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NAME
    EStateIndiciesFingerprints.pl - Generate E-state indicies fingerprints
    for SD files

SYNOPSIS
    EStateIndiciesFingerprints.pl SDFile(s)...

    EStateIndiciesFingerprints.pl [--AromaticityModel
    *AromaticityModelType*] [--CompoundID *DataFieldName or
    LabelPrefixString*] [--CompoundIDLabel *text*] [--CompoundIDMode
    *DataField | MolName | LabelPrefix | MolNameOrLabelPrefix*]
    [--DataFields *"FieldLabel1,FieldLabel2,..."*] [-d, --DataFieldsMode
    *All | Common | Specify | CompoundID*] [-e, --EStateAtomTypesSetToUse
    *ArbitrarySize or FixedSize*] [-f, --Filter *Yes | No*]
    [--FingerprintsLabelMode *FingerprintsLabelOnly |
    FingerprintsLabelWithIDs*] [--FingerprintsLabel *text*] [-h, --help]
    [-k, --KeepLargestComponent *Yes | No*] [--OutDelim *comma | tab |
    semicolon*] [--output *SD | FP | text | all*] [-o, --overwrite] [-q,
    --quote *Yes | No*] [-r, --root *RootName*] [-s, --size *number*]
    [--ValuesPrecision *number*] [-v, --VectorStringFormat
    *IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
    ValuesAndIDsPairsString*] [-w, --WorkingDir *DirName*]

DESCRIPTION
    Generate E-state indicies fingerprints [ Ref 75-78 ] for *SDFile(s)* and
    create appropriate SD, FP, or CSV/TSV text file(s) containing
    fingerprints bit-vector or vector strings corresponding to molecular
    fingerprints.

    Multiple SDFile names are separated by spaces. The valid file extensions
    are *.sdf* and *.sd*. All other file names are ignored. All the SD files
    in a current directory can be specified either by **.sdf* or the current
    directory name.

    E-state atom types are assigned to all non-hydrogen atoms in a molecule
    using module AtomTypes::EStateAtomTypes.pm and E-state values are
    calculated using module AtomicDescriptors::EStateValues.pm. Using
    E-state atom types and E-state values, EStateIndiciesFingerprints
    constituting sum of E-state values for E-sate atom types is generated.

    Two types of E-state atom types set size are allowed:

        ArbitrarySize - Corresponds to only E-state atom types detected
                        in molecule
        FixedSize - Corresponds to fixed number of E-state atom types previously
                    defined

    Module AtomTypes::EStateAtomTypes.pm, used to assign E-state atom types
    to non-hydrogen atoms in the molecule, is able to assign atom types to
    any valid atom group. However, for *FixedSize* value of
    EStateAtomTypesSetToUse, only a fixed set of E-state atom types
    corresponding to specific atom groups [ Appendix III in Ref 77 ] are
    used for fingerprints.

    The fixed size E-state atom type set size used during generation of
    fingerprints contains 87 E-state non-hydrogen atom types in
    EStateAtomTypes.csv data file distributed with MayaChemTools.

    Combination of Type and EStateAtomTypesSetToUse allow generation of 2
    different types of E-state indicies fingerprints:

        Type                        EStateAtomTypesSetToUse

        EStateIndicies              ArbitrarySize      [ default fingerprints ]
        EStateIndicies              FixedSize

    Example of *SD* file containing E-state indicies fingerprints string
    data:

        ... ...
        ... ...
        $$$$
        ... ...
        ... ...
        ... ...
        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
        ... ...
        2  3  1  0  0  0  0
        ... ...
        M  END
        >  <CmpdID>
        Cmpd1

        >  <EStateIndiciesFingerprints>
        FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDsA
        ndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssNH
        SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3.02
        4 -2.270

        $$$$
        ... ...
        ... ...

    Example of *FP* file containing E-state indicies fingerprints string
    data:

        #
        # Package = MayaChemTools 7.4
        # Release Date = Oct 21, 2010
        #
        # TimeStamp = Fri Mar 11 14:35:11 2011
        #
        # FingerprintsStringType = FingerprintsVector
        #
        # Description = EStateIndicies:ArbitrarySize
        # VectorStringFormat = IDsAndValuesString
        # VectorValuesType = NumericalValues
        #
        Cmpd1 11;SaaCH SaasC SaasN SdO SdssC...;24.778 4.387 1.993 25.023 -1...
        Cmpd2 9;SdNH SdO SdssC SsCH3 SsNH...;7.418 22.984 -1.583 5.387 5.400...
        ... ...
        ... ..

