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.\" ========================================================================
.\"
.IX Title "ESTATEINDICIESFINGERPRINTS 1"
.TH ESTATEINDICIESFINGERPRINTS 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"
EStateIndiciesFingerprints.pl \- Generate E\-state indicies fingerprints for SD files
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
EStateIndiciesFingerprints.pl SDFile(s)...
.PP
EStateIndiciesFingerprints.pl [\fB\-\-AromaticityModel\fR \fIAromaticityModelType\fR]
[\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR]
[\fB\-\-CompoundIDLabel\fR \fItext\fR] [\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR]
[\fB\-\-DataFields\fR \fI\*(L"FieldLabel1,FieldLabel2,...\*(R"\fR] [\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR]
[\fB\-e, \-\-EStateAtomTypesSetToUse\fR \fIArbitrarySize or FixedSize\fR] [\fB\-f, \-\-Filter\fR \fIYes | No\fR]
[\fB\-\-FingerprintsLabelMode\fR \fIFingerprintsLabelOnly | FingerprintsLabelWithIDs\fR] [\fB\-\-FingerprintsLabel\fR \fItext\fR]
[\fB\-h, \-\-help\fR] [\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR]
[\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR] [\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR] [\fB\-o, \-\-overwrite\fR]
[\fB\-q, \-\-quote\fR \fIYes | No\fR] [\fB\-r, \-\-root\fR \fIRootName\fR] [\fB\-s, \-\-size\fR \fInumber\fR] [\fB\-\-ValuesPrecision\fR \fInumber\fR]
[\fB\-v, \-\-VectorStringFormat\fR \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR]
[\fB\-w, \-\-WorkingDir\fR \fIDirName\fR]
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Generate E\-state indicies fingerprints [ Ref 75\-78 ] for \fISDFile(s)\fR and create appropriate \s-1SD\s0,
\&\s-1FP\s0, or \s-1CSV/TSV\s0 text file(s) containing fingerprints bit-vector or vector strings corresponding to
molecular fingerprints.
.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
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,
\&\fBEStateIndiciesFingerprints\fR constituting sum of E\-state values for E\-sate atom types
is generated.
.PP
Two types of E\-state atom types set size are allowed:
.PP
.Vb 4
\&    ArbitrarySize \- Corresponds to only E\-state atom types detected
\&                    in molecule
\&    FixedSize \- Corresponds to fixed number of E\-state atom types previously
\&                defined
.Ve
.PP
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 \fIFixedSize\fR value of \fBEStateAtomTypesSetToUse\fR, only a
fixed set of E\-state atom types corresponding to specific atom groups [ Appendix \s-1III\s0 in
Ref 77 ] are used for fingerprints.
.PP
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.
.PP
Combination of Type and EStateAtomTypesSetToUse allow generation of 2 different types of
E\-state indicies fingerprints:
.PP
.Vb 1
\&    Type                        EStateAtomTypesSetToUse
\&
\&    EStateIndicies              ArbitrarySize      [ default fingerprints ]
\&    EStateIndicies              FixedSize
.Ve
.PP
Example of \fI\s-1SD\s0\fR file containing E\-state indicies fingerprints string data:
.PP
.Vb 10
\&    ... ...
\&    ... ...
\&    $$$$
\&    ... ...
\&    ... ...
\&    ... ...
\&    41 44  0  0  0  0  0  0  0  0999 V2000
\&     \-3.3652    1.4499    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
\&    ... ...
\&    2  3  1  0  0  0  0
\&    ... ...
\&    M  END
\&    >  <CmpdID>
\&    Cmpd1
\&
\&    >  <EStateIndiciesFingerprints>
\&    FingerprintsVector;EStateIndicies:ArbitrarySize;11;NumericalValues;IDsA
\&    ndValuesString;SaaCH SaasC SaasN SdO SdssC SsCH3 SsF SsOH SssCH2 SssNH
\&    SsssCH;24.778 4.387 1.993 25.023 \-1.435 3.975 14.006 29.759 \-0.073 3.02
\&    4 \-2.270
\&
\&    $$$$
\&    ... ...
\&    ... ...
.Ve
.PP
Example of \fI\s-1FP\s0\fR file containing E\-state indicies fingerprints string data:
.PP
.Vb 10
\&    #
\&    # 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...
