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.\" 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" MACCSKeysFingerprints.pl \- Generate MACCS key fingerprints for SD files .SH "SYNOPSIS" .IX Header "SYNOPSIS" MACCSKeysFingerprints.pl SDFile(s)... .PP MACCSKeysFingerprints.pl [\fB\-\-AromaticityModel\fR \fIAromaticityModelType\fR] [\fB\-\-BitsOrder\fR \fIAscending | Descending\fR] [\fB\-b, \-\-BitStringFormat\fR \fIBinaryString | HexadecimalString\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\-f, \-\-Filter\fR \fIYes | No\fR] [\fB\-\-FingerprintsLabel\fR \fItext\fR] [\fB\-h, \-\-help\fR] [\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR] [\fB\-m, \-\-mode\fR \fIMACCSKeyBits | MACCSKeyCount\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\-v, \-\-VectorStringFormat\fR \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR] [\fB\-w, \-\-WorkingDir\fR \fIDirName\fR] .SH "DESCRIPTION" .IX Header "DESCRIPTION" Generate \s-1MACCS\s0 (Molecular ACCess System) keys fingerprints [ Ref 45\-47 ] 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 For each \s-1MACCS\s0 keys definition, atoms are processed to determine their membership to the key and the appropriate molecular fingerprints strings are generated. An atom can belong to multiple \&\s-1MACCS\s0 keys. .PP For \fIMACCSKeyBits\fR value of \fB\-m, \-\-mode\fR option, a fingerprint bit-vector string containing zeros and ones is generated and for \fIMACCSKeyCount\fR value, a fingerprint vector string corresponding to number of \s-1MACCS\s0 keys [ Ref 45\-47 ] is generated. .PP \&\fIMACCSKeyBits | MACCSKeyCount\fR values for \fB\-m, \-\-mode\fR option along with two possible \&\fI166 | 322\fR values of \fB\-s, \-\-size\fR supports generation of four different types of \s-1MACCS\s0 keys fingerprint: \fIMACCS166KeyBits, MACCS166KeyCount, MACCS322KeyBits, MACCS322KeyCount\fR. .PP Example of \fI\s-1SD\s0\fR file containing \s-1MAACS\s0 keys fingerprints string data: .PP .Vb 10 \& ... ... \& ... ... \& $$$$ \& ... ... \& ... ... \& ... ... \& 41 44 0 0 0 0 0 0 0 0999 V2000 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 \& ... ... \& 2 3 1 0 0 0 0 \& ... ... \& M END \& > <CmpdID> \& Cmpd1 \& \& > <MACCSKeysFingerprints> \& FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;000000000 \& 00000000000000000000000000000000100100001001000000001001000000001110001 \& 00101010111100011011000100110110000011011110100110111111111111011111111 \& 11111111110111000 \& \& $$$$ \& ... ... \& ... ... .Ve .PP Example of \fI\s-1FP\s0\fR file containing \s-1MAACS\s0 keys fingerprints string data: .PP .Vb 10 \& # \& # Package = MayaChemTools 7.4 \& # Release Date = Oct 21, 2010 \& # \& # TimeStamp = Fri Mar 11 14:57:24 2011 \& # \& # FingerprintsStringType = FingerprintsBitVector \& # \& # Description = MACCSKeyBits \& # Size = 166 \& # BitStringFormat = BinaryString \& # BitsOrder = Ascending \& # \& Cmpd1 00000000000000000000000000000000000000000100100001001000000001... \& Cmpd2 00000000000000000000000010000000001000000010000000001000000000... \& ... ... \& ... .. .Ve .PP Example of \s-1CSV\s0 \fIText\fR file containing \s-1MAACS\s0 keys fingerprints string data: .PP .Vb 7 \& "CompoundID","MACCSKeysFingerprints" \& "Cmpd1","FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending; \& 00000000000000000000000000000000000000000100100001001000000001001000000 \& 00111000100101010111100011011000100110110000011011110100110111111111111 \& 01111111111111111110111000" \& ... ... \& ... ... .Ve .PP The current release of MayaChemTools generates the following types of \s-1MACCS\s0 keys fingerprints bit-vector and vector strings: .PP .Vb 4 \& FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000 \& 0000000000000000000000000000000001001000010010000000010010000000011100 \& 0100101010111100011011000100110110000011011110100110111111111111011111 \& 11111111111110111000 \& \& FingerprintsBitVector;MACCSKeyBits;166;HexadecimalString;Ascending;000 \& 000000021210210e845f8d8c60b79dffbffffd1 \& \& FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011 \& 1110011111100101111111000111101100110000000000000011100010000000000000 \& 0000000000000000000000000000000000000000000000101000000000000000000000 \& 0000000000000000000000000000000000000000000000000000000000000000000000 \& 0000000000000000000000000000000000000011000000000000000000000000000000 \& 0000000000000000000000000000000000000000 \& \& FingerprintsBitVector;MACCSKeyBits;322;HexadecimalString;Ascending;7d7 \& e7af3edc000c1100000000000000500000000000000000000000000000000300000000 \& 000000000 \& \& FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri \& ng;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 1 0 0 3 0 0 0 0 4 0 0 2 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0 \& 0 0 0 0 1 1 8 0 0 0 1 0 0 1 0 1 0 1 0 3 1 3 1 0 0 0 1 2 0 11 1 0 0 0 \& 5 0 0 1 2 0 1 1 0 0 0 0 0 1 1 0 1 1 1 1 0 4 0 0 1 1 0 4 6 1 1 1 2 1 1 \& 3 5 2 2 0 5 3 5 1 1 2 5 1 2 1 2 4 8 3 5 5 2 2 0 3 5 4 1 \& \& FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri \& ng;14 8 2 0 2 0 4 4 2 1 4 0 0 2 5 10 5 2 1 0 0 2 0 5 13 3 28 5 5 3 0 0 \& 0 4 2 1 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 3 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 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 ... .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\-\-BitsOrder\fR \fIAscending | Descending\fR" 4 .IX Item "--BitsOrder Ascending | Descending" Bits order to use during generation of fingerprints bit-vector string for \fIMACCSKeyBits\fR value of \&\fB\-m, \-\-mode\fR option. Possible values: \fIAscending, Descending\fR. Default: \fIAscending\fR. .Sp \&\fIAscending\fR bit order which corresponds to first bit in each byte as the lowest bit as opposed to the highest bit. .Sp Internally, bits are stored in \fIAscending\fR order using Perl vec function. Regardless of machine order, big-endian or little-endian, vec function always considers first string byte as the lowest byte and first bit within each byte as the lowest bit. .IP "\fB\-b, \-\-BitStringFormat\fR \fIBinaryString | HexadecimalString\fR" 4 .IX Item "-b, --BitStringFormat BinaryString | HexadecimalString" Format of fingerprints bit-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 during \fIMACCSKeyBits\fR value of \fB\-m, \-\-mode\fR option. Possible values: \fIBinaryString, HexadecimalString\fR. Default value: \fIBinaryString\fR. .Sp \&\fIBinaryString\fR corresponds to an \s-1ASCII\s0 