diff docs/scripts/txt/MACCSKeysFingerprints.txt @ 0:4816e4a8ae95 draft default tip

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author deepakjadmin
date Wed, 20 Jan 2016 09:23:18 -0500
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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 <msud@san.rr.com>
+
+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.
+