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1 #Comments after SMARTS
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2 # Extracted from RDKit r1553 Nov 2010 rdkit/Chem/MACCSKeys.py
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3 #
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4 # Copyright (C) 2001-2008 greg Landrum and Rational Discovery LLC
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5 #
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6 # @@ All Rights Reserved @@
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7 # This file is part of the RDKit.
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8 # The contents are covered by the terms of the BSD license
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9 # which is included in the file license.txt, found at the root
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10 # of the RDKit source tree.
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11 #
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12 # SMARTS definitions for the publically available MACCS keys
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13
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14 # I compared the MACCS fingerprints generated here with those from two
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15 # other packages (not MDL, unfortunately). Of course there are
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16 # disagreements between the various fingerprints still, but I think
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17 # these definitions work pretty well. Some notes:
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18
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19 # 1) most of the differences have to do with aromaticity
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20 # 2) there's a discrepancy sometimes because the current RDKit
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21 # definitions do not require multiple matches to be distinct. e.g. the
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22 # SMILES C(=O)CC(=O) can match the (hypothetical) key O=CC twice in my
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23 # definition. It's not clear to me what the correct behavior is.
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24 # 3) Some keys are not fully defined in the MDL documentation
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25 # 4) Two keys, 125 and 166, have to be done outside of SMARTS.
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26 # 5) Key 1 (ISOTOPE) isn't defined
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27
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28 # these are SMARTS patterns corresponding to the MDL MACCS keys
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29 1:('?',0), # ISOTOPE
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30 #2:('[#103,#104,#105,#106,#107,#106,#109,#110,#111,#112]',0), # ISOTOPE Not complete
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31 2:('[#103,#104]',0), # ISOTOPE Not complete
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32 3:('[Ge,As,Se,Sn,Sb,Te,Tl,Pb,Bi]',0), # Group IVa,Va,VIa Periods 4-6 (Ge...) *NOTE* spec wrong
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33 4:('[Ac,Th,Pa,U,Np,Pu,Am,Cm,Bk,Cf,Es,Fm,Md,No,Lr]',0), # actinide
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34 5:('[Sc,Ti,Y,Zr,Hf]',0), # Group IIIB,IVB (Sc...) *NOTE* spec wrong
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35 6:('[La,Ce,Pr,Nd,Pm,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu]',0), # Lanthanide
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36 7:('[V,Cr,Mn,Nb,Mo,Tc,Ta,W,Re]',0), # Group VB,VIB,VIIB (V...) *NOTE* spec wrong
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37 8:('[!#6;!#1]1~*~*~*~1',0), # QAAA@1
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38 9:('[Fe,Co,Ni,Ru,Rh,Pd,Os,Ir,Pt]',0), # Group VIII (Fe...)
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39 10:('[Be,Mg,Ca,Sr,Ba,Ra]',0), # Group IIa (Alkaline earth)
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40 11:('*1~*~*~*~1',0), # 4M Ring
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41 12:('[Cu,Zn,Ag,Cd,Au,Hg]',0), # Group IB,IIB (Cu..)