string containing 1s and 0s. \fIHexadecimalString\fR contains bit values in \s-1ASCII\s0 hexadecimal format. .Sp Examples: .Sp .Vb 4 \& FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;00000000 \& 0000000000000000000000000000000001001000010010000000010010000000011100 \& 0100101010111100011011000100110110000011011110100110111111111111011111 \& 11111111111110111000 \& \& FingerprintsBitVector;MACCSKeyBits;166;HexadecimalString;Ascending;000 \& 000000021210210e845f8d8c60b79dffbffffd1 \& \& FingerprintsBitVector;MACCSKeyBits;322;BinaryString;Ascending;11101011 \& 1110011111100101111111000111101100110000000000000011100010000000000000 \& 0000000000000000000000000000000000000000000000101000000000000000000000 \& 0000000000000000000000000000000000000000000000000000000000000000000000 \& 0000000000000000000000000000000000000011000000000000000000000000000000 \& 0000000000000000000000000000000000000000 \& \& FingerprintsBitVector;MACCSKeyBits;322;HexadecimalString;Ascending;7d7 \& e7af3edc000c1100000000000000500000000000000000000000000000000300000000 \& 000000000 .Ve .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\-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\-\-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: \fIMACCSKeyFingerprints\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\-m, \-\-mode\fR \fIMACCSKeyBits | MACCSKeyCount\fR" 4 .IX Item "-m, --mode MACCSKeyBits | MACCSKeyCount" Specify type of \s-1MACCS\s0 keys [ Ref 45\-47 ] fingerprints to generate for molecules in \fISDFile(s)\fR. Possible values: \fIMACCSKeyBits, MACCSKeyCount\fR. Default value: \fIMACCSKeyBits\fR. .Sp For \fIMACCSKeyBits\fR value of \fB\-m, \-\-mode\fR option, a fingerprint bit-vector string containing zeros and ones is generated and for \fIMACCSKeyCount\fR value, a fingerprint vector string corresponding to number of \s-1MACCS\s0 keys is generated. .Sp \&\fIMACCSKeyBits | MACCSKeyCount\fR values for \fB\-m, \-\-mode\fR option along with two possible \&\fI166 | 322\fR values of \fB\-s, \-\-size\fR supports generation of four different types of \s-1MACCS\s0 keys fingerprint: \fIMACCS166KeyBits, MACCS166KeyCount, MACCS322KeyBits, MACCS322KeyCount\fR. .Sp Definition of \s-1MACCS\s0 keys uses the following atom and bond symbols to define atom and bond environments: .Sp .Vb 1 \& Atom symbols for 166 keys [ Ref 47 ]: \& \& A : Any valid periodic table element symbol \& Q : Hetro atoms; any non\-C or non\-H atom \& X : Halogens; F, Cl, Br, I \& Z : Others; other than H, C, N, O, Si, P, S, F, Cl, Br, I \& \& Atom symbols for 322 keys [ Ref 46 ]: \& \& A : Any valid periodic table element symbol \& Q : Hetro atoms; any non\-C or non\-H atom \& X : Others; other than H, C, N, O, Si, P, S, F, Cl, Br, I \& Z is neither defined nor used \& \& Bond types: \& \& \- : Single \& = : Double \& T : Triple \& # : Triple \& ~ : Single or double query bond \& % : An aromatic query bond \& \& None : Any bond type; no explicit bond specified \& \& $ : Ring bond; $ before a bond type specifies ring bond \& ! : Chain or non\-ring bond; ! before a bond type specifies chain bond \& \& @ : A ring linkage and the number following it specifies the \& atoms position in the line, thus @1 means linked back to the first \& atom in the list. \& \& Aromatic: Kekule or Arom5 \& \& Kekule: Bonds in 6\-membered rings with alternate single/double bonds \& or perimeter bonds \& Arom5: Bonds in 5\-membered rings with two double bonds and a hetro \& atom at the apex of the ring. .Ve .Sp \&\s-1MACCS\s0 166 keys [ Ref 45\-47 ] are defined as follows: .Sp .Vb 1 \& Key Description \& \& 1 ISOTOPE \& 2 103 < ATOMIC NO. < 256 \& 3 GROUP IVA,VA,VIA PERIODS 4\-6 (Ge...) \& 4 ACTINIDE \& 5 GROUP IIIB,IVB (Sc...) \& 6 LANTHANIDE \& 7 GROUP VB,VIB,VIIB (V...) \& 8 QAAA@1 \& 9 GROUP VIII (Fe...) \& 10 GROUP IIA (ALKALINE EARTH) \& 11 4M RING \& 12 GROUP IB,IIB (Cu...) \& 13 ON(C)C \& 14 S\-S \& 15 OC(O)O \& 16 QAA@1 \& 17 CTC \& 18 GROUP IIIA (B...) \& 19 7M RING \& 20 SI \& 21 C=C(Q)Q \& 22 3M RING \& 23 NC(O)O \& 24 N\-O \& 25 NC(N)N \& 26 C$=C($A)$A \& 27 I \& 28 QCH2Q \& 29 P \& 30 CQ(C)(C)A \& 31 QX \& 32 CSN \& 33 NS \& 34 CH2=A \& 35 GROUP IA (ALKALI METAL) \& 36 S HETEROCYCLE \& 37 NC(O)N \& 38 NC(C)N \& 39 OS(O)O \& 40 S\-O \& 41 CTN \& 42 F \& 43 QHAQH \& 44 OTHER \& 45 C=CN \& 46 BR \& 47 SAN \& 48 OQ(O)O \& 49 CHARGE \& 50 C=C(C)C \& 51 CSO \& 52 NN \& 53 QHAAAQH \& 54 QHAAQH \& 55 OSO \& 56 ON(O)C \& 57 O HETEROCYCLE \& 58 QSQ \& 59 Snot%A%A \& 60 S=O \& 61 AS(A)A \& 62 A$A!A$A \& 63 N=O \& 64 A$A!S \& 65 C%N \& 66 CC(C)(C)A \& 67 QS \& 68 QHQH (&...) \& 69 QQH \& 70 QNQ \& 71 NO \& 72 OAAO \& 73 S=A \& 74 CH3ACH3 \& 75 A!N$A \& 76 C=C(A)A \& 77 NAN \& 78 C=N \& 79 NAAN \& 80 NAAAN \& 81 SA(A)A \& 82 ACH2QH \& 83 QAAAA@1 \& 84 NH2 \& 85 CN(C)C \& 86 CH2QCH2 \& 87 X!A$A \& 88 S \& 89 OAAAO \& 90 QHAACH2A \& 91 QHAAACH2A \& 92 OC(N)C \& 93 QCH3 \& 94 QN \& 95 NAAO \& 96 5M RING \& 97 NAAAO \& 98 QAAAAA@1 \& 99 C=C \& 100 ACH2N \& 101 8M RING \& 102 QO \& 103 CL \& 104 QHACH2A \& 105 A$A($A)$A \& 106 QA(Q)Q \& 107 XA(A)A \& 108 CH3AAACH2A \& 109 ACH2O \& 110 NCO \& 111 NACH2A \& 112 AA(A)(A)A \& 113 Onot%A%A \& 114 CH3CH2A \& 115 CH3ACH2A \& 116 CH3AACH2A \& 117 NAO \& 118 ACH2CH2A > 1 \& 119 N=A \& 120 HETEROCYCLIC ATOM > 1 (&...) \& 121 N HETEROCYCLE \& 122 AN(A)A \& 123 OCO \& 124 QQ \& 125 AROMATIC RING > 1 \& 126 A!O!A \& 127 A$A!O > 1 (&...) \& 128 ACH2AAACH2A \& 129 ACH2AACH2A \& 130 QQ > 1 (&...) \& 131 QH > 1 \& 132 OACH2A \& 133 A$A!N \& 134 X (HALOGEN) \& 135 Nnot%A%A \& 136 O=A > 1 \& 137 HETEROCYCLE \& 138 QCH2A > 1 (&...) \& 139 OH \& 140 O > 3 (&...) \& 141 CH3 > 2 (&...) \& 142 N > 1 \& 143 A$A!O \& 144 Anot%A%Anot%A \& 145 6M RING > 1 \& 146 O > 2 \& 147 ACH2CH2A \& 148 AQ(A)A \& 149 CH3 > 1 \& 150 A!A$A!A \& 151 NH \& 152 OC(C)C \& 153 QCH2A \& 154 C=O \& 155 A!CH2!A \& 156 NA(A)A \& 157 C\-O \& 158 C\-N \& 159 O > 1 \& 160 CH3 \& 161 N \& 162 AROMATIC \& 163 6M RING \& 164 O \& 165 RING \& 166 FRAGMENTS .Ve .Sp \&\s-1MACCS\s0 322 keys set as defined in tables 1, 2 and 3 [ Ref 46 ] include: .Sp .Vb 3 \& . 26 atom properties of type P, as listed in Table 1 \& . 32 one\-atom environments, as listed in Table 3 \& . 