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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/man1/MACCSKeysFingerprints.1 Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,1202 @@ +.\" 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.