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date Fri, 02 Sep 2011 08:48:21 -0400
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#Comments after SMARTS
# Extracted from RDKit Jul 2008 release (r747) Python/Chem/MACCSKeys.py
#
# Copyright (C) 2001-2006 greg Landrum and Rational Discovery LLC
#
#   @@ All Rights Reserved  @@
#
#Redistribution and use in source and binary forms, with or without
#modification, are permitted provided that the following conditions are
#met: 
#
#    * Redistributions of source code must retain the above copyright 
#      notice, this list of conditions and the following disclaimer.
#    * Redistributions in binary form must reproduce the above
#      copyright notice, this list of conditions and the following 
#      disclaimer in the documentation and/or other materials provided 
#      with the distribution.
#    * Neither the name of Rational Discovery nor the names of its 
#      contributors may be used to endorse or promote products derived 
#      from this software without specific prior written permission.
#
#THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
#"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
#LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
#A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
#OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
#SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
#LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
#DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
#THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
#(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
#OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

# 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:('[!C;!c;!#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 *NOTE* Was '*1~*~*~*~1' This and 9 others changed by CM because OB didn't like it
  12:('[Cu,Zn,Ag,Cd,Au,Hg]',0), # Group IB,IIB (Cu..)
  13:('[O,o]~[N,n](~[C,c])~[C,c]',0), # ON(C)C
  14:('[S,s]-[S,s]',0), # S-S
  15:('[O,o]~[C,c](~[O,o])~[O,o]',0), # OC(O)O
  16:('[!C;!c;!#1]1~*~*~*1',0), # QAA@1
  17:('[C,c]#[C,c]',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:('[C,c]=[C,c](~[!C;!c;!#1])~[!C;!c;!#1]',0), # C=C(Q)Q
  22:('*1~*~*~*1',0), # 3M Ring
  23:('[N,n]~[C,c](~[O,o])~[O,o]',0), # NC(O)O
  24:('[N,n]-[O,o]',0), # N-O
  25:('[N,n]~[C,c](~[N,n])~[N,n]',0), # NC(N)N
  26:('[C,c]=;@[C,c](@*)@*',0), # C$=C($A)$A
  27:('[I]',0), # I
  28:('[!C;!c;!#1]~[CH2]~[!C;!c;!#1]',0), # QCH2Q
  29:('P',0),# P
  30:('[C,c]~[!C;!c;!#1](~[C,c])(~[C,c])~*',0), # CQ(C)(C)A
  31:('[!C;!c;!#1]~[F,Cl,Br,I]',0), # QX
  32:('[C,c]~[S,s]~[N,n]',0), # CSN
  33:('[N,n]~[S,s]',0), # NS