264 atom\-bond\-atom combinations listed in Table 4 .Ve .Sp Total number of keys in three tables is : 322 .Sp Atom symbol, X, used for 322 keys [ Ref 46 ] doesn't refer to Halogens as it does for 166 keys. In order to keep the definition of 322 keys consistent with the published definitions, the symbol X is used to imply \*(L"others\*(R" atoms, but it's internally mapped to symbol X as defined for 166 keys during the generation of key values. .Sp Atom properties-based keys (26): .Sp .Vb 10 \& Key Description \& 1 A(AAA) or AA(A)A \- atom with at least three neighbors \& 2 Q \- heteroatom \& 3 Anot%not\-A \- atom involved in one or more multiple bonds, not aromatic \& 4 A(AAAA) or AA(A)(A)A \- atom with at least four neighbors \& 5 A(QQ) or QA(Q) \- atom with at least two heteroatom neighbors \& 6 A(QQQ) or QA(Q)Q \- atom with at least three heteroatom neighbors \& 7 QH \- heteroatom with at least one hydrogen attached \& 8 CH2(AA) or ACH2A \- carbon with at least two single bonds and at least \& two hydrogens attached \& 9 CH3(A) or ACH3 \- carbon with at least one single bond and at least three \& hydrogens attached \& 10 Halogen \& 11 A(\-A\-A\-A) or A\-A(\-A)\-A \- atom has at least three single bonds \& 12 AAAAAA@1 > 2 \- atom is in at least two different six\-membered rings \& 13 A($A$A$A) or A$A($A)$A \- atom has more than two ring bonds \& 14 A$A!A$A \- atom is at a ring/chain boundary. When a comparison is done \& with another atom the path passes through the chain bond. \& 15 Anot%A%Anot%A \- atom is at an aromatic/nonaromatic boundary. When a \& comparison is done with another atom the path \& passes through the aromatic bond. \& 16 A!A!A \- atom with more than one chain bond \& 17 A!A$A!A \- atom is at a ring/chain boundary. When a comparison is done \& with another atom the path passes through the ring bond. \& 18 A%Anot%A%A \- atom is at an aromatic/nonaromatic boundary. When a \& comparison is done with another atom the \& path passes through the nonaromatic bond. \& 19 HETEROCYCLE \- atom is a heteroatom in a ring. \& 20 rare properties: atom with five or more neighbors, atom in \& four or more rings, or atom types other than \& H, C, N, O, S, F, Cl, Br, or I \& 21 rare properties: atom has a charge, is an isotope, has two or \& more multiple bonds, or has a triple bond. \& 22 N \- nitrogen \& 23 S \- sulfur \& 24 O \- oxygen \& 25 A(AA)A(A)A(AA) \- atom has two neighbors, each with three or \& more neighbors (including the central atom). \& 26 CHACH2 \- atom has two hydrocarbon (CH2) neighbors .Ve .Sp Atomic environments properties-based keys (32): .Sp .Vb 10 \& Key Description \& 27 C(CC) \& 28 C(CCC) \& 29 C(CN) \& 30 C(CCN) \& 31 C(NN) \& 32 C(NNC) \& 33 C(NNN) \& 34 C(CO) \& 35 C(CCO) \& 36 C(NO) \& 37 C(NCO) \& 38 C(NNO) \& 39 C(OO) \& 40 C(COO) \& 41 C(NOO) \& 42 C(OOO) \& 43 Q(CC) \& 44 Q(CCC) \& 45 Q(CN) \& 46 Q(CCN) \& 47 Q(NN) \& 48 Q(CNN) \& 49 Q(NNN) \& 50 Q(CO) \& 51 Q(CCO) \& 52 Q(NO) \& 53 Q(CNO) \& 54 Q(NNO) \& 55 Q(OO) \& 56 Q(COO) \& 57 Q(NOO) \& 58 Q(OOO) .Ve .Sp Note: The first symbol is the central atom, with atoms bonded to the central atom listed in parentheses. Q is any non-C, non-H atom. If only two atoms are in parentheses, there is no implication concerning the other atoms bonded to the central atom. .Sp Atom-Bond-Atom properties-based keys: (264) .Sp .Vb 10 \& Key Description \& 59 C\-C \& 60 C\-N \& 61 C\-O \& 62 C\-S \& 63 C\-Cl \& 64 C\-P \& 65 C\-F \& 66 C\-Br \& 67 C\-Si \& 68 C\-I \& 69 C\-X \& 70 N\-N \& 