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#include <BALL/STRUCTURE/logP.h>
using namespace std;
namespace BALL
{
LogP::LogP()
{
molecular_similarity_ = new MolecularSimilarity("fragments/functionalGroups.smarts");
addRule("[$([CH4]),$([CH3]C),$([CH2](C)C)]",0.14441); // C1
addRule("[$([CH](C)(C)C),$([C](C)(C)(C)C)]",0.00000); // C2
addRule("[$([CH3][#7,#8,#15,#16,#9,Cl,Br,I]),$([CH2X4][#7,#8,#15,#16,#9,Cl,Br,I])]",-0.2035); // C3
addRule("[$([CH1X4][#7,#8,#15,#16,#9,Cl,Br,I]),$([CH0X4][#7,#8,#15,#16,#9,Cl,Br,I])]",-0.2051); // C4
addRule("[C]=[A;!#1;!#6]",-0.2783); // C5, ali. heteroatom
addRule("[$([CH2]=C),$([CH1](=C)A),$([CH0](=C)(A)A),$([C](=C)=C)]",0.1551); // C6
addRule("[CX2]#A",0.00170); // C7
addRule("[CH3]c",0.08452); // C8
addRule("[CH3][a;!#1;!#6]",-0.1444); // C9, aro. heteroatom
addRule("[CH2X4]a",-0.0516); // C10
addRule("[CHX4]a",0.1193); // C11
addRule("[CH0X4]a",-0.0967); // C12
addRule("[cH0]-[!#6;!#7;!#8;!#16;!#9;!Cl;!Br;!I]",-0.5443); // C13
//"[$([c][#5],$([c][#14]),$([c][#15]),$([c][#33]),$([c][#34]),$([c][#50]),$([c][#80])]" // C13 alternative
addRule("[c][#9]",0.0000); // C14
addRule("[c][#17]",0.2450); // C15
addRule("[c][#35]",0.1980); // C16
addRule("[c][#53]",0.0000); // C17
addRule("[cH]",0.1581); // C18
addRule("[c](:a)(:a):a",0.2955); // C19
addRule("[c](:a)(:a)-a",0.2713); // C20
addRule("[c](:a)(:a)-C",0.1360); // C21
addRule("[c](:a)(:a)-N",0.4619); // C22
addRule("[c](:a)(:a)-O",0.5437); // C23
addRule("[c](:a)(:a)-S",0.1893); // C24
addRule("[$([c](:a)(:a)=C),$([c](:a)(:a)=N),$([c](:a)(:a)=O)]",-0.8186); // C25
addRule("[$([C](=C)(a)A),$([C](=C)(c)a),$([CH](=C)a),$([C]=c)]",0.2640); // C26
addRule("[CX4][!#5;!#7;!#8;!#15;!#16;!#9;!Cl;!Br;!I]",0.2148); // C27
addRule("remaining [C,c]",0.08129);
addRule("[$([H,h][#6]),$([H,h][H,h])]",0.1230); // H1, hydrocarbon
addRule("[$([H,h]O[CX4]),$([H,h]Oc),$([H,h]O[!#6;!#7;!#8;!16]),$([H,h][!#6;!#7;!#8])]",-0.2677); // H2, alcohol
addRule("[$([H,h][#7]),$([H,h]O[#7])]",0.2142); // H3, amine
addRule("[$([H,h]OC=[#6]),$([H,h]OC=[#7]),$([H,h]OC=O),$([H,h]OC=S),$([H,h]OO),$([H,h]OS)]",0.2980); // H4, acid
addRule("remaining [H,h]",0.1125);
addRule("[NH2+0]A",-1.0190); // N1
addRule("[NH+0](A)A",-0.7096); // N2
addRule("[NH2+0]a",-1.0270); // N3
addRule("[$([NH+0](A)a),$([NH+0](a)a)]",-0.5188); // N4
addRule("[$([NH+0]=A),$([NH+0]=a)]",0.08387); // N5
addRule("[$([N+0](=A)A),$([N+0](=A)a),$([N+0](=a)A),$([N+0](=a)a)]",0.1836); // N6
