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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/AtomNeighborhoodsFingerprints.txt Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,636 @@ +NAME + AtomNeighborhoodsFingerprints.pl - Generate atom neighborhoods + fingerprints for SD files + +SYNOPSIS + AtomNeighborhoodsFingerprints.pl SDFile(s)... + + AtomNeighborhoodsFingerprints.pl [--AromaticityModel + *AromaticityModelType*] [-a, --AtomIdentifierType + *AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | + MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | + UFFAtomTypes*] [--AtomicInvariantsToUse + *"AtomicInvariant,AtomicInvariant..."*] [--FunctionalClassesToUse + *"FunctionalClass1,FunctionalClass2..."*] [--CompoundID *DataFieldName + or LabelPrefixString*] [--CompoundIDLabel *text*] [--CompoundIDMode] + [--DataFields *"FieldLabel1,FieldLabel2,..."*] [-d, --DataFieldsMode + *All | Common | Specify | CompoundID*] [-f, --Filter *Yes | No*] + [--FingerprintsLabel *text*] [-h, --help] [-k, --KeepLargestComponent + *Yes | No*] [--MinNeighborhoodRadius *number*] [--MaxNeighborhoodRadius + *number*] [--OutDelim *comma | tab | semicolon*] [--output *SD | FP | + text | all*] [-o, --overwrite] [-q, --quote *Yes | No*] [-r, --root + *RootName*] [-w, --WorkingDir dirname] SDFile(s)... + +DESCRIPTION + Generate atom neighborhoods fingerprints [ Ref 53-56, Ref 73 ] for + *SDFile(s)* and create appropriate SD, FP or CSV/TSV text file(s) + containing fingerprints 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. + + The current release of MayaChemTools supports generation of atom + neighborhoods fingerprints corresponding to following -a, + --AtomIdentifierTypes: + + AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, + FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, + SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes + + Based on the values specified for -a, --AtomIdentifierType and + --AtomicInvariantsToUse, initial atom types are assigned to all + non-hydrogen atoms in a molecule. Using atom neighborhoods around each + non-hydrogen central atom corresponding to radii between specified + values --MinNeighborhoodRadius and --MaxNeighborhoodRadius, unique atom + types at each radii level are counted and an atom neighborhood + identifier is generated. + + The format of an atom neighborhood identifier around a central + non-hydrogen atom at a specific radius is: + + NR<n>-<AtomType>-ATC<n> + + NR: Neighborhood radius + AtomType: Assigned atom type + ATC: Atom type count + + The atom neighborhood identifier for a non-hydrogen central atom + corresponding to all specified radii is generated by concatenating + neighborhood identifiers at each radii by colon as a delimiter: + + NR<n>-<AtomType>-ATC<n>:NR<n>-<AtomType>-ATC<n>:... + + The atom neighborhood identifiers for all non-hydrogen central atoms at + all specified radii are concatenated using space as a delimiter and + constitute atom neighborhood fingerprint of the molecule. + + Example of *SD* file containing atom neighborhood fingerprints string + data: + + ... ... + ... ... + $$$$ + ... ... + ... ... + ... ... + 41 44 0 0 0 0 0 0 0 0999 V2000 + -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + ... ... + 2 3 1 0 0 0 0 + ... ... + M END + > <CmpdID> + Cmpd1 + + > <AtomNeighborhoodsFingerprints> + FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadiu + s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-ATC1 + :NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X1.B + O1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 + NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C... + + $$$$ + ... ... + ... ... + + Example of *FP* file containing atom neighborhood fingerprints string + data: + + # + # Package = MayaChemTools 7.4 + # Release Date = Oct 21, 2010 + # + # TimeStamp = Fri Mar 11 14:15:27 2011 + # + # FingerprintsStringType = FingerprintsVector + # + # Description = AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadiu... + # VectorStringFormat = ValuesString + # VectorValuesType = AlphaNumericalValues + # + Cmpd1 41;NR0-C.X1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-A... + Cmpd2 23;NR0-C.X1.BO1.H3-ATC1:NR1-C.X2.BO2.H2-ATC1:NR2-C.X3.BO3.H1-A... + ... ... + ... .. + + Example of CSV *Text* file containing atom neighborhood fingerprints + string data: + + "CompoundID","AtomNeighborhoodsFingerprints" + "Cmpd1","FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes + :MinRadius0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.B + O1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 + NR0-C.X1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3 + .BO4-ATC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1..." + ... ... + ... ... + + The current release of MayaChemTools generates the following types of + atom neighborhoods fingerprints vector strings: + + FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi + us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT + C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X + 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A + TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2 + -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B... + + FingerprintsVector;AtomNeighborhoods:DREIDINGAtomTypes:MinRadius0:MaxR + adius2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1: + NR1-O_2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N + _3-ATC1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-AT + C1:NR2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR + 1-N_R-ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-... + + FingerprintsVector;AtomNeighborhoods:EStateAtomTypes:MinRadius0:MaxRad + ius2;41;AlphaNumericalValues;ValuesString;NR0-aaCH-ATC1:NR1-aaCH-ATC1: + NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-aaCH-ATC1:NR + 1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0- + aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 NR0- + aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 N... + + FingerprintsVector;AtomNeighborhoods:FunctionalClassAtomTypes:MinRadiu + s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-Ar-ATC1:NR1-Ar- + ATC1:NR1-Ar.HBA-ATC1:NR1-None-ATC1:NR2-Ar-ATC2:NR2-None-ATC4 NR0-Ar-AT + C1:NR1-Ar-ATC2:NR1-Ar.HBA-ATC1:NR2-Ar-ATC5:NR2-None-ATC1 NR0-Ar-ATC1:N + R1-Ar-ATC2:NR1-HBD-ATC1:NR2-Ar-ATC2:NR2-None-ATC1 NR0-Ar-ATC1:NR1-Ar-A + TC2:NR1-Hal-ATC1:NR2-Ar-ATC2 NR0-Ar-ATC1:NR1-Ar-ATC2:NR1-None-ATC1:... + + FingerprintsVector;AtomNeighborhoods:MMFF94AtomTypes:MinRadius0:MaxRad + ius2;41;AlphaNumericalValues;ValuesString;NR0-C5A-ATC1:NR1-C5B-ATC1:NR + 1-CB-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C5B-ATC1:NR2-CB-ATC3:NR2-CR-ATC + 1 NR0-C5A-ATC1:NR1-C5B-ATC1:NR1-CR-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C + 5B-ATC1:NR2-C=ON-ATC1:NR2-CR-ATC3 NR0-C5B-ATC1:NR1-C5A-ATC1:NR1-C5B-AT + C1:NR1-C=ON-ATC1:NR2-C5A-ATC1:NR2-CB-ATC1:NR2-CR-ATC1:NR2-N5-ATC1:N... + + FingerprintsVector;AtomNeighborhoods:SLogPAtomTypes:MinRadius0:MaxRadi + us2;41;AlphaNumericalValues;ValuesString;NR0-C1-ATC1:NR1-C10-ATC1:NR1- + CS-ATC1:NR2-C1-ATC1:NR2-N11-ATC1:NR2-O2-ATC1 NR0-C1-ATC1:NR1-C11-ATC1: + NR2-C1-ATC1:NR2-C21-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:NR2-C1-ATC1:NR2-C21- + ATC1 NR0-C1-ATC1:NR1-C5-ATC1:NR1-CS-ATC1:NR2-C1-ATC1:NR2-O2-ATC2:NR2-O + 9-ATC1 NR0-C1-ATC1:NR1-CS-ATC2:NR2-C1-ATC2:NR2-O2-ATC2 NR0-C10-ATC1... + + FingerprintsVector;AtomNeighborhoods:SYBYLAtomTypes:MinRadius0:MaxRadi + us2;41;AlphaNumericalValues;ValuesString;NR0-C.2-ATC1:NR1-C.3-ATC1:NR1 + -O.co2-ATC2:NR2-C.3-ATC1 NR0-C.2-ATC1:NR1-C.ar-ATC1:NR1-N.am-ATC1:NR1- + O.2-ATC1:NR2-C.ar-ATC3 NR0-C.3-ATC1:NR1-C.2-ATC1:NR1-C.3-ATC1:NR2-C.3- + ATC1:NR2-O.3-ATC1:NR2-O.co2-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR1-N.ar-AT + C1:NR2-C.3-ATC1:NR2-C.ar-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR2-C.3-ATC... + + FingerprintsVector;AtomNeighborhoods:TPSAAtomTypes:MinRadius0:MaxRadiu + s2;41;AlphaNumericalValues;ValuesString;NR0-N21-ATC1:NR1-None-ATC3:NR2 + -None-ATC5 NR0-N7-ATC1:NR1-None-ATC2:NR2-None-ATC3:NR2-O3-ATC1 NR0-Non + e-ATC1:NR1-N21-ATC1:NR1-None-ATC1:NR2-None-ATC3 NR0-None-ATC1:NR1-N21- + ATC1:NR1-None-ATC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N21-ATC1:NR1-None-A + TC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N7-ATC1:NR1-None-ATC1:NR1-O3-AT... + + FingerprintsVector;AtomNeighborhoods:UFFAtomTypes:MinRadius0:MaxRadius + 2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:NR1-O + _2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N_3-AT + C1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-ATC1:NR + 2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR1-N_R + -ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-C_3-A... + +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. + + -a, --AtomIdentifierType *AtomicInvariantsAtomTypes | DREIDINGAtomTypes + | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | + SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes* + Specify atom identifier type to use for assignment of initial atom + identifier to non-hydrogen atoms during calculation of atom + neighborhoods fingerprints. Possible values in the current release + are: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, + FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, + SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*. Default value: + *AtomicInvariantsAtomTypes*. + + --AtomicInvariantsToUse *"AtomicInvariant,AtomicInvariant..."