Notes.txt

The RDKit was not able to parse some of the SMARTS in the structural_alerts table in ChEMBL.  I modified the SMARTS so that
the patterns could be parsed.  I'm pretty sure I didn't alter the original intent of the SMARTS.  This document lists the
changes I made and why I made them.  Each record consists of
* The rule number
* The original SMARTS
* The reason the RDKit couldn't parse the SMARTS
* My new version of the SMARTS
The file alert_collection.csv contains the edited SMARTS where applicable.

rule 194
[F,Cl,Br,I,$(O(S(=O)(=O)))]-[CH,CH2;!$(CF2)]-[N,n]
As Andrew Dalke pointed out, CF2 should actually be C(F)F
[F,Cl,Br,I,$(O(S(=O)(=O)))]-[CH,CH2;!$(C(F)F)]-[N,n]


rule 196
Parse Error: unclosed ring for input: '[N,n,O,S;!$(S(=O)(=O))]-[CH,CH2;!$(CF2)][F,Cl,Br,I,$(O(S(=O)(=O)))]'
The RDKit isn't happy when CF2 is not in brackets make it [CF2]
[N,n,O,S;!$(S(=O)(=O))]-[CH,CH2;!$([CF2])][F,Cl,Br,I,$(O(S(=O)(=O)))]

rule 245
SMARTS Parse Error: unclosed ring for input: '[CH2,$(CF2);R0][CH2,$(CF2);R0][CH2,$(CF2);R0][CH2,$(CF2);R0][CH2,$(CF2);R0][CH2,$(CF2);R0][CH2,$(CF2);R0][CH2,$(CF2);R0]'
The RDKit isn't happy when CF2 is not in brackets make it [CF2]
[CH2,$([CF2]);R0][CH2,$([CF2]);R0][CH2,$([CF2]);R0][CH2,$([CF2]);R0][CH2,$([CF2]);R0][CH2,$([CF2]);R0][CH2,$([CF2]);R0][CH2,$([CF2]);R0]

rule 339
[17:05:35] SMARTS Parse Error: syntax error for input: '[[CH;!R];!$(C-N)]=C([$(S(=O)(=O)),$(C(F)(F)(F)),$(C#N),$(N(=O)(=O)),$([N+](=O)[O-]),$(C(=O))])([$(S(=O)(=O)),$(C(F)(F)(F)),$(C#N),$(N(=O)(=O)),$([N+](=O)[O-]),$(C(=O))])'
Remove unnecessary square breackets at the beginning on [CH;!R]
[CH;!R;!$(C-N)]=C([$(S(=O)(=O)),$(C(F)(F)(F)),$(C#N),$(N(=O)(=O)),$([N+](=O)[O-]),$(C(=O))])([$(S(=O)(=O)),$(C(F)(F)(F)),$(C#N),$(N(=O)(=O)),$([N+](=O)[O-]),$(C(=O))])

rule 983
SMARTS Parse Error: syntax error for input: '[2H,3H,11C,11c,14C,14c,125I,32P,33P,35S]'
Versions of the RDKit prior to 2018-06 could not handle deuterium as [2H] or tritium as [3H] changed to [2#1] and [3#1]
[2#1,3#1,11C,11c,14C,14c,125I,32P,33P,35S]

rule 1040
SMARTS Parse Error: syntax error for input: '[N,C,S,O]-&!@[N,C,S,O]&!@[N,C,S,O]&!@[N,C,S,O]&!@[N,C,S,O]&!@[N,C,S,O]&!@[N,C,S,O]'
The RDKit doesn't like implict bond orders when specifying non-ring bonds e.g. "&!@" replace with "-&!@"
[N,C,S,O]-&!@[N,C,S,O]-&!@[N,C,S,O]-&!@[N,C,S,O]-&!@[N,C,S,O]-&!@[N,C,S,O]-&!@[N,C,S,O]

rule 1053
SMARTS Parse Error: syntax error for input: 'ac-*=&!@*-&!@C(=O)&!@ca'
The RDKit doesn't like implict bond orders when specifying non-ring bonds e.g. "&!@" replace with "-&!@"
ac-*=&!@*-&!@C(=O)-&!@ca

rule 1072
SMARTS Parse Error: syntax error for input: '[#6,#7]&!@[#6](=&!@[CH])&!@C(=O)-&!@[C,N,O,S]'
The RDKit doesn't like implict bond orders when specifying non-ring bonds e.g. "&!@" replace with "-&!@"
[#6,#7]-&!@[#6](=&!@[CH])-&!@C(=O)-&!@[C,N,O,S]

rule 1079
SMARTS Parse Error: syntax error for input: '*-C(=O)-&!@[NH]-C&!@C(=O)-&!@[NH]-*'
The RDKit doesn't like implict bond orders when specifying non-ring bonds e.g. "&!@" replace with "-&!@"
*-C(=O)-&!@[NH]-C-&!@C(=O)-&!@[NH]-*

rule 1085
SMARTS Parse Error: syntax error for input: '([#6]OP(=O)(*)O[#6].[#6]OP(=O)(*)O[#6].[#6]OP(=O)(*)O[#6])'
Removed unnecessary leading and trailing parens
[#6]OP(=O)(*)O[#6].[#6]OP(=O)(*)O[#6].[#6]OP(=O)(*)O[#6]

rule 1092
SMARTS Parse Error: syntax error for input: 'c12cccc(C(=O)N(&!@C)C(=O)3)c2c3ccc1'
The RDKit doesn't like implict bond orders when specifying non-ring bonds e.g. "&!@" replace with "-&!@"
c12cccc(C(=O)N(-&!@C)C(=O)3)c2c3ccc1

rule 1137
[2H,3H,13C,14C,15N,125I,23F,22Na,32P,33P,35S,45Ca,57Co,103Ru,141Ce]
Versions of the RDKit prior to 2018-06 could not handle deuterium as [2H] or tritium as [3H] changed to [2#1] and [3#1]
[2#1,3#1,13C,14C,15N,125I,23F,22Na,32P,33P,35S,45Ca,57Co,103Ru,141Ce]

rule 1140
SMARTS Parse Error: syntax error for input: 'Si~O'
The RDKit can't handle silicon with out brackets change to [Si]
[Si]~O