NAME
    MACCSKeys

SYNOPSIS
    use Fingerprints::MACCSKeys;

    use Fingerprints::MACCSKeys qw(:all);

DESCRIPTION
    MACCSKeys [ Ref 45-47 ] class provides the following methods:

    new, GenerateFingerprints, GenerateMACCSKeys, GetDescription, SetSize,
    SetType, StringifyMACCSKeys

    MACCSKeys is derived from Fingerprints class which in turn is derived
    from ObjectProperty base class that provides methods not explicitly
    defined in MACCSKeys, Fingerprints or ObjectProperty classes using
    Perl's AUTOLOAD functionality. These methods are generated on-the-fly
    for a specified object property:

        Set<PropertyName>(<PropertyValue>);
        $PropertyValue = Get<PropertyName>();
        Delete<PropertyName>();

    For each MACCS (Molecular ACCess System) 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 Type 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 or MACCSKeyCount* values for Type along with two possible
    *166 | 322* values of Size supports generation of four different types
    of MACCS keys fingerprint: *MACCS166KeyBits, MACCS166KeyCount,
    MACCS322KeyBits, MACCS322KeyCount*.

    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 ...

  METHODS
    new
            $NewMACCSKeys = new MACCSKeys(%NamesAndValues);

        Using specified *MACCSKeys* property names and values hash, new
        method creates a new object and returns a reference to newly created
        PathLengthFingerprints object. By default, the following properties
        are initialized:

            Molecule = '';
            Type = ''
            Size = ''

        Examples:

            $MACCSKeys = new MACCSKeys('Molecule' => $Molecule,
                                       'Type' => 'MACCSKeyBits',
                                       'Size' => 166);

            $MACCSKeys = new MACCSKeys('Molecule' => $Molecule,
                                       'Type' => 'MACCSKeyCount',
                                       'Size' => 166);

            $MACCSKeys = new MACCSKeys('Molecule' => $Molecule,
                                       'Type' => 'MACCSKeyBit',
                                       'Size' => 322);

            $MACCSKeys = new MACCSKeys('Molecule' => $Molecule,
                                       'Type' => 'MACCSKeyCount',
                                       'Size' => 322);

            $MACCSKeys->GenerateMACCSKeys();
            print "$MACCSKeys\n";

    GetDescription
            $Description = $MACCSKeys->GetDescription();

        Returns a string containing description of MACCS keys fingerprints.

    GenerateMACCSKeys or GenerateFingerprints
            $MACCSKeys = $MACCSKeys->GenerateMACCSKeys();

        Generates MACCS keys fingerprints and returns *MACCSKeys*.

        For *MACCSKeyBits* value of Type, 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 or MACCSKeyCount* values for Type option along with
        two possible *166 | 322* values of 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:

            o 26 atom properties of type P, as listed in Table 1
            o 32 one-atom environments, as listed in Table 3
            o 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

    SetSize
            $MACCSKeys->SetSize($Size);

        Sets size of MACCS keys and returns *MACCSKeys*. Possible values:
        *166 or 322*.

    SetType
            $MACCSKeys->SetType($Type);

        Sets type of MACCS keys and returns *MACCSKeys*. Possible values:
        *MACCSKeysBits or MACCSKeysCount*.

    StringifyMACCSKeys
            $String = $MACCSKeys->StringifyMACCSKeys();

        Returns a string containing information about *MACCSKeys* object.

AUTHOR
    Manish Sud <msud@san.rr.com>

SEE ALSO
    Fingerprints.pm, FingerprintsStringUtil.pm,
    AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm,
    EStateIndiciesFingerprints.pm, ExtendedConnectivityFingerprints.pm,
    PathLengthFingerprints.pm, TopologicalAtomPairsFingerprints.pm,
    TopologicalAtomTripletsFingerprints.pm,
    TopologicalAtomTorsionsFingerprints.pm,
    TopologicalPharmacophoreAtomPairsFingerprints.pm,
    TopologicalPharmacophoreAtomTripletsFingerprints.pm

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.

