Mercurial > repos > marcel > caddsuite_mac10_6
diff CADDSuite-1.0.1/data/OpenBabel/MACCS.txt @ 5:e30a41af9d2b
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| author | marcel |
|---|---|
| date | Tue, 15 Nov 2011 10:53:16 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite-1.0.1/data/OpenBabel/MACCS.txt Tue Nov 15 10:53:16 2011 -0500 @@ -0,0 +1,199 @@ +#Comments after SMARTS +# Extracted from RDKit r1553 Nov 2010 rdkit/Chem/MACCSKeys.py +# +# Copyright (C) 2001-2008 greg Landrum and Rational Discovery LLC +# +# @@ All Rights Reserved @@ +# This file is part of the RDKit. +# The contents are covered by the terms of the BSD license +# which is included in the file license.txt, found at the root +# of the RDKit source tree. +# +# SMARTS definitions for the publically available MACCS keys + +# I compared the MACCS fingerprints generated here with those from two +# other packages (not MDL, unfortunately). Of course there are +# disagreements between the various fingerprints still, but I think +# these definitions work pretty well. Some notes: + +# 1) most of the differences have to do with aromaticity +# 2) there's a discrepancy sometimes because the current RDKit +# definitions do not require multiple matches to be distinct. e.g. the +# SMILES C(=O)CC(=O) can match the (hypothetical) key O=CC twice in my +# definition. It's not clear to me what the correct behavior is. +# 3) Some keys are not fully defined in the MDL documentation +# 4) Two keys, 125 and 166, have to be done outside of SMARTS. +# 5) Key 1 (ISOTOPE) isn't defined + +# these are SMARTS patterns corresponding to the MDL MACCS keys + 1:('?',0), # ISOTOPE + #2:('[#103,#104,#105,#106,#107,#106,#109,#110,#111,#112]',0), # ISOTOPE Not complete + 2:('[#103,#104]',0), # ISOTOPE Not complete + 3:('[Ge,As,Se,Sn,Sb,Te,Tl,Pb,Bi]',0), # Group IVa,Va,VIa Periods 4-6 (Ge...) *NOTE* spec wrong + 4:('[Ac,Th,Pa,U,Np,Pu,Am,Cm,Bk,Cf,Es,Fm,Md,No,Lr]',0), # actinide + 5:('[Sc,Ti,Y,Zr,Hf]',0), # Group IIIB,IVB (Sc...) *NOTE* spec wrong + 6:('[La,Ce,Pr,Nd,Pm,Sm,Eu,Gd,Tb,Dy,Ho,Er,Tm,Yb,Lu]',0), # Lanthanide + 7:('[V,Cr,Mn,Nb,Mo,Tc,Ta,W,Re]',0), # Group VB,VIB,VIIB (V...) *NOTE* spec wrong + 8:('[!#6;!#1]1~*~*~*~1',0), # QAAA@1 + 9:('[Fe,Co,Ni,Ru,Rh,Pd,Os,Ir,Pt]',0), # Group VIII (Fe...) + 10:('[Be,Mg,Ca,Sr,Ba,Ra]',0), # Group IIa (Alkaline earth) + 11:('*1~*~*~*~1',0), # 4M Ring + 12:('[Cu,Zn,Ag,Cd,Au,Hg]',0), # Group IB,IIB (Cu..) + 13:('[#8]~[#7](~[#6])~[#6]',0), # ON(C)C + 14:('[#16]-[#16]',0), # S-S + 15:('[#8]~[#6](~[#8])~[#8]',0), # OC(O)O + 16:('[!#6;!#1]1~*~*~1',0), # QAA@1 + 17:('[#6]#[#6]',0), #CTC + 18:('[B,Al,Ga,In,Tl]',0), # Group IIIA (B...) *NOTE* spec wrong + 19:('*1~*~*~*~*~*~*~1',0), # 7M Ring + 20:('[Si]',0), #Si + 21:('[#6]=[#6](~[!#6;!#1])~[!#6;!#1]',0), # C=C(Q)Q + 22:('*1~*~*~1',0), # 3M Ring + 23:('[#7]~[#6](~[#8])~[#8]',0), # NC(O)O + 24:('[#7]-[#8]',0), # N-O + 25:('[#7]~[#6](~[#7])~[#7]',0), # NC(N)N + 26:('[#6]=;@[#6](@*)@*',0), # C$=C($A)$A + 27:('[I]',0), # I + 28:('[!