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42 13:('[#8]~[#7](~[#6])~[#6]',0), # ON(C)C
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43 14:('[#16]-[#16]',0), # S-S
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44 15:('[#8]~[#6](~[#8])~[#8]',0), # OC(O)O
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45 16:('[!#6;!#1]1~*~*~1',0), # QAA@1
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46 17:('[#6]#[#6]',0), #CTC
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47 18:('[B,Al,Ga,In,Tl]',0), # Group IIIA (B...) *NOTE* spec wrong
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48 19:('*1~*~*~*~*~*~*~1',0), # 7M Ring
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49 20:('[Si]',0), #Si
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50 21:('[#6]=[#6](~[!#6;!#1])~[!#6;!#1]',0), # C=C(Q)Q
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51 22:('*1~*~*~1',0), # 3M Ring
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52 23:('[#7]~[#6](~[#8])~[#8]',0), # NC(O)O
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53 24:('[#7]-[#8]',0), # N-O
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54 25:('[#7]~[#6](~[#7])~[#7]',0), # NC(N)N
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55 26:('[#6]=;@[#6](@*)@*',0), # C$=C($A)$A
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56 27:('[I]',0), # I
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57 28:('[!#6;!#1]~[CH2]~[!#6;!#1]',0), # QCH2Q
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58 29:('[#15]',0),# P
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59 30:('[#6]~[!#6;!#1](~[#6])(~[#6])~*',0), # CQ(C)(C)A
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60 31:('[!#6;!#1]~[F,Cl,Br,I]',0), # QX
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61 32:('[#6]~[#16]~[#7]',0), # CSN
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62 33:('[#7]~[#16]',0), # NS
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63 34:('[CH2]=*',0), # CH2=A
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64 35:('[Li,Na,K,Rb,Cs,Fr]',0), # Group IA (Alkali Metal)
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65 36:('[#16R]',0), # S Heterocycle
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66 37:('[#7]~[#6](~[#8])~[#7]',0), # NC(O)N
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67 38:('[#7]~[#6](~[#6])~[#7]',0), # NC(C)N
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68 39:('[#8]~[#16](~[#8])~[#8]',0), # OS(O)O
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69 40:('[#16]-[#8]',0), # S-O
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70 41:('[#6]#[#7]',0), # CTN
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71 42:('F',0), # F
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72 43:('[!C;!c;!#1;!H0]~*~[!C;!c;!#1;!H0]',0), # QHAQH
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73 44:('?',0), # OTHER
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74 45:('[#6]=[#6]~[#7]',0), # C=CN
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75 46:('Br',0), # BR
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76 47:('[#16]~*~[#7]',0), # SAN
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77 48:('[#8]~[!#6;!#1](~[#8])(~[#8])',0), # OQ(O)O
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78 49:('[!+0]',0), # CHARGE
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79 50:('[#6]=[#6](~[#6])~[#6]',0), # C=C(C)C
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80 51:('[#6]~[#16]~[#8]',0), # CSO
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81 52:('[#7]~[#7]',0), # NN
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82 53:('[!#6;!#1;!H0]~*~*~*~[!#6;!#1;!H0]',0), # QHAAAQH
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83 54:('[!#6;!#1;!H0]~*~*~[!#6;!#1;!H0]',0), # QHAAQH
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84 55:('[#8]~[#16]~[#8]',0), #OSO
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85 56:('[#8]~[#7](~[#8])~[#6]',0), # ON(O)C
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86 57:('[#8R]',0), # O Heterocycle
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87 58:('[!#6;!#1]~[#16]~[!#6;!#1]',0), # QSQ
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88 59:('[#16]!:*:*',0), # Snot%A%A
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89 60:('[#16]=[#8]',0), # S=O
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90 61:('*~[#16](~*)~*',0), # AS(A)A
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91 62:('*@*!@*@*',0), # A$!A$A
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92 63:('[#7]=[#8]',0), # N=O
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93 64:('*@*!@[#16]',0), # A$A!S
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94 65:('c:n',0), # C%N
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95 66:('[#6]~[#6](~[#6])(~[#6])~*',0), # CC(C)(C)A
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96 67:('[!#6;!#1]~[#16]',0), # QS
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97 68:('[!#6;!#1;!H0]~[!#6;!#1;!H0]',0), # QHQH (&...) FIX: incomplete definition
