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diff docs/scripts/txt/EStateIndiciesFingerprints.txt @ 0:4816e4a8ae95 draft default tip
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/txt/EStateIndiciesFingerprints.txt Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,447 @@ +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 <msud@san.rr.com> + +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. +