  34:('[CH2]=*',0), # CH2=A
  35:('[Li,Na,K,Rb,Cs,Fr]',0), # Group IA (Alkali Metal)
  36:('[$(S@*),$(s@*)]',0), # S Heterocycle
  37:('[N,n]~[C,c](~[O,o])~[N,n]',0), # NC(O)N
  38:('[N,n]~[C,c](~[C,c])~[N,n]',0), # NC(C)N
  39:('[O,o]~[S,s](~[O,o])~[O,o]',0), # OS(O)O
  40:('[S,s]-[O,o]',0), # S-O
  41:('[C,c]#[N,n]',0), # CTN
  42:('F',0), # F
  43:('[!C;!c;!#1;H,H2,H3,H4]~*~[!C;!c;!#1;H,H2,H3,H4]',0), # QHAQH FIX: possibly incomplete
  44:('?',0), # OTHER
  45:('[C,c]=[C,c]~[N,n]',0), # C=CN
  46:('Br',0), # BR
  47:('[S,s]~*~[N,n]',0), # SAN
  48:('[O,o]~[!C;!c;!#1](~[O,o])(~[O,o])~*',0), # OQ(O)O
  49:('[-,-2,-3,-4,+,+2,+3,+4]',0), # CHARGE  FIX: possibly incomplete
  50:('[C,c]=[C,c](~[C,c])~[C,c]',0), # C=C(C)C
  51:('[C,c]~[S,s]~[O,o]',0), # CSO
  52:('[N,n]~[N,n]',0), # NN
  53:('[!#6;!#1;!H0]~*~*~*~[!#6;!#1;!H0]',0), # QHAAAQH FIX: possibly incomplete
  54:('[!#6;!#1;!H0]~*~*~[!#6;!#1;!H0]',0), # QHAAQH FIX: possibly incomplete
  55:('[O,o]~[S,s]~[O,o]',0), #OSO
  56:('[O,o]~[N,n](~[O,o])~[C,c]',0), # ON(O)C
  57:('[$(O@*),$(o@*)]',0), # O Heterocycle
  58:('[!C;!c;!#1]~[S,s]~[!C;!c;!#1]',0), # QSQ
  59:('[S,s]!:*:*',0), # Snot%A%A
  60:('[S,s]=[O,o]',0), # S=O
  61:('*~[S,s](~*)~*',0), # AS(A)A
  62:('*@*!@*@*',0), # A$!A$A
  63:('[N,n]=[O,o]',0), # N=O
  64:('*@*!@[S,s]',0), # A$A!S
  65:('[C,c]:[N,n]',0), # C%N
  66:('[C,c]~[C,c](~[C,c])(~[C,c])~*',0), # CC(C)(C)A
  67:('[!C;!c;!#1]~[S,s]',0), # QS
  68:('[!#6;!#1;!H0]~[!#6;!#1;!H0]',0), # QHQH FIX: possibly incomplete
  69:('[!C;!c;!#1]~[!#6;!#1;!H0]',0), # QQH FIX: possibly incomplete
  70:('[!C;!c;!#1]~[N,n]~[!C;!c;!#1]',0), # QNQ
  71:('[N,n]~[O,o]',0), # NO
  72:('[O,o]~*~*~[O,o]',0), # OAAO
  73:('[S,s]=*',0), # S=A
  74:('[CH3]~*~[CH3]',0), # CH3ACH3
  75:('*!@[N,n]@*',0), # A!N$A
  76:('[C,c]=[C,c](~*)~*',0), # C=C(A)A
  77:('[N,n]~*~[N,n]',0), # NAN
  78:('[C,c]=[N,n]',0), # C=N
  79:('[N,n]~*~*~[N,n]',0), # NAAN
  80:('[N,n]~*~*~*~[N,n]',0), # NAAAN
  81:('[S,s]~*(~*)~*',0), # SA(A)A
  82:('*~[CH2]~[!#6;!#1;!H0]',0), # ACH2QH
  83:('[!C;!c;!#1]1~*~*~*~*~*1',0), # QAAAA@1
  84:('[NH2]',0), #NH2
  85:('[C,c]~[N,n](~[C,c])~[C,c]',0), # CN(C)C
  86:('[CH2][!C;!c;!#1][CH2]',0), # CH2QCH2
  87:('[F,Cl,Br,I]!@*@*',0), # X!A$A
  88:('[S,s]',0), # S
  89:('[O,o]~*~*~*~[O,o]',0), # OAAAO
  90:('[!#6;!#1;!H0]~*~*~[CH2]~*',0), # QHAACH2A
  91:('[!#6;!#1;!H0]~*~*~*~[CH2]~*',0), # QHAAACH2A
  92:('[O,o]~[C,c](~[N,n])~[C,c]',0), # OC(N)C
  93:('[!C;!c;!#1]~[CH3]',0), # QCH3
  94:('[!C;!c;!#1]~[N,n]',0), # QN
  95:('[N,n]~*~*~[O,o]',0), # NAAO
  96:('*1~*~*~*~*~*1',0), # 5 M ring
  97:('[N,n]~*~*~*~[O,o]',0), # NAAAO
  98:('[!C;!c;!#1]1~*~*~*~*~*~*1',0), # QAAAAA@1
  99:('[C,c]=[C,c]',0), # C=C