    Example of CSV *Text* file containing E-state indicies fingerprints
    string data:

        "CompoundID","EStateIndiciesFingerprints"
        "Cmpd1","FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalVa
        lues;IDsAndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssC
        H2 SssNH SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0
        .073 3.024 -2.270"
        "Cmpd2","FingerprintsVector;EStateIndicies:ArbitrarySize;9;NumericalVal
        ues;IDsAndValuesString;SdNH SdO SdssC SsCH3 SsNH2 SsOH SssCH2 SssNH Sss
        sCH;7.418 22.984 -1.583 5.387 5.400 19.852 1.737 5.624 -3.319"
        ... ...
        ... ...

    The current release of MayaChemTools generates the following types of
    E-state fingerprints vector strings:

        FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
        AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
        H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
        .024 -2.270

        FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
        ValuesString;0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435
        4.387 0 0 0 0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 1
        4.006 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
        0 0 0 0 0 0 0 0 0 0 0 0 0 0

        FingerprintsVector;EStateIndicies:FixedSize;87;OrderedNumericalValues;
        IDsAndValuesString;SsLi SssBe SssssBem SsBH2 SssBH SsssB SssssBm SsCH3
        SdCH2 SssCH2 StCH SdsCH SaaCH SsssCH SddC StsC SdssC SaasC SaaaC Sssss
        C SsNH3p SsNH2 SssNH2p SdNH SssNH SaaNH StN SsssNHp SdsN SaaN SsssN Sd
        0 0 0 0 0 0 0 3.975 0 -0.073 0 0 24.778 -2.270 0 0 -1.435 4.387 0 0 0
        0 0 0 3.024 0 0 0 0 0 0 0 1.993 0 29.759 25.023 0 0 0 0 14.006 0 0 0 0
        0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...

OPTIONS
    --AromaticityModel *MDLAromaticityModel | TriposAromaticityModel |
    MMFFAromaticityModel | ChemAxonBasicAromaticityModel |
    ChemAxonGeneralAromaticityModel | DaylightAromaticityModel |
    MayaChemToolsAromaticityModel*
        Specify aromaticity model to use during detection of aromaticity.
        Possible values in the current release are: *MDLAromaticityModel,
        TriposAromaticityModel, MMFFAromaticityModel,
        ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel,
        DaylightAromaticityModel or MayaChemToolsAromaticityModel*. Default
        value: *MayaChemToolsAromaticityModel*.

        The supported aromaticity model names along with model specific
        control parameters are defined in AromaticityModelsData.csv, which
        is distributed with the current release and is available under
        lib/data directory. Molecule.pm module retrieves data from this file
        during class instantiation and makes it available to method
        DetectAromaticity for detecting aromaticity corresponding to a
        specific model.

    --CompoundID *DataFieldName or LabelPrefixString*
        This value is --CompoundIDMode specific and indicates how compound
        ID is generated.

        For *DataField* value of --CompoundIDMode 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, *Cmpd*, generates compound
        IDs which look like Cmpd<Number>.

        Examples for *DataField* value of --CompoundIDMode:

            MolID
            ExtReg

        Examples for *LabelPrefix* or *MolNameOrLabelPrefix* value of
        --CompoundIDMode:

            Compound

        The value specified above generates compound IDs which correspond to
        Compound<Number> instead of default value of Cmpd<Number>.

    --CompoundIDLabel *text*
        Specify compound ID column label for FP or CSV/TSV text file(s) used
        during *CompoundID* value of --DataFieldsMode option. Default:
        *CompoundID*.

    --CompoundIDMode *DataField | MolName | LabelPrefix |
    MolNameOrLabelPrefix*
        Specify how to generate compound IDs and write to FP or CSV/TSV text
        file(s) along with generated fingerprints for *FP | text | all*
        values of --output option: use a *SDFile(s)* datafield value; use
        molname line from *SDFile(s)*; generate a sequential ID with
        specific prefix; use combination of both MolName and LabelPrefix
        with usage of LabelPrefix values for empty molname lines.

        Possible values: *DataField | MolName | LabelPrefix |
        MolNameOrLabelPrefix*. Default: *LabelPrefix*.