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98 69:('[!#6;!#1]~[!#6;!#1;!H0]',0), # QQH
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99 70:('[!#6;!#1]~[#7]~[!#6;!#1]',0), # QNQ
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100 71:('[#7]~[#8]',0), # NO
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101 72:('[#8]~*~*~[#8]',0), # OAAO
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102 73:('[#16]=*',0), # S=A
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103 74:('[CH3]~*~[CH3]',0), # CH3ACH3
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104 75:('*!@[#7]@*',0), # A!N$A
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105 76:('[#6]=[#6](~*)~*',0), # C=C(A)A
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106 77:('[#7]~*~[#7]',0), # NAN
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107 78:('[#6]=[#7]',0), # C=N
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108 79:('[#7]~*~*~[#7]',0), # NAAN
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109 80:('[#7]~*~*~*~[#7]',0), # NAAAN
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110 81:('[#16]~*(~*)~*',0), # SA(A)A
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111 82:('*~[CH2]~[!#6;!#1;!H0]',0), # ACH2QH
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112 83:('[!#6;!#1]1~*~*~*~*~1',0), # QAAAA@1
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113 84:('[NH2]',0), #NH2
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114 85:('[#6]~[#7](~[#6])~[#6]',0), # CN(C)C
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115 86:('[C;H2,H3][!#6;!#1][C;H2,H3]',0), # CH2QCH2
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116 87:('[F,Cl,Br,I]!@*@*',0), # X!A$A
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117 88:('[#16]',0), # S
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118 89:('[#8]~*~*~*~[#8]',0), # OAAAO
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119 90:('[$([!#6;!#1;!H0]~*~*~[CH2]~*),$([!#6;!#1;!H0;R]1@[R]@[R]@[CH2;R]1),$([!#6;!#1;!H0]~[R]1@[R]@[CH2;R]1)]',0), # QHAACH2A
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120 91:('[$([!#6;!#1;!H0]~*~*~*~[CH2]~*),$([!#6;!#1;!H0;R]1@[R]@[R]@[R]@[CH2;R]1),$([!#6;!#1;!H0]~[R]1@[R]@[R]@[CH2;R]1),$([!#6;!#1;!H0]~*~[R]1@[R]@[CH2;R]1)]',0), # QHAAACH2A
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121 92:('[#8]~[#6](~[#7])~[#6]',0), # OC(N)C
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122 93:('[!#6;!#1]~[CH3]',0), # QCH3
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123 94:('[!#6;!#1]~[#7]',0), # QN
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124 95:('[#7]~*~*~[#8]',0), # NAAO
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125 96:('*1~*~*~*~*~1',0), # 5 M ring
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126 97:('[#7]~*~*~*~[#8]',0), # NAAAO
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127 98:('[!#6;!#1]1~*~*~*~*~*~1',0), # QAAAAA@1
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128 99:('[#6]=[#6]',0), # C=C
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129 100:('*~[CH2]~[#7]',0), # ACH2N
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130 101:('[$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1),$([R]@1@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]@[R]1)]',0), # 8M Ring or larger. This only handles up to ring sizes of 14
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131 102:('[!#6;!#1]~[#8]',0), # QO
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132 103:('Cl',0), # CL
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133 104:('[!#6;!#1;!H0]~*~[CH2]~*',0), # QHACH2A
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134 105:('*@*(@*)@*',0), # A$A($A)$A
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135 106:('[!#6;!#1]~*(~[!#6;!#1])~[!#6;!#1]',0), # QA(Q)Q
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136 107:('[F,Cl,Br,I]~*(~*)~*',0), # XA(A)A
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137 108:('[CH3]~*~*~*~[CH2]~*',0), # CH3AAACH2A
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138 109:('*~[CH2]~[#8]',0), # ACH2O
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139 110:('[#7]~[#6]~[#8]',0), # NCO
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140 111:('[#7]~*~[CH2]~*',0), # NACH2A
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141 112:('*~*(~*)(~*)~*',0), # AA(A)(A)A
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142 113:('[#8]!:*:*',0), # Onot%A%A
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143 114:('[CH3]~[CH2]~*',0), # CH3CH2A
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144 115:('[CH3]~*~[CH2]~*',0), # CH3ACH2A
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145 116:('[$([CH3]~*~*~[CH2]~*),$([CH3]~*1~*~[CH2]1)]',0), # CH3AACH2A
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146 117:('[#7]~*~[#8]',0), # NAO
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147 118:('[$(*~[CH2]~[CH2]~*),$(*1~[CH2]~[CH2]1)]',1), # ACH2CH2A > 1
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148 119:('[#7]=*',0), # N=A