  100:('*~[CH2]~[N,n]',0), # ACH2N
  101:('[r8,r9,r10,r11,r12]',0), # 8M Ring or larger FIX: This is not exhaustive and it appears that oelib doesn't do this right
  102:('[!C;!c;!#1]~[O,o]',0), # QO
  103:('Cl',0), # CL
  104:('[!#6;!#1;!H0]~*~[CH2]~*',0), # QHACH2A
  105:('[!C;!c;!#1]@*(@*)@*',0), # A$A($A)$A
  106:('[!C;!c;!#1]~*(~[!C;!c;!#1])~[!C;!c;!#1]',0), # QA(Q)Q
  107:('[F,Cl,Br,I]~*(~*)~*',0), # XA(A)A
  108:('[CH3]~*~*~*~[CH2]~*',0), # CH3AAACH2A
  109:('*~[CH2]~[O,o]',0), # ACH2O
  110:('[N,n]~[C,c]~[O,o]',0), # NCO
  111:('[N,n]~*~[CH2]~*',0), # NACH2A
  112:('*~*(~*)(~*)~*',0), # AA(A)(A)A
  113:('[O,o]!:*:*',0), # Onot%A%A
  114:('[CH3]~[CH2]~*',0), # CH3CH2A
  115:('[CH3]~*~[CH2]~*',0), # CH3ACH2A
  116:('[CH3]~*~*~[CH2]~*',0), # CH3AACH2A
  117:('[N,n]~*~[O,o]',0), # NAO
  118:('*~[CH2]~[CH2]~*',1), # ACH2CH2A > 1
  119:('[N,n]=*',0), # N=A
  120:('[!C;!c;R]',1), # Heterocyclic atom > 1
  121:('[$(N@*),$(n@*)]',0), # N Heterocycle
  122:('*~[N,n](~*)~*',0), # AN(A)A
  123:('[O,o]~[C,c]~[O,o]',0), # OCO
  124:('[!C;!c;!#1]~[!C;!c;!#1]',0), # QQ
  125:('?',0), # Aromatic Ring > 1
  126:('*!@[O,o]!@*',0), # A!O!A
  127:('*@*!@[O,o]',1), # A$A!O > 1
  128:('*~[CH2]~*~*~*~[CH2]~*',0), # ACH2AAACH2A
  129:('*~[CH2]~*~*~[CH2]~*',0), # ACH2AACH2A
  130:('[!C;!c;!#1]~[!C;!c;!#1]',1), # QQ > 1 (&...)
  131:('[!#6;!#1;!H0]',1), # QH > 1
  132:('[O,o]~*~[CH2]~*',0), # OACH2A
  133:('*@*!:[N,n]',0), # A$A!N
  134:('[F,Cl,Br,I]',0), # X (HALOGEN)
  135:('[N,n]!:*:*',0), # Nnot%A%A
  136:('[O,o]=*',1), # O=A>1 FIX: maybe not right key
  137:('[!C;!c;R]',0), # Heterocycle
  138:('[!C;!c;!#1]~[CH2]~*',1), # QCH2A>1 (&...)
  139:('[OH,OH2,OH3]',0), # OH
  140:('[O,o]',3), # O > 3
  141:('[CH3]',2), # CH3 > 2
  142:('[N,n]',1), # N > 1
  143:('*@*!@[O,o]',0), # A$A!O
  144:('*!:*:*!:*',0), # Anot%A%Anot%A
  145:('*1~*~*~*~*~*~*1',1), # 6M ring > 1
  146:('[O,o]',2), # O > 2
  147:('*~[CH2]~[CH2]~*',0), # ACH2CH2A
  148:('*~[!C;!c;!#1](~*)~*',0), # AQ(A)A
  149:('[CH3]',1), # CH3 > 1
  150:('*!@*@*!@*',0), # A!A$A!A
  151:('[N!H0]',0), # NH
  152:('[O,o]~[C,c](~[C,c])~[C,c]',0), # OC(C)C
  153:('[!C;!c;!#1]~[CH2]~*',0), # QCH2A
  154:('[C,c]=[O,o]',0), # C=O
  155:('*!@[CH2]!@*',0), # A!CH2!A
  156:('[N,n]~*(~*)~*',0), # NA(A)A
  157:('[C,c]-[O,o]',0), # C-O
  158:('[C,c]-[N,n]',0), # C-N
  159:('[O,o]',1), # O>1
  160:('[CH3]',0), #CH3
  161:('[N,n]',0), # N
  162:('a',0), # Aromatic
  163:('*1~*~*~*~*~*~*1',0), # 6M Ring
  164:('[O,o]',0), # O
  165:('[R]',0), # Ring
  166:('?',0), # Fragments  FIX: this should be (*).(*), but that doesn't work properly in oelib

# Output with SMILES "CNO"
#>	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