\&    ... ...
\&    ... ..
.Ve
.PP
Example of \s-1CSV\s0 \fIText\fR file containing E\-state indicies fingerprints string data:
.PP
.Vb 10
\&    "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"
\&    ... ...
\&    ... ...
.Ve
.PP
The current release of MayaChemTools generates the following types of E\-state
fingerprints vector strings:
.PP
.Vb 4
\&    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...
.Ve
.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-1FP\s0 or \s-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value
of \fB\-\-DataFieldsMode\fR option. Default: \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-1FP\s0 or \s-1CSV/TSV\s0 text file(s) along with generated
fingerprints for \fI\s-1FP\s0 | text | all\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: \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 generated fingerprints for \fItext | all\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 generated fingerprints for \fItext | all\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\-e, \-\-EStateAtomTypesSetToUse\fR \fIArbitrarySize | FixedSize\fR" 4
.IX Item "-e, --EStateAtomTypesSetToUse ArbitrarySize | FixedSize"
E\-state atom types set size to use during generation of E\-state indicies fingerprints.
Possible values: \fIArbitrarySize | FixedSize\fR; Default value: \fIArbitrarySize\fR.
.Sp
\&\fIArbitrarySize\fR corrresponds to only E\-state atom types detected in molecule; \fIFixedSize\fR
corresponds to fixed number of previously defined E\-state atom types.
.Sp
For \fIEStateIndicies\fR, a fingerprint vector string is generated. The vector string corresponding to
\&\fIEStateIndicies\fR contains sum of E\-state values for E\-state atom types.
.Sp
Module \fBAtomTypes::EStateAtomTypes.pm\fR 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 \fIFixedSize\fR value of \fBEStateAtomTypesSetToUse\fR,
only a fixed set of E\-state atom types corresponding to specific atom groups [ Appendix
\&\s-1III\s0 in Ref 77 ] are used for fingerprints.
.Sp
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.
.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 fingerprints and compounds containing
atom data corresponding to non-element symbols or no atom data are ignored.
.IP "\fB\-\-FingerprintsLabelMode\fR \fIFingerprintsLabelOnly | FingerprintsLabelWithIDs\fR" 4
.IX Item "--FingerprintsLabelMode FingerprintsLabelOnly | FingerprintsLabelWithIDs"
Specify how fingerprints label is generated in conjunction with \fB\-\-FingerprintsLabel\fR option value:
use fingerprints label generated only by \fB\-\-FingerprintsLabel\fR option value or append E\-state
atom type value IDs to \fB\-\-FingerprintsLabel\fR option value.
.Sp
Possible values: \fIFingerprintsLabelOnly | FingerprintsLabelWithIDs\fR. Default value:
\&\fIFingerprintsLabelOnly\fR.
.Sp
This option is only used for \fIFixedSize\fR value of \fB\-e, \-\-EStateAtomTypesSetToUse\fR option during
generation of \fIEStateIndicies\fR E\-state fingerprints.
.Sp
E\-state atom type IDs appended to \fB\-\-FingerprintsLabel\fR value during \fIFingerprintsLabelWithIDs\fR
values of \fB\-\-FingerprintsLabelMode\fR correspond to fixed number of previously defined E\-state
atom types.
.IP "\fB\-\-FingerprintsLabel\fR \fItext\fR" 4
.IX Item "--FingerprintsLabel text"
\&\s-1SD\s0 data label or text file column label to use for fingerprints string in output \s-1SD\s0 or
\&\s-1CSV/TSV\s0 text file(s) specified by \fB\-\-output\fR. Default value: \fIEStateIndiciesFingerprints\fR.
.IP "\fB\-h, \-\-help\fR" 4
.IX Item "-h, --help"
Print this help message.
.IP "\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR" 4
.IX Item "-k, --KeepLargestComponent Yes | No"
Generate fingerprints for only the largest component in molecule. Possible values:
\&\fIYes or No\fR. Default value: \fIYes\fR.
.Sp
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.
.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 | \s-1FP\s0 | text | all\fR" 4
.IX Item "--output SD | FP | text | all"
Type of output files to generate. Possible values: \fI\s-1SD\s0, \s-1FP\s0, text, or all\fR. Default value: \fItext\fR.