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149 120:('[!#6;R]',1), # Heterocyclic atom > 1 (&...) FIX: incomplete definition
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150 121:('[#7;R]',0), # N Heterocycle
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151 122:('*~[#7](~*)~*',0), # AN(A)A
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152 123:('[#8]~[#6]~[#8]',0), # OCO
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153 124:('[!#6;!#1]~[!#6;!#1]',0), # QQ
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154 125:('?',0), # Aromatic Ring > 1
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155 126:('*!@[#8]!@*',0), # A!O!A
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156 127:('*@*!@[#8]',1), # A$A!O > 1 (&...) FIX: incomplete definition
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157 128:('[$(*~[CH2]~*~*~*~[CH2]~*),$([R]1@[CH2;R]@[R]@[R]@[R]@[CH2;R]1),$(*~[CH2]~[R]1@[R]@[R]@[CH2;R]1),$(*~[CH2]~*~[R]1@[R]@[CH2;R]1)]',0), # ACH2AAACH2A
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158 129:('[$(*~[CH2]~*~*~[CH2]~*),$([R]1@[CH2]@[R]@[R]@[CH2;R]1),$(*~[CH2]~[R]1@[R]@[CH2;R]1)]',0), # ACH2AACH2A
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159 130:('[!#6;!#1]~[!#6;!#1]',1), # QQ > 1 (&...) FIX: incomplete definition
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160 131:('[!#6;!#1;!H0]',1), # QH > 1
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161 132:('[#8]~*~[CH2]~*',0), # OACH2A
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162 133:('*@*!@[#7]',0), # A$A!N
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163 134:('[F,Cl,Br,I]',0), # X (HALOGEN)
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164 135:('[#7]!:*:*',0), # Nnot%A%A
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165 136:('[#8]=*',1), # O=A>1
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166 137:('[!C;!c;R]',0), # Heterocycle
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167 138:('[!#6;!#1]~[CH2]~*',1), # QCH2A>1 (&...) FIX: incomplete definition
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168 139:('[O;!H0]',0), # OH
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169 140:('[#8]',3), # O > 3 (&...) FIX: incomplete definition
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170 141:('[CH3]',2), # CH3 > 2 (&...) FIX: incomplete definition
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171 142:('[#7]',1), # N > 1
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172 143:('*@*!@[#8]',0), # A$A!O
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173 144:('*!:*:*!:*',0), # Anot%A%Anot%A
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174 145:('*1~*~*~*~*~*~1',1), # 6M ring > 1
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175 146:('[#8]',2), # O > 2
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176 147:('[$(*~[CH2]~[CH2]~*),$([R]1@[CH2;R]@[CH2;R]1)]',0), # ACH2CH2A
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177 148:('*~[!#6;!#1](~*)~*',0), # AQ(A)A
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178 149:('[C;H3,H4]',1), # CH3 > 1
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179 150:('*!@*@*!@*',0), # A!A$A!A
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180 151:('[#7;!H0]',0), # NH
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181 152:('[#8]~[#6](~[#6])~[#6]',0), # OC(C)C
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182 153:('[!#6;!#1]~[CH2]~*',0), # QCH2A
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183 154:('[#6]=[#8]',0), # C=O
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184 155:('*!@[CH2]!@*',0), # A!CH2!A
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185 156:('[#7]~*(~*)~*',0), # NA(A)A
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186 157:('[#6]-[#8]',0), # C-O
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187 158:('[#6]-[#7]',0), # C-N
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188 159:('[#8]',1), # O>1
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189 160:('[C;H3,H4]',0), #CH3
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190 161:('[#7]',0), # N
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191 162:('a',0), # Aromatic
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192 163:('*1~*~*~*~*~*~1',0), # 6M Ring
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193 164:('[#8]',0), # O
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194 165:('[R]',0), # Ring
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195 166:('?',0), # Fragments FIX: this can't be done in SMARTS
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196
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197 # obabel -:"CNO" -oftp -xs
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198 # 24: N-O 68: QHQH (&...) 69: QQH 71: NO 93: QCH3 94: QN 102: QO
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199 # 124: QQ 131: QH > 1 *2 139: OH 151: NH 158: C-N 160: CH3 161: N 164: O
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