#6;!#1]~[CH2]~[!#6;!#1]',0), # QCH2Q + 29:('[#15]',0),# P + 30:('[#6]~[!#6;!#1](~[#6])(~[#6])~*',0), # CQ(C)(C)A + 31:('[!#6;!#1]~[F,Cl,Br,I]',0), # QX + 32:('[#6]~[#16]~[#7]',0), # CSN + 33:('[#7]~[#16]',0), # NS + 34:('[CH2]=*',0), # CH2=A + 35:('[Li,Na,K,Rb,Cs,Fr]',0), # Group IA (Alkali Metal) + 36:('[#16R]',0), # S Heterocycle + 37:('[#7]~[#6](~[#8])~[#7]',0), # NC(O)N + 38:('[#7]~[#6](~[#6])~[#7]',0), # NC(C)N + 39:('[#8]~[#16](~[#8])~[#8]',0), # OS(O)O + 40:('[#16]-[#8]',0), # S-O + 41:('[#6]#[#7]',0), # CTN + 42:('F',0), # F + 43:('[!C;!c;!#1;!H0]~*~[!C;!c;!#1;!H0]',0), # QHAQH + 44:('?',0), # OTHER + 45:('[#6]=[#6]~[#7]',0), # C=CN + 46:('Br',0), # BR + 47:('[#16]~*~[#7]',0), # SAN + 48:('[#8]~[!#6;!#1](~[#8])(~[#8])',0), # OQ(O)O + 49:('[!+0]',0), # CHARGE + 50:('[#6]=[#6](~[#6])~[#6]',0), # C=C(C)C + 51:('[#6]~[#16]~[#8]',0), # CSO + 52:('[#7]~[#7]',0), # NN + 53:('[!#6;!#1;!H0]~*~*~*~[!#6;!#1;!H0]',0), # QHAAAQH + 54:('[!#6;!#1;!H0]~*~*~[!#6;!#1;!H0]',0), # QHAAQH + 55:('[#8]~[#16]~[#8]',0), #OSO + 56:('[#8]~[#7](~[#8])~[#6]',0), # ON(O)C + 57:('[#8R]',0), # O Heterocycle + 58:('[!#6;!#1]~[#16]~[!#6;!#1]',0), # QSQ + 59:('[#16]!:*:*',0), # Snot%A%A + 60:('[#16]=[#8]',0), # S=O + 61:('*~[#16](~*)~*',0), # AS(A)A + 62:('*@*!@*@*',0), # A$!A$A + 63:('[#7]=[#8]',0), # N=O + 64:('*@*!@[#16]',0), # A$A!S + 65:('c:n',0), # C%N + 66:('[#6]~[#6](~[#6])(~[#6])~*',0), # CC(C)(C)A + 67:('[!#6;!#1]~[#16]',0), # QS + 68:('[!#6;!#1;!H0]~[!#6;!#1;!H0]',0), # QHQH (&...) FIX: incomplete definition + 69:('[!#6;!#1]~[!#6;!#1;!H0]',0), # QQH + 70:('[!#6;!#1]~[#7]~[!#6;!#1]',0), # QNQ + 71:('[#7]~[#8]',0), # NO + 72:('[#8]~*~*~[#8]',0), # OAAO + 73:('[#16]=*',0), # S=A + 74:('[CH3]~*~[CH3]',0), # CH3ACH3 + 75:('*!@[#7]@*',0), # A!N$A + 76:('[#6]=[#6](~*)~*',0), # C=C(A)A + 77:('[#7]~*~[#7]',0), # NAN + 78:('[#6]=[#7]',0), # C=N + 79:('[#7]~*~*~[#7]',0), # NAAN + 80:('[#7]~*~*~*~[#7]',0), # NAAAN + 81:('[#16]~*(~*)~*',0), # SA(A)A + 82:('*~[CH2]~[!#6;!#1;!H0]',0), # ACH2QH + 83:('[!#6;!#1]1~*~*~*~*~1',0), # QAAAA@1 + 84:('[NH2]',0), #NH2 + 85:('[#6]~[#7](~[#6])~[#6]',0), # CN(C)C + 86:('[C;H2,H3][!#6;!#1][C;H2,H3]',0), # CH2QCH2 + 87:('[F,Cl,Br,I]!@*@*',0), # X!A$A + 88:('[#16]',0), # S + 89:('[#8]~*~*~*~[#8]',0), # OAAAO + 90:('[$([!#6;!#1;!H0]~*~*~[CH2]~*),$([!#6;!#1;!H0;R]1@[R]@[R]@[CH2;R]1),$([!#6;!#1;!H0]~[R]1@[R]@[CH2;R]1)]',0), # QHAACH2A + 91:('[$([!#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),$([!#6;!#1;!H0]~*~[R]1@[R]@[CH2;R]1)]',0), # QHAAACH2A + 92:('[#8]~[#6](~[#7])~[#6]',0), # OC(N)C + 93:('[!#6;!#1]~[CH3]',0), # QCH3 + 94:('[!#6;!#1]~[#7]',0), # QN + 95:('[#7]~*~*~[#8]',0), # NAAO + 96:('*1~*~*~*~*~1',0), # 5 M ring + 97:('[#7]~*~*~*~[#8]',0), # NAAAO + 98:('[!#6;!