.IP "\fB\-o, \-\-overwrite\fR" 4
.IX Item "-o, --overwrite"
Overwrite existing files.
.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><EStateIndiciesFP>.<Ext>. The file type determines <Ext> value.
The sdf, fpf, csv, and tsv <Ext> values are used for \s-1SD\s0, \s-1FP\s0, comma/semicolon, and tab
delimited text files, respectively.This option is ignored for multiple input files.
.IP "\fB\-\-ValuesPrecision\fR \fInumber\fR" 4
.IX Item "--ValuesPrecision number"
Precision of values for E\-state indicies option. Default value: up to \fI3\fR decimal places.
Valid values: positive integers.
.IP "\fB\-v, \-\-VectorStringFormat\fR \fIValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR" 4
.IX Item "-v, --VectorStringFormat ValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString"
Format of fingerprints vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by
\&\fB\-\-output\fR used for \fIEStateIndicies\fR. Possible values: \fIValuesString, IDsAndValuesString,
IDsAndValuesPairsString, ValuesAndIDsString, ValuesAndIDsPairsString\fR.
.Sp
Default value during \fIArbitrarySize\fR value of \fB\-e, \-\-EStateAtomTypesSetToUse\fR
option: \fIIDsAndValuesString\fR. Default value during \fIFixedSize\fR value of
\&\fB\-e, \-\-EStateAtomTypesSetToUse\fR option: \fIValuesString\fR.
.Sp
Examples:
.Sp
.Vb 4
\&    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
.Ve
.IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4
.IX Item "-w, --WorkingDir DirName"
Location of working directory. Default: current directory.
.SH "EXAMPLES"
.IX Header "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:
.PP
.Vb 1
\&    % EStateIndiciesFingerprints.pl \-r SampleESFP \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 2
\&    % EStateIndiciesFingerprints.pl \-e FixedSize \-r SampleESFP
\&      \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 2
\&    % EStateIndiciesFingerprints.pl \-e FixedSize \-v IDsAndValuesString
\&      \-r SampleESFP \-o Sample.sdf
.Ve
.PP
To generate E\-state fingerprints of fixed size in vector string format
and create a SampleESFP.csv file containing compound \s-1ID\s0 from molecule
name line along with fingerprints vector strings data, type
.PP
.Vb 3
\&    % EStateIndiciesFingerprints.pl \-e FixedSize
\&      \-\-DataFieldsMode CompoundID \-\-CompoundIDMode MolName
\&      \-r SampleESFP \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 3
\&    % EStateIndiciesFingerprints.pl \-e FixedSize
\&      \-\-DataFieldsMode CompoundID \-\-CompoundIDMode DataField \-\-CompoundID
\&      Mol_ID \-r SampleESFP \-o Sample.sdf
.Ve
.PP
To generate E\-state fingerprints of fixed size in vector string format
and create a SampleESFP.csv file containing compound \s-1ID\s0 using combination
of molecule name line and an explicit compound prefix along with fingerprints vector
strings data, type:
.PP
.Vb 3
\&    % EStateIndiciesFingerprints.pl \-e FixedSize
\&      \-\-DataFieldsMode CompoundID \-\-CompoundIDMode MolnameOrLabelPrefix
\&      \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleESFP \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 3
\&    % EStateIndiciesFingerprints.pl \-e FixedSize
\&      \-\-DataFieldsMode Specify \-\-DataFields Mol_ID \-r SampleESFP
\&      \-o Sample.sdf
.Ve
.PP
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:
.PP
.Vb 2
\&    % EStateIndiciesFingerprints.pl \-e FixedSize
\&     \-\-DataFieldsMode Common \-r SampleESFP \-o Sample.sdf
.Ve
.PP
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 \s-1CSV\s0 file along with fingerprints vector strings data, type:
.PP
.Vb 2
\&    % EStateIndiciesFingerprints.pl \-e FixedSize
\&     \-\-DataFieldsMode All \-\-output all \-r SampleESFP \-o Sample.sdf
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Manish Sud <[e-mail]>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
ExtendedConnectivityFingerprints.pl, MACCSKeysFingeprints.pl, PathLengthFingerprints.pl,
TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.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.