71 N\-O \& 72 N\-S \& 73 N\-Cl \& 74 N\-P \& 75 N\-F \& 76 N\-Br \& 77 N\-Si \& 78 N\-I \& 79 N\-X \& 80 O\-O \& 81 O\-S \& 82 O\-Cl \& 83 O\-P \& 84 O\-F \& 85 O\-Br \& 86 O\-Si \& 87 O\-I \& 88 O\-X \& 89 S\-S \& 90 S\-Cl \& 91 S\-P \& 92 S\-F \& 93 S\-Br \& 94 S\-Si \& 95 S\-I \& 96 S\-X \& 97 Cl\-Cl \& 98 Cl\-P \& 99 Cl\-F \& 100 Cl\-Br \& 101 Cl\-Si \& 102 Cl\-I \& 103 Cl\-X \& 104 P\-P \& 105 P\-F \& 106 P\-Br \& 107 P\-Si \& 108 P\-I \& 109 P\-X \& 110 F\-F \& 111 F\-Br \& 112 F\-Si \& 113 F\-I \& 114 F\-X \& 115 Br\-Br \& 116 Br\-Si \& 117 Br\-I \& 118 Br\-X \& 119 Si\-Si \& 120 Si\-I \& 121 Si\-X \& 122 I\-I \& 123 I\-X \& 124 X\-X \& 125 C=C \& 126 C=N \& 127 C=O \& 128 C=S \& 129 C=Cl \& 130 C=P \& 131 C=F \& 132 C=Br \& 133 C=Si \& 134 C=I \& 135 C=X \& 136 N=N \& 137 N=O \& 138 N=S \& 139 N=Cl \& 140 N=P \& 141 N=F \& 142 N=Br \& 143 N=Si \& 144 N=I \& 145 N=X \& 146 O=O \& 147 O=S \& 148 O=Cl \& 149 O=P \& 150 O=F \& 151 O=Br \& 152 O=Si \& 153 O=I \& 154 O=X \& 155 S=S \& 156 S=Cl \& 157 S=P \& 158 S=F \& 159 S=Br \& 160 S=Si \& 161 S=I \& 162 S=X \& 163 Cl=Cl \& 164 Cl=P \& 165 Cl=F \& 166 Cl=Br \& 167 Cl=Si \& 168 Cl=I \& 169 Cl=X \& 170 P=P \& 171 P=F \& 172 P=Br \& 173 P=Si \& 174 P=I \& 175 P=X \& 176 F=F \& 177 F=Br \& 178 F=Si \& 179 F=I \& 180 F=X \& 181 Br=Br \& 182 Br=Si \& 183 Br=I \& 184 Br=X \& 185 Si=Si \& 186 Si=I \& 187 Si=X \& 188 I=I \& 189 I=X \& 190 X=X \& 191 C#C \& 192 C#N \& 193 C#O \& 194 C#S \& 195 C#Cl \& 196 C#P \& 197 C#F \& 198 C#Br \& 199 C#Si \& 200 C#I \& 201 C#X \& 202 N#N \& 203 N#O \& 204 N#S \& 205 N#Cl \& 206 N#P \& 207 N#F \& 208 N#Br \& 209 N#Si \& 210 N#I \& 211 N#X \& 212 O#O \& 213 O#S \& 214 O#Cl \& 215 O#P \& 216 O#F \& 217 O#Br \& 218 O#Si \& 219 O#I \& 220 O#X \& 221 S#S \& 222 S#Cl \& 223 S#P \& 224 S#F \& 225 S#Br \& 226 S#Si \& 227 S#I \& 228 S#X \& 229 Cl#Cl \& 230 Cl#P \& 231 Cl#F \& 232 Cl#Br \& 233 Cl#Si \& 234 Cl#I \& 235 Cl#X \& 236 P#P \& 237 P#F \& 238 P#Br \& 239 P#Si \& 240 P#I \& 241 P#X \& 242 F#F \& 243 F#Br \& 244 F#Si \& 245 F#I \& 246 F#X \& 247 Br#Br \& 248 Br#Si \& 249 Br#I \& 250 Br#X \& 251 Si#Si \& 252 Si#I \& 253 Si#X \& 254 I#I \& 255 I#X \& 256 X#X \& 257 C$C \& 258 C$N \& 259 C$O \& 260 C$S \& 261 C$Cl \& 262 C$P \& 263 C$F \& 264 C$Br \& 265 C$Si \& 266 C$I \& 267 C$X \& 268 N$N \& 269 N$O \& 270 N$S \& 271 N$Cl \& 272 N$P \& 273 N$F \& 274 N$Br \& 275 N$Si \& 276 N$I \& 277 N$X \& 278 O$O \& 279 O$S \& 280 O$Cl \& 281 O$P \& 282 O$F \& 283 O$Br \& 284 O$Si \& 285 O$I \& 286 O$X \& 287 S$S \& 288 S$Cl \& 289 S$P \& 290 S$F \& 291 S$Br \& 292 S$Si \& 293 S$I \& 294 S$X \& 295 Cl$Cl \& 296 Cl$P \& 297 Cl$F \& 298 Cl$Br \& 299 Cl$Si \& 300 Cl$I \& 301 Cl$X \& 302 P$P \& 303 P$F \& 304 P$Br \& 305 P$Si \& 306 P$I \& 307 P$X \& 308 F$F \& 309 F$Br \& 310 F$Si \& 311 F$I \& 312 F$X \& 313 Br$Br \& 314 Br$Si \& 315 Br$I \& 316 Br$X \& 317 Si$Si \& 318 Si$I \& 319 Si$X \& 320 I$I \& 321 I$X \& 322 X$X .Ve .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><MACCSKeysFP>.<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\-s, \-\-size\fR \fInumber\fR" 4 .IX Item "-s, --size number" Size of \s-1MACCS\s0 keys [ Ref 45\-47 ] set to use during fingerprints generation. Possible values: \fI166 or 322\fR. Default value: \fI166\fR. .