#1]1~*~*~*~*~*~1',0), # QAAAAA@1 + 99:('[#6]=[#6]',0), # C=C + 100:('*~[CH2]~[#7]',0), # ACH2N + 101:('[$([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 + 102:('[!#6;!#1]~[#8]',0), # QO + 103:('Cl',0), # CL + 104:('[!#6;!#1;!H0]~*~[CH2]~*',0), # QHACH2A + 105:('*@*(@*)@*',0), # A$A($A)$A + 106:('[!#6;!#1]~*(~[!#6;!#1])~[!#6;!#1]',0), # QA(Q)Q + 107:('[F,Cl,Br,I]~*(~*)~*',0), # XA(A)A + 108:('[CH3]~*~*~*~[CH2]~*',0), # CH3AAACH2A + 109:('*~[CH2]~[#8]',0), # ACH2O + 110:('[#7]~[#6]~[#8]',0), # NCO + 111:('[#7]~*~[CH2]~*',0), # NACH2A + 112:('*~*(~*)(~*)~*',0), # AA(A)(A)A + 113:('[#8]!:*:*',0), # Onot%A%A + 114:('[CH3]~[CH2]~*',0), # CH3CH2A + 115:('[CH3]~*~[CH2]~*',0), # CH3ACH2A + 116:('[$([CH3]~*~*~[CH2]~*),$([CH3]~*1~*~[CH2]1)]',0), # CH3AACH2A + 117:('[#7]~*~[#8]',0), # NAO + 118:('[$(*~[CH2]~[CH2]~*),$(*1~[CH2]~[CH2]1)]',1), # ACH2CH2A > 1 + 119:('[#7]=*',0), # N=A + 120:('[!#6;R]',1), # Heterocyclic atom > 1 (&...) FIX: incomplete definition + 121:('[#7;R]',0), # N Heterocycle + 122:('*~[#7](~*)~*',0), # AN(A)A + 123:('[#8]~[#6]~[#8]',0), # OCO + 124:('[!#6;!#1]~[!#6;!#1]',0), # QQ + 125:('?',0), # Aromatic Ring > 1 + 126:('*!@[#8]!@*',0), # A!O!A + 127:('*@*!@[#8]',1), # A$A!O > 1 (&...) FIX: incomplete definition + 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 + 129:('[$(*~[CH2]~*~*~[CH2]~*),$([R]1@[CH2]@[R]@[R]@[CH2;R]1),$(*~[CH2]~[R]1@[R]@[CH2;R]1)]',0), # ACH2AACH2A + 130:('[!#6;!#1]~[!#6;!#1]',1), # QQ > 1 (&...) FIX: incomplete definition + 131:('[!#6;!#1;!H0]',1), # QH > 1 + 132:('[#8]~*~[CH2]~*',0), # OACH2A + 133:('*@*!@[#7]',0), # A$A!N + 134:('[F,Cl,Br,I]',0), # X (HALOGEN) + 135:('[#7]!:*:*',0), # Nnot%A%A + 136:('[#8]=*',1), # O=A>1 + 137:('[!C;!c;R]',0), # Heterocycle + 138:('[!#6;!#1]~[CH2]~*',1), # QCH2A>1 (&...) FIX: incomplete definition + 139:('[O;!H0]',0), # OH + 140:('[#8]',3), # O > 3 (&...) FIX: incomplete definition + 141:('[CH3]',2), # CH3 > 2 (&...) FIX: incomplete definition + 142:('[#7]',1), # N > 1 + 143:('*@*!@[#8]',0), # A$A!O + 144:('*!:*:*!:*',0), # Anot%A%Anot%A + 145:('*1~*~*~*~*~*~1',1), # 6M ring > 1 + 146:('[#8]',2), # O > 2 + 147:('[$(*~[CH2]~[CH2]~*),$([R]1@[CH2;R]@[CH2;R]1)]',0), # ACH2CH2A + 148:('*~[!#6;!#1](~*)~*',0), # AQ(A)A + 149:('[C;H3,H4]',1), # CH3 > 1 + 150:('*!@*@*!@*',0), # A!A$A!A + 151:('[#7;!H0]',0), # NH + 152:('[#8]~[#6](~[#6])~[#6]',0), # OC(C)C + 153:('[!#6;!#1]~[CH2]~*',0), # QCH2A + 154:('[#6]=[#8]',0), # C=O + 155:('*!@[CH2]!@*',0), # A!CH2!A + 156:('[#7]~*(~*)~*',0), # NA(A)A + 157:('[#6]-[#8]',0), # C-O + 158:('[#6]-[#7]',0), # C-N + 159:('[#8]',1), # O>1 + 160:('[C;H3,H4]',0), #CH3 + 161:('[#7]',0), # N + 162:('a',0), # Aromatic + 163:('*1~*~*~*~*~*~1',0), # 6M Ring + 164:('[#8]',0), # O + 165:('[R]',0), # Ring + 166:('?',0), # Fragments FIX: this can't be done in SMARTS + +# obabel -:"CNO" -oftp -xs +# 24: N-O 68: QHQH (&...) 69: QQH 71: NO 93: QCH3 94: QN 102: QO +# 124: QQ 131: QH > 1 *2 139: OH 151: NH 158: C-N 160: CH3 161: N 164: O