* + This value is used during *AtomicInvariantsAtomTypes* value of a, + --AtomIdentifierType option. It's a list of comma separated valid + atomic invariant atom types. + + Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB, + TB, H, Ar, RA, FC, MN, SM*. Default value: *AS,X,BO,H,FC*. + + The atomic invariants abbreviations correspond to: + + 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) + + Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class + corresponds to: + + AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n> + + Except for AS 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. + + In addition to usage of abbreviations for specifying atomic + invariants, the following descriptive words are also allowed: + + 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 + + *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign + atomic invariant atom types. + + --FunctionalClassesToUse *"FunctionalClass1,FunctionalClass2..."* + This value is used during *FunctionalClassAtomTypes* value of a, + --AtomIdentifierType option. It's a list of comma separated valid + functional classes. + + Possible values for atom functional classes are: *Ar, CA, H, HBA, + HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]: + *HBD,HBA,PI,NI,Ar,Hal*. + + The functional class abbreviations correspond to: + + 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 + + *AtomTypes::FunctionalClassAtomTypes* module is used to assign + functional class atom types. It uses following definitions [ Ref + 60-61, Ref 65-66 ]: + + HydrogenBondDonor: NH, NH2, OH + HydrogenBondAcceptor: N[!H], O + PositivelyIonizable: +, NH2 + NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH + + --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*. + + -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. + + --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: *AtomNeighborhoodsFingerprints*. + + -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. + + --MinNeighborhoodRadius *number* + Minimum atom neighborhood radius for generating atom neighborhoods. + Default value: *0*. Valid values: positive integers and less than + --MaxNeighborhoodRadius. Neighborhood radius of zero corresponds to + list of non-hydrogen atoms. + + --MaxNeighborhoodRadius *number* + Maximum atom neighborhood radius for generating atom neighborhoods. + Default value: *2*. Valid values: positive integers and greater than + --MineighborhoodRadius. + + --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><AtomNeighborhoodsFP>.<Ext>. The file + type determines <Ext> value. The sdf, fpf, csv, and tsv <Ext> values + are used for SD, comma/semicolon, and tab delimited text files, + respectively.This option is ignored for multiple input files. + + -w, --WorkingDir *DirName* + Location of working directory. Default: current directory. + +EXAMPLES + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 0 to 2 using atomic invariants atom types in + vector string format and create a SampleANFP.csv file containing + sequential compound IDs along with fingerprints vector strings data, + type: + + % AtomNeighborhoodsFingerprints.pl -r SampleANFP -o Sample.sdf + + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 0 to 2 using DREIDING atom types in vector + string format and create a SampleANFP.csv file containing sequential + compound IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a DREIDINGAtomTypes -r SampleANFP + -o Sample.sdf + + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 0 to 2 using EStateAtomTypes types in vector + string format and create a SampleANFP.csv file containing sequential + compound IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a EStateAtomTypes -r SampleANFP + -o Sample.sdf + + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 0 to 2 using SYBYL atom types in vector string + format and create a SampleANFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a SYBYLAtomTypes -r SampleANFP + -o Sample.sdf + + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 0 to 2 using FunctionalClass atom types in + vector string format and create a SampleANFP.csv file containing + sequential compound IDs along with fingerprints vector strings data, + type: + + % AtomNeighborhoodsFingerprints.pl -a FunctionalClassAtomTypes + -r SampleANFP -o Sample.sdf + + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 0 to 2 using MMFF94 atom types in vector string + format and create a SampleANFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a MMFF94AtomTypes -r