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 during \fIMACCSKeyCount\fR value of \fB\-m, \-\-mode\fR option. Possible values: \fIValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR. Defaultvalue: \fIValuesString\fR. .Sp Examples: .Sp .Vb 6 \& FingerprintsVector;MACCSKeyCount;166;OrderedNumericalValues;ValuesStri \& ng;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 1 0 0 3 0 0 0 0 4 0 0 2 0 0 0 0 0 0 0 0 2 0 0 2 0 0 0 0 \& 0 0 0 0 1 1 8 0 0 0 1 0 0 1 0 1 0 1 0 3 1 3 1 0 0 0 1 2 0 11 1 0 0 0 \& 5 0 0 1 2 0 1 1 0 0 0 0 0 1 1 0 1 1 1 1 0 4 0 0 1 1 0 4 6 1 1 1 2 1 1 \& 3 5 2 2 0 5 3 5 1 1 2 5 1 2 1 2 4 8 3 5 5 2 2 0 3 5 4 1 \& \& FingerprintsVector;MACCSKeyCount;322;OrderedNumericalValues;ValuesStri \& ng;14 8 2 0 2 0 4 4 2 1 4 0 0 2 5 10 5 2 1 0 0 2 0 5 13 3 28 5 5 3 0 0 \& 0 4 2 1 1 0 1 1 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 5 3 0 0 0 1 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 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 2 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 ... .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 \s-1MACCS\s0 keys fingerprints of size 166 in binary bit-vector string format and create a SampleMACCS166FPBin.csv file containing sequential compound IDs along with fingerprints bit-vector strings data, type: .PP .Vb 1 \& % MACCSKeysFingerprints.pl \-r SampleMACCS166FPBin \-o Sample.sdf .Ve .PP To generate \s-1MACCS\s0 keys fingerprints of size 166 in binary bit-vector string format and create SampleMACCS166FPBin.sdf, SampleMACCS166FPBin.csv and SampleMACCS166FPBin.csv files containing sequential compound IDs in \s-1CSV\s0 file along with fingerprints bit-vector strings data, type: .PP .Vb 2 \& % MACCSKeysFingerprints.pl \-\-output all \-r SampleMACCS166FPBin \& \-o Sample.sdf .Ve .PP To generate \s-1MACCS\s0 keys fingerprints of size 322 in binary bit-vector string format and create a SampleMACCS322FPBin.csv file containing sequential compound IDs along with fingerprints bit-vector strings data, type: .PP .Vb 1 \& % MACCSKeysFingerprints.pl \-size 322 \-r SampleMACCS322FPBin \-o Sample.sdf .Ve .PP To generate \s-1MACCS\s0 keys fingerprints of size 166 corresponding to count of keys in ValuesString format and create a SampleMACCS166FPCount.csv file containing sequential compound IDs along with fingerprints vector strings data, type: .PP .Vb 2 \& % MACCSKeysFingerprints.pl \-m MACCSKeyCount \-r SampleMACCS166FPCount \& \-o Sample.sdf .Ve .PP To generate \s-1MACCS\s0 keys fingerprints of size 322 corresponding to count of keys in ValuesString format and create a SampleMACCS322FPCount.csv file containing sequential compound IDs along with fingerprints vector strings data, type: .PP .Vb 2 \& % MACCSKeysFingerprints.pl \-m MACCSKeyCount \-size 322 \& \-r SampleMACCS322FPCount \-o Sample.sdf .Ve .PP To generate \s-1MACCS\s0 keys fingerprints of size 166 in hexadecimal bit-vector string format with ascending bits order and create a SampleMACCS166FPHex.csv file containing compound IDs from MolName along with fingerprints bit-vector strings data, type: .PP .Vb 3 \& % MACCSKeysFingerprints.pl \-m MACCSKeyBits \-\-size 166 \-\-BitStringFormat \& HexadecimalString \-\-BitsOrder