        For *MolNameAndLabelPrefix* value of --CompoundIDMode, molname line
        in *SDFile(s)* takes precedence over sequential compound IDs
        generated using *LabelPrefix* and only empty molname values are
        replaced with sequential compound IDs.

        This is only used for *CompoundID* value of --DataFieldsMode option.

    --DataFields *"FieldLabel1,FieldLabel2,..."*
        Comma delimited list of *SDFiles(s)* data fields to extract and
        write to CSV/TSV text file(s) along with generated fingerprints for
        *text | all* values of --output option.

        This is only used for *Specify* value of --DataFieldsMode option.

        Examples:

            Extreg
            MolID,CompoundName

    -d, --DataFieldsMode *All | Common | Specify | CompoundID*
        Specify how data fields in *SDFile(s)* are transferred to output
        CSV/TSV text file(s) along with generated fingerprints for *text |
        all* values of --output 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: *All | Common |
        specify | CompoundID*. Default value: *CompoundID*.

    -e, --EStateAtomTypesSetToUse *ArbitrarySize | FixedSize*
        E-state atom types set size to use during generation of E-state
        indicies fingerprints. Possible values: *ArbitrarySize | FixedSize*;
        Default value: *ArbitrarySize*.

        *ArbitrarySize* corrresponds to only E-state atom types detected in
        molecule; *FixedSize* corresponds to fixed number of previously
        defined E-state atom types.

        For *EStateIndicies*, a fingerprint vector string is generated. The
        vector string corresponding to *EStateIndicies* contains sum of
        E-state values for E-state atom types.

        Module AtomTypes::EStateAtomTypes.pm is used to assign E-state atom
        types to non-hydrogen atoms in the molecule which is able to assign
        atom types to any valid atom group. However, for *FixedSize* value
        of EStateAtomTypesSetToUse, only a fixed set of E-state atom types
        corresponding to specific atom groups [ Appendix III in Ref 77 ] are
        used for fingerprints.

        The fixed size E-state atom type set size used during generation of
        fingerprints contains 87 E-state non-hydrogen atom types in
        EStateAtomTypes.csv data file distributed with MayaChemTools.

    -f, --Filter *Yes | No*
        Specify whether to check and filter compound data in SDFile(s).
        Possible values: *Yes or No*. Default value: *Yes*.

        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.

    --FingerprintsLabelMode *FingerprintsLabelOnly |
    FingerprintsLabelWithIDs*
        Specify how fingerprints label is generated in conjunction with
        --FingerprintsLabel option value: use fingerprints label generated
        only by --FingerprintsLabel option value or append E-state atom type
        value IDs to --FingerprintsLabel option value.

        Possible values: *FingerprintsLabelOnly | FingerprintsLabelWithIDs*.
        Default value: *FingerprintsLabelOnly*.

        This option is only used for *FixedSize* value of -e,
        --EStateAtomTypesSetToUse option during generation of
        *EStateIndicies* E-state fingerprints.

        E-state atom type IDs appended to --FingerprintsLabel value during
        *FingerprintsLabelWithIDs* values of --FingerprintsLabelMode
        correspond to fixed number of previously defined E-state atom types.

    --FingerprintsLabel *text*
        SD data label or text file column label to use for fingerprints
        string in output SD or CSV/TSV text file(s) specified by --output.
        Default value: *EStateIndiciesFingerprints*.

    -h, --help
        Print this help message.

    -k, --KeepLargestComponent *Yes | No*
        Generate fingerprints for only the largest component in molecule.
        Possible values: *Yes or No*. Default value: *Yes*.

        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.

    --OutDelim *comma | tab | semicolon*
        Delimiter for output CSV/TSV text file(s). Possible values: *comma,
        tab, or semicolon* Default value: *comma*.

    --output *SD | FP | text | all*
        Type of output files to generate. Possible values: *SD, FP, text, or
        all*. Default value: *text*.

    -o, --overwrite
        Overwrite existing files.

    -q, --quote *Yes | No*
        Put quote around column values in output CSV/TSV text file(s).
        Possible values: *Yes or No*. Default value: *Yes*.

    -r, --root *RootName*
        New file name is generated using the root: <Root>.<Ext>. Default for
        new file names: <SDFileName><EStateIndiciesFP>.<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.

    --ValuesPrecision *number*
        Precision of values for E-state indicies option. Default value: up
        to *3* decimal places. Valid values: positive integers.

