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diff mayachemtools/docs/scripts/man1/EStateIndiciesFingerprints.1 @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/scripts/man1/EStateIndiciesFingerprints.1 Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,567 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. 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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 <msud@san.rr.com> +.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.