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID  \-r SampleAllProperties
\&      \-o Sample.sdf
.Ve
.PP
To calculate all available physicochemical properties and generate a SampleAllProperties.csv
file containing specific data fields columns along with with properties data, type:
.PP
.Vb 3
\&    % CalculatePhysicochemicalProperties.pl \-m All
\&      \-\-DataFieldsMode Specify \-\-DataFields Mol_ID \-r SampleAllProperties
\&      \-o Sample.sdf
.Ve
.PP
To calculate all available physicochemical properties and generate a SampleAllProperties.csv
file containing common data fields columns along with with properties data, type:
.PP
.Vb 2
\&    % CalculatePhysicochemicalProperties.pl \-m All
\&      \-\-DataFieldsMode Common \-r SampleAllProperties \-o Sample.sdf
.Ve
.PP
To calculate all available physicochemical properties and generate both SampleAllProperties.csv
and \s-1CSV\s0 files containing all data fields columns in \s-1CSV\s0 files along with with properties data, type:
.PP
.Vb 3
\&    % CalculatePhysicochemicalProperties.pl \-m All
\&      \-\-DataFieldsMode All  \-\-output both \-r SampleAllProperties
\&      \-o Sample.sdf
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Manish Sud <[e-mail]>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
ExtractFromSDtFiles.pl, ExtractFromTextFiles.pl, InfoSDFiles.pl, InfoTextFiles.pl
.SH "COPYRIGHT"
.IX Header "COPYRIGHT"
Copyright (C) 2015 Manish Sud. All rights reserved.
.PP
This file is part of MayaChemTools.
.PP
MayaChemTools is free software; you can redistribute it and/or modify it under
the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
Software Foundation; either version 3 of the License, or (at your option)
any later version.