On 06/11/2010 16:12, Andrew Dalke wrote:
Hi all,
I've found some rather serious problems in the OB MACCS definitions in the
2.3 release.
I'm working more on my fingerprint generation codes, in preparation for my
poster at the GCC conference in Goslar. In order to test the bit order, I
constructed SMILES strings designed to hit specific bits in the MACCS keys.
The test case "C1CCC1" should produce a "1" at position 11 (bit 10 if you
count from 0). RDKit and OEChem both do this, but OpenBabel does not. I looked up the OB's pattern
definition and found:
11:('*1~*~*~*~*1',0), # 4M Ring *NOTE* Was '*1~*~*~*~1' This and 9 others
changed by CM because OB didn't like it
This pattern is incorrect. It matches a 5-membered ring. I tested the MACCS fingerprint
with the 5 membered ring "C1CCCC1" and sure enough, OB gives a 1 for position
11.
With the 4-membered ring C1CCC1 I see that OB sets position 22 (bit 21) to 1,
when it should be 0. Here's the OB SMARTS definition for that position
22:('*1~*~*~*1',0), # 3M Ring
Here's the corresponding line from rdkit/Chem/MACCSkeys.py
22:('*1~*~*~1',0), # 3M Ring
You can see that here also the modified OB definition is looking for one too
many atoms.
I haven't done a full analysis of which other bits are incorrect in this way,
but what I've found is enough to say that people shouldn't use OB's MACCS
definitions until they've been reviewed and fixed.
Andrew
Thanks for raising this.
I have updated the data file MACCS.txt from the RDKit trunk and the
SMARTS patterns are now exactly the same.
The data file with corrected data is attached and can just replace the
original in OpenBabel v2.3.0 and earlier.
Although the modifications were rather unintelligently carried out,
they were originally necessary because the OB's SMARTS parser required
a ring digit to follow an atom, but it seems that now it can follow a
bond.
Chris
#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), # q...@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), # q...@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$A
76:('[#6]=[#6](~*)~*',0), # C=C(A)A
77:('[#7]~*~[#7]',0), # NAN
78:('[#6]=[#7]',0), # C=N
79:('[#7]~*~*~[#7]',0), # NAAN
80:('[#7]~*~*~*~[#7]',0), # NAAAN
81:('[#16]~*(~*)~*',0), # SA(A)A
82:('*~[CH2]~[!#6;!#1;!H0]',0), # ACH2QH
83:('[!#6;!#1]1~*~*~*~*~1',0), # qa...@1
84:('[NH2]',0), #NH2
85:('[#6]~[#7](~[#6])~[#6]',0), # CN(C)C
86:('[C;H2,H3][!#6;!#1][C;H2,H3]',0), # CH2QCH2
87:('[F,Cl,Br,i...@*@*',0), # X!A$A
88:('[#16]',0), # S
89:('[#8]~*~*~*~[#8]',0), # OAAAO
90:('[$([!#6;!#1;!H0]~*~*~[CH2]~*),$([!#6;!#1;!H0;r...@[r]@[...@[ch2;R]1),$([!#6;!#1;!h0]~[...@[r]@[CH2;R]1)]',0),
# QHAACH2A
91:('[$([!#6;!#1;!H0]~*~*~*~[CH2]~*),$([!#6;!#1;!H0;r...@[r]@[...@[r]@[CH2;R]1),$([!#6;!#1;!h0]~[...@[r]@[...@[ch2;R]1),$([!#6;!#1;!h0]~*~[...@[r]@[CH2;R]1)]',0),
# QHAAACH2A
92:('[#8]~[#6](~[#7])~[#6]',0), # OC(N)C
93:('[!#6;!#1]~[CH3]',0), # QCH3
94:('[!#6;!#1]~[#7]',0), # QN
95:('[#7]~*~*~[#8]',0), # NAAO
96:('*1~*~*~*~*~1',0), # 5 M ring
97:('[#7]~*~*~*~[#8]',0), # NAAAO
98:('[!#6;!#1]1~*~*~*~*~*~1',0), # qaa...@1
99:('[#6]=[#6]',0), # C=C
100:('*~[CH2]~[#7]',0), # ACH2N
101:('[$([...@1@[...@[r]@[...@[r]@[...@[r]@[R]1),$([...@1@[...@[r]@[...@[r]@[...@[r]@[...@[r]1),$([...@1@[...@[r]@[...@[r]@[...@[r]@[...@[r]@[R]1),$([...@1@[...@[r]@[...@[r]@[...@[r]@[...@[r]@[...@[r]1),$([...@1@[...@[r]@[...@[r]@[...@[r]@[...@[r]@[...@[r]@[R]1),$([...@1@[...@[r]@[...@[r]@[...@[r]@[...@[r]@[...@[r]@[...@[r]1),$([...@1@[...@[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:('[$(*~[CH2]~*~*~*~[CH2]~*),$([...@[ch2;r...@[r]@[...@[r]@[CH2;R]1),$(*~[ch2]~[...@[r]@[...@[ch2;R]1),$(*~[ch2]~*~[...@[r]@[CH2;R]1)]',0),
# ACH2AAACH2A
129:('[$(*~[CH2]~*~*~[CH2]~*),$([...@[ch2]@[...@[r]@[CH2;R]1),$(*~[ch2]~[...@[r]@[CH2;R]1)]',0),
# ACH2AACH2A
130:('[!#6;!#1]~[!#6;!#1]',1), # QQ > 1 (&...) FIX: incomplete definition
131:('[!#6;!#1;!H0]',1), # QH > 1
132:('[#8]~*~[CH2]~*',0), # OACH2A
133:('*...@*!@[#7]',0), # A$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]~*),$([...@[ch2;r...@[ch2;R]1)]',0), # ACH2CH2A
148:('*~[!#6;!#1](~*)~*',0), # AQ(A)A
149:('[C;H3,H4]',1), # CH3 > 1
150:('*...@*@*...@*',0), # A!A$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
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