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NAME
    MACCSKeysFingerprints.pl - Generate MACCS key fingerprints for SD files

SYNOPSIS
    MACCSKeysFingerprints.pl SDFile(s)...

    MACCSKeysFingerprints.pl [--AromaticityModel *AromaticityModelType*]
    [--BitsOrder *Ascending | Descending*] [-b, --BitStringFormat
    *BinaryString | HexadecimalString*] [--CompoundID *DataFieldName or
    LabelPrefixString*] [--CompoundIDLabel *text*] [--CompoundIDMode
    *DataField | MolName | LabelPrefix | MolNameOrLabelPrefix*]
    [--DataFields *"FieldLabel1,FieldLabel2,..."*] [-d, --DataFieldsMode
    *All | Common | Specify | CompoundID*] [-f, --Filter *Yes | No*]
    [--FingerprintsLabel *text*] [-h, --help] [-k, --KeepLargestComponent
    *Yes | No*] [-m, --mode *MACCSKeyBits | MACCSKeyCount*] [--OutDelim
    *comma | tab | semicolon*] [--output *SD | FP | text | all*] [-o,
    --overwrite] [-q, --quote *Yes | No*] [-r, --root *RootName*] [-s,
    --size *number*] [-v, --VectorStringFormat *IDsAndValuesString |
    IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString*]
    [-w, --WorkingDir *DirName*]

DESCRIPTION
    Generate MACCS (Molecular ACCess System) keys fingerprints [ Ref 45-47 ]
    for *SDFile(s)* and create appropriate SD, FP or CSV/TSV text file(s)
    containing fingerprints bit-vector or vector strings corresponding to
    molecular fingerprints.

    Multiple SDFile names are separated by spaces. The valid file extensions
    are *.sdf* and *.sd*. All other file names are ignored. All the SD files
    in a current directory can be specified either by **.sdf* or the current
    directory name.

    For each MACCS 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 MACCS keys.

    For *MACCSKeyBits* value of -m, --mode option, a fingerprint bit-vector
    string containing zeros and ones is generated and for *MACCSKeyCount*
    value, a fingerprint vector string corresponding to number of MACCS keys
    [ Ref 45-47 ] is generated.

    *MACCSKeyBits | MACCSKeyCount* values for -m, --mode option along with
    two possible *166 | 322* values of -s, --size supports generation of
    four different types of MACCS keys fingerprint: *MACCS166KeyBits,
    MACCS166KeyCount, MACCS322KeyBits, MACCS322KeyCount*.

    Example of *SD* file containing MAACS keys 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

        >  <MACCSKeysFingerprints>
        FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;000000000
        00000000000000000000000000000000100100001001000000001001000000001110001
        00101010111100011011000100110110000011011110100110111111111111011111111
        11111111110111000

        $$$$
        ... ...
        ... ...

    Example of *FP* file containing MAACS keys fingerprints string data:

        #
        # 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...
        ... ...
        ... ..

    Example of CSV *Text* file containing MAACS keys fingerprints string
    data:

        "CompoundID","MACCSKeysFingerprints"
        "Cmpd1","FingerprintsBitVector;MACCSKeyBits;166;BinaryString;Ascending;
        00000000000000000000000000000000000000000100100001001000000001001000000
        00111000100101010111100011011000100110110000011011110100110111111111111
        01111111111111111110111000"
        ... ...
        ... ...

    The current release of MayaChemTools generates the following types of
    MACCS keys fingerprints bit-vector and vector strings:

        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 ...

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.

    --BitsOrder *Ascending | Descending*
        Bits order to use during generation of fingerprints bit-vector
        string for *MACCSKeyBits* value of -m, --mode option. Possible
        values: *Ascending, Descending*. Default: *Ascending*.

        *Ascending* bit order which corresponds to first bit in each byte as
        the lowest bit as opposed to the highest bit.

        Internally, bits are stored in *Ascending* 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.

    -b, --BitStringFormat *BinaryString | HexadecimalString*
        Format of fingerprints bit-vector string data in output SD, FP or
        CSV/TSV text file(s) specified by --output used during
        *MACCSKeyBits* value of -m, --mode option. Possible values:
        *BinaryString, HexadecimalString*. Default value: *BinaryString*.

        *BinaryString* corresponds to an ASCII string containing 1s and 0s.
        *HexadecimalString* contains bit values in ASCII hexadecimal format.

        Examples:

            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

    --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: *MACCSKeyFingerprints*.

    -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.

    -m, --mode *MACCSKeyBits | MACCSKeyCount*
        Specify type of MACCS keys [ Ref 45-47 ] fingerprints to generate
        for molecules in *SDFile(s)*. Possible values: *MACCSKeyBits,
        MACCSKeyCount*. Default value: *MACCSKeyBits*.

        For *MACCSKeyBits* value of -m, --mode option, a fingerprint
        bit-vector string containing zeros and ones is generated and for
        *MACCSKeyCount* value, a fingerprint vector string corresponding to
        number of MACCS keys is generated.