Ascending \-\-DataFieldsMode CompoundID \& \-\-CompoundIDMode MolName \-r SampleMACCS166FPBin \-o Sample.sdf .Ve .PP To generate \s-1MACCS\s0 keys fingerprints of size 166 corresponding to count of keys in IDsAndValuesString format and create a SampleMACCS166FPCount.csv file containing compound IDs from MolName line along with fingerprints vector strings data, type: .PP .Vb 3 \& % MACCSKeysFingerprints.pl \-m MACCSKeyCount \-\-size 166 \& \-\-VectorStringFormat IDsAndValuesString \-\-DataFieldsMode CompoundID \& \-\-CompoundIDMode MolName \-r SampleMACCS166FPCount \-o Sample.sdf .Ve .PP To generate \s-1MACCS\s0 keys fingerprints of size 166 corresponding to count of keys in IDsAndValuesString format and create a SampleMACCS166FPCount.csv file containing compound IDs using specified data field along with fingerprints vector strings data, type: .PP .Vb 4 \& % MACCSKeysFingerprints.pl \-m MACCSKeyCount \-\-size 166 \& \-\-VectorStringFormat IDsAndValuesString \-\-DataFieldsMode CompoundID \& \-\-CompoundIDMode DataField \-\-CompoundID Mol_ID \-r \& SampleMACCS166FPCount \-o Sample.sdf .Ve .PP To generate \s-1MACCS\s0 keys fingerprints of size 322 corresponding to count of keys in ValuesString format and create a SampleMACCS322FPCount.tsv file containing compound IDs derived from combination of molecule name line and an explicit compound prefix along with fingerprints vector strings data in a column labels MACCSKeyCountFP, type: .PP .Vb 4 \& % MACCSKeysFingerprints.pl \-m MACCSKeyCount \-size 322 \-\-DataFieldsMode \& CompoundID \-\-CompoundIDMode MolnameOrLabelPrefix \-\-CompoundID Cmpd \& \-\-CompoundIDLabel MolID \-\-FingerprintsLabel MACCSKeyCountFP \-\-OutDelim \& Tab \-r SampleMACCS322FPCount \-o Sample.sdf .Ve .PP To generate \s-1MACCS\s0 keys fingerprints of size 166 corresponding to count of keys in ValuesString format and create a SampleMACCS166FPCount.csv file containing specific data fields columns along with fingerprints vector strings data, type: .PP .Vb 3 \& % MACCSKeysFingerprints.pl \-m MACCSKeyCount \-\-size 166 \& \-\-VectorStringFormat ValuesString \-\-DataFieldsMode Specify \-\-DataFields \& Mol_ID \-r SampleMACCS166FPCount \-o Sample.sdf .Ve .PP To generate \s-1MACCS\s0 keys fingerprints of size 322 corresponding to count of keys in ValuesString format and create a SampleMACCS322FPCount.csv file containing common data fields columns along with fingerprints vector strings data, type: .PP .Vb 3 \& % MACCSKeysFingerprints.pl \-m MACCSKeyCount \-\-size 322 \& \-\-VectorStringFormat ValuesString \-\-DataFieldsMode Common \-r \& SampleMACCS322FPCount \-o Sample.sdf .Ve .PP To generate \s-1MACCS\s0 keys fingerprints of size 166 corresponding to count of keys in ValuesString format and create SampleMACCS166FPCount.sdf, SampleMACCS166FPCount.fpf and SampleMACCS166FPCount.csv files containing all data fields columns in \s-1CSV\s0 file along with fingerprints vector strings data, type: .PP .Vb 3 \& % MACCSKeysFingerprints.pl \-m MACCSKeyCount \-\-size 166 \-\-output all \& \-\-VectorStringFormat ValuesString \-\-DataFieldsMode All \-r \& SampleMACCS166FPCount \-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, 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.