void constructBRICSAtomTypes(std::map<unsigned int,std::string> &defs,
std::map<unsigned int,ROMOL_SPTR> *environs){
/*
After some discussion, the L2 definitions ("N.pl3" in the original
paper) have been removed and incorporated into a (almost) general
purpose amine definition in L5 ("N.sp3" in the paper).
The problem is one of consistency.
Based on the original definitions you should get the following
fragmentations:
C1CCCCC1NC(=O)C -> C1CCCCC1N[2*].[1*]C(=O)C
c1ccccc1NC(=O)C -> c1ccccc1[16*].[2*]N[2*].[1*]C(=O)C
This difference just didn't make sense to us. By switching to
the unified definition we end up with:
C1CCCCC1NC(=O)C -> C1CCCCC1[15*].[5*]N[5*].[1*]C(=O)C
c1ccccc1NC(=O)C -> c1ccccc1[16*].[5*]N[5*].[1*]C(=O)C
*/
const std::string BRICSdefs="1 [C;D3]([#0,#6,#7,#8])(=O)\n\
3 [O;D2]-;!@[#0,#6,#1]\n\
5 [N;!D1;!$(N=*);!$(N-[!#6;!#16;!#0;!#1]);!$([N;R]@[C;R]=O)]\n\
9 [n;+0;$(n(:[c,n,o,s]):[c,n,o,s])]\n\
10 [N;R;$(N(@C(=O))@[C,N,O,S])]\n\
11 [S;D2](-;!@[#0,#6])\n\
12 [S;D4]([#6,#0])(=O)(=O)\n\
6 [C;D3;!R](=O)-;!@[#0,#6,#7,#8]\n\
13 [C;$(C(-;@[C,N,O,S])-;@[N,O,S])]\n\
14 [c;$(c(:[c,n,o,s]):[n,o,s])]\n\
15 [C;$(C(-;@C)-;@C)]\n\
4 [C;!D1;!$(C=*)]-;!@[#6]\n\
7 [C;D2,D3]-[#6]\n\
8 [C;!R;!D1;!$(C!-*)]\n\
16 [c;$(c(:c):c)]";
constructFragmenterAtomTypes(BRICSdefs,defs,"//",true,environs);
}
void constructFragmenterAtomTypes(
const std::string &str, std::map<unsigned int, std::string> &defs,
const std::string &comment, bool validate,
std::map<unsigned int, ROMOL_SPTR> *environs) {
std::stringstream istr(str);
constructFragmenterAtomTypes(&istr, defs, comment, validate, environs);
}