        *MACCSKeyBits | MACCSKeyCount* values for -m, --mode option along
        with two possible *166 | 322* values of -s, --size supports
        generation of four different types of MACCS keys fingerprint:
        *MACCS166KeyBits, MACCS166KeyCount, MACCS322KeyBits,
        MACCS322KeyCount*.

        Definition of MACCS keys uses the following atom and bond symbols to
        define atom and bond environments:

            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.

        MACCS 166 keys [ Ref 45-47 ] are defined as follows:

            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

        MACCS 322 keys set as defined in tables 1, 2 and 3 [ Ref 46 ]
        include:

            . 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

        Total number of keys in three tables is : 322

        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 "others" atoms, but it's internally mapped to symbol X
        as defined for 166 keys during the generation of key values.

        Atom properties-based keys (26):

            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

        Atomic environments properties-based keys (32):

            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)

        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.

        Atom-Bond-Atom properties-based keys: (264)

            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

    --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><MACCSKeysFP>.<Ext>. The file type
        determines <Ext> value. The sdf, fpf, csv, and tsv <Ext> values are
        used for SD, FP, comma/semicolon, and tab delimited text files,
        respectively.This option is ignored for multiple input files.

    -s, --size *number*
        Size of MACCS keys [ Ref 45-47 ] set to use during fingerprints
        generation. Possible values: *166 or 322*. Default value: *166*.

    -v, --VectorStringFormat *ValuesString | IDsAndValuesString |
    IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString*
        Format of fingerprints vector string data in output SD, FP or
        CSV/TSV text file(s) specified by --output used during
        *MACCSKeyCount* value of -m, --mode option. Possible values:
        *ValuesString, IDsAndValuesString | IDsAndValuesPairsString |
        ValuesAndIDsString | ValuesAndIDsPairsString*. Defaultvalue:
        *ValuesString*.

        Examples:

            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 ...

    -w, --WorkingDir *DirName*
        Location of working directory. Default: current directory.

EXAMPLES
    To generate MACCS 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:

        % MACCSKeysFingerprints.pl -r SampleMACCS166FPBin -o Sample.sdf

    To generate MACCS 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 CSV file along with fingerprints bit-vector
    strings data, type:

        % MACCSKeysFingerprints.pl --output all -r SampleMACCS166FPBin
          -o Sample.sdf

    To generate MACCS 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:

        % MACCSKeysFingerprints.pl -size 322 -r SampleMACCS322FPBin -o Sample.sdf

    To generate MACCS 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:

        % MACCSKeysFingerprints.pl -m MACCSKeyCount -r SampleMACCS166FPCount
          -o Sample.sdf

    To generate MACCS 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:

        % MACCSKeysFingerprints.pl -m MACCSKeyCount -size 322
          -r SampleMACCS322FPCount -o Sample.sdf

    To generate MACCS 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:

        % MACCSKeysFingerprints.pl -m MACCSKeyBits --size 166 --BitStringFormat
          HexadecimalString --BitsOrder Ascending --DataFieldsMode CompoundID
          --CompoundIDMode MolName -r SampleMACCS166FPBin -o Sample.sdf

    To generate MACCS 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:

        % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166
          --VectorStringFormat IDsAndValuesString  --DataFieldsMode CompoundID
          --CompoundIDMode MolName -r SampleMACCS166FPCount -o Sample.sdf

    To generate MACCS 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:

        % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166
          --VectorStringFormat IDsAndValuesString  --DataFieldsMode CompoundID
          --CompoundIDMode DataField --CompoundID Mol_ID -r
          SampleMACCS166FPCount -o Sample.sdf

    To generate MACCS 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:

        % MACCSKeysFingerprints.pl -m MACCSKeyCount -size 322 --DataFieldsMode
          CompoundID --CompoundIDMode MolnameOrLabelPrefix --CompoundID Cmpd
          --CompoundIDLabel MolID --FingerprintsLabel MACCSKeyCountFP --OutDelim
          Tab -r SampleMACCS322FPCount -o Sample.sdf

    To generate MACCS 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:

        % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166
          --VectorStringFormat ValuesString --DataFieldsMode Specify --DataFields
          Mol_ID  -r SampleMACCS166FPCount -o Sample.sdf

    To generate MACCS 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:

        % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 322
          --VectorStringFormat ValuesString --DataFieldsMode Common -r
          SampleMACCS322FPCount -o Sample.sdf

    To generate MACCS 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 CSV file along with fingerprints vector
    strings data, type:

        % MACCSKeysFingerprints.pl -m MACCSKeyCount --size 166 --output all
          --VectorStringFormat ValuesString --DataFieldsMode All -r
          SampleMACCS166FPCount -o Sample.sdf

AUTHOR
    Manish Sud <[e-mail]>

SEE ALSO
    InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl,
    AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.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.