    -v, --VectorStringFormat *ValuesString | IDsAndValuesString |
    IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString*
        Format of fingerprints vector string data in output SD, FP or
        CSV/TSV text file(s) specified by --output used for
        *EStateIndicies*. Possible values: *ValuesString,
        IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString,
        ValuesAndIDsPairsString*.

        Default value during *ArbitrarySize* value of -e,
        --EStateAtomTypesSetToUse option: *IDsAndValuesString*. Default
        value during *FixedSize* value of -e, --EStateAtomTypesSetToUse
        option: *ValuesString*.

        Examples:

            FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDs
            AndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssN
            H SsssCH;24.778 4.387 1.993 25.023 -1.435 3.975 14.006 29.759 -0.073 3
            .024 -2.270

    -w, --WorkingDir *DirName*
        Location of working directory. Default: current directory.

EXAMPLES
    To generate E-state fingerprints of arbitrary size in vector string
    format and create a SampleESFP.csv file containing sequential compound
    IDs along with fingerprints vector strings data, type:

        % EStateIndiciesFingerprints.pl -r SampleESFP -o Sample.sdf

    To generate E-state fingerprints of fixed size in vector string format
    and create a SampleESFP.csv file containing sequential compound IDs
    along with fingerprints vector strings data, type:

        % EStateIndiciesFingerprints.pl -e FixedSize -r SampleESFP
          -o Sample.sdf

    To generate E-state fingerprints of fixed size in vector string with
    IDsAndValues format and create a SampleESFP.csv file containing
    sequential compound IDs along with fingerprints vector strings data,
    type:

        % EStateIndiciesFingerprints.pl -e FixedSize -v IDsAndValuesString
          -r SampleESFP -o Sample.sdf

    To generate E-state fingerprints of fixed size in vector string format
    and create a SampleESFP.csv file containing compound ID from molecule
    name line along with fingerprints vector strings data, type

        % EStateIndiciesFingerprints.pl -e FixedSize
          --DataFieldsMode CompoundID --CompoundIDMode MolName
          -r SampleESFP -o Sample.sdf

    To generate E-state fingerprints of fixed size in vector string format
    and create a SampleESFP.csv file containing compound IDs using specified
    data field along with fingerprints vector strings data, type:

        % EStateIndiciesFingerprints.pl -e FixedSize
          --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID
          Mol_ID -r SampleESFP -o Sample.sdf

    To generate E-state fingerprints of fixed size in vector string format
    and create a SampleESFP.csv file containing compound ID using
    combination of molecule name line and an explicit compound prefix along
    with fingerprints vector strings data, type:

        % EStateIndiciesFingerprints.pl -e FixedSize
          --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix
          --CompoundID Cmpd --CompoundIDLabel MolID -r SampleESFP -o Sample.sdf

    To generate E-state fingerprints of fixed size in vector string format
    and create a SampleESFP.csv file containing specific data fields columns
    along with fingerprints vector strings data, type:

        % EStateIndiciesFingerprints.pl -e FixedSize
          --DataFieldsMode Specify --DataFields Mol_ID -r SampleESFP
          -o Sample.sdf

    To generate E-state fingerprints of fixed size in vector string format
    and create a SampleESFP.csv file containing common data fields columns
    along with fingerprints vector strings data, type:

        % EStateIndiciesFingerprints.pl -e FixedSize
         --DataFieldsMode Common -r SampleESFP -o Sample.sdf

    To generate E-state fingerprints of fixed size in vector string format
    and create SampleESFP.sdf, SampleESFP.fpf, and SampleESFP.csv files
    containing all data fields columns in CSV file along with fingerprints
    vector strings data, type:

        % EStateIndiciesFingerprints.pl -e FixedSize
         --DataFieldsMode All --output all -r SampleESFP -o Sample.sdf

AUTHOR
    Manish Sud <[e-mail]>

SEE ALSO
    InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl,
    AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl,
    MACCSKeysFingeprints.pl, PathLengthFingerprints.pl,
    TopologicalAtomPairsFingerprints.pl,
    TopologicalAtomTorsionsFingerprints.pl,
    TopologicalPharmacophoreAtomPairsFingerprints.pl,
    TopologicalPharmacophoreAtomTripletsFingerprints.pl

COPYRIGHT
    Copyright (C) 2015 Manish Sud. All rights reserved.

    This file is part of MayaChemTools.

    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.