SampleANFP + -o Sample.sdf + + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 0 to 2 using SLogP atom types in vector string + format and create a SampleANFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a SLogPAtomTypes -r SampleANFP + -o Sample.sdf + + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 0 to 2 using SYBYL atom types in vector string + format and create a SampleANFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a SYBYLAtomTypes -r SampleANFP + -o Sample.sdf + + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 0 to 2 using TPSA atom types in vector string + format and create a SampleANFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a TPSAAtomTypes -r SampleANFP + -o Sample.sdf + + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 0 to 2 using UFF atom types in vector string + format and create a SampleANFP.csv file containing sequential compound + IDs along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a UFFAtomTypes -r SampleANFP + -o Sample.sdf + + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 0 to 2 using atomic invariants atom types in + vector string format and create SampleANFP.sdf, SampleANFP.fpf and + SampleANFP.csv files containing sequential compound IDs in CSV file + along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl --output all -r SampleANFP + -o Sample.sdf + + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 1 to 3 using atomic invariants atom types in + vector string format and create a SampleANFP.csv file containing + sequential compound IDs along with fingerprints vector strings data, + type: + + % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes + --MinNeighborhoodRadius 1 --MaxNeighborhoodRadius 3 -r SampleANFP + -o Sample.sdf + + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 0 to 2 using only AS,X atomic invariants atom + types in vector string format and create a SampleANFP.csv file + containing sequential compound IDs along with fingerprints vector + strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes + --AtomicInvariantsToUse "AS,X" --MinNeighborhoodRadius 0 + --MaxNeighborhoodRadius 3 -r SampleANFP -o Sample.sdf + + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 0 to 2 using atomic invariants atom types in + vector string format and create a SampleANFP.csv file containing + compound ID from molecule name line along with fingerprints vector + strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID --CompoundIDMode MolName + -r SampleANFP -o Sample.sdf + + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 0 to 2 using atomic invariants atom types in + vector string format and create a SampleANFP.csv file containing + compound IDs using specified data field along with fingerprints vector + strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID + Mol_ID -r SampleANFP -o Sample.sdf + + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 0 to 2 using atomic invariants atom types in + vector string format and create a SampleANFP.csv file containing + compound ID using combination of molecule name line and an explicit + compound prefix along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix + --CompoundID Cmpd --CompoundIDLabel MolID -r SampleANFP -o Sample.sdf + + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 0 to 2 using atomic invariants atom types in + vector string format and create a SampleANFP.csv file containing + specific data fields columns along with fingerprints vector strings + data, type: + + % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode Specify --DataFields Mol_ID -r SampleANFP + -o Sample.sdf + + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 0 to 2 using atomic invariants atom types in + vector string format and create a SampleANFP.csv file containing common + data fields columns along with fingerprints vector strings data, type: + + % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode Common -r SampleANFP -o Sample.sdf + + To generate atom neighborhoods fingerprints corresponding to atom + neighborhood radii from 0 to 2 using atomic invariants atom types in + vector string format and create SampleANFP.sdf, SampleANFP.fpf and + SampleANFP.csv files containing all data fields columns in CSV file + along with fingerprints data, type: + + % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes + --DataFieldsMode All --output all -r SampleANFP + -o Sample.sdf + +AUTHOR + Manish Sud <msud@san.rr.com> + +SEE ALSO + InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, + SimilaritySearchingFingerprints.pl, ExtendedConnectivityFingerprints.pl, + MACCSKeysFingerprints.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. +