addRule("[N+0](A)(A)A",-0.3187); // N7
addRule("[$([N+0](a)(A)A),$([N+0](a)(a)A),$([N+0](a)(a)a)]",-0.4458); // N8
addRule("[N+0]#A",0.01508); // N9
addRule("[$([NH3+*]),$([NH2+*]),$([NH+*])]",-1.950); // N10
addRule("[n+0]",-0.3239); // N11
addRule("[n+*]",-1.119); // N12
addRule("[$([NH0+*](A)(A)(A)A),$([NH0+*](=A)(A)A),$([NH0+*](=A)(A)a),$([NH0+*](=[#6])=[#7])]",-0.3396); // N13
addRule("[$([N+*]#A),$([N-*]),$([N+*](=[N-*])=N)]",0.2887); // N14
addRule("remaining [N,n]",-0.4806);
addRule("[o]",0.1552); // O1
addRule("[$([OH]),$([OH2])]",-0.2893); // O2, alcohol
addRule("[$([O](C)C),$([O](C)[A;N,O,P,S,F,Cl,Br,I]),$([O]([A;N,O,P,S,F,Cl,Br,I])[A;N,O,P,S,F,Cl,Br,I])]",-0.0684); // O3, ali. ether
addRule("[$([O](A)a),$([O](a)a)]",-0.4195); // O4, aro. ether
addRule("[$([O]=[#8]),$([O]=[#7]),$([OX1-*][#7])]",0.0335); // O5, oxide
addRule("[OX1-*][#16]",-0.3339); // O6, oxide
addRule("[OX1-*][!N;!S]",-1.189); // O7, oxide
addRule("[O]=c",0.1788); // O8, aro. carbonyl
addRule("[$([O]=[CH]C),$([O]=C(C)C),$([O]=C(C)[A;!#1;!#6]),$([O]=[CH]N),$([O]=[CH]O),$([O]=[CH2]),$([O]=[CX2]=O)]",-0.1525); // O9, carbonyl ali.
addRule("[$([O]=[CH]c),$([O]=C(C)c),$([O]=C(c)c),$([O]=C(c)[a;!#1;!#6]),$([O]=C(c)[A;!#1;!#6]),$([O]=C(C)[a;!#1;!#6])]",0.1129); // O10, carbonyl aro.
addRule("[$([O]=C([A;!#1;!#6])[A;!#1;!#6]),$([O]=C([A;!#1;!#6])[a;!#1;!#6]),$([O]=C([a;!#1;!#6])[a;!#1;!#6])]",0.4833); // O11, carbonyl heteroatom
addRule("[O-1]C(=O)",-1.326); // O12, acid
addRule("remaining [O,o]",-0.1188);
addRule("[#9-0]",0.4202); // flourine
addRule("remaining [#9]",-2.996);
addRule("[#17-0]",0.6895); // chlorine
addRule("remaining [#17]",-2.996);
addRule("[#35-0]",0.8456); // bromine
addRule("remaining [#35]",-2.996);
addRule("[#53-0]",0.8857); // iodine
addRule("remaining [#53]",-2.996);
addRule("[#15]",0.8612); // phosphorous
addRule("[S-0]",0.6482); // aliphatic sulfur
addRule("[$([S-*]),$([S-*])]",-0.0024); // ionic sulfur
addRule("[s]",0.6237); // aromatic sulfur
addRule("[B,Si,Ga,Ge,As,Se,Sn,Te,Pb,Ne,Ar,Kr,Xe,Rn]",-0.3808); // remaining p-block elements
addRule("[Fe,Cu,Zn,Tc,Cd,Pt,Au,Hg]",-0.0025); // remaining d-block elements
}
LogP::~LogP()
{
delete molecular_similarity_;
}
void LogP::addRule(String smarts, double value)
{
rules_.push_back(make_pair(smarts,value));
}
double LogP::calculate(const String& usmile)
{
double logP = 0;
Size match_sum = 0;
for(Size i=0; i<rules_.size(); i++)
{
if(!rules_[i].first.hasPrefix("remaining"))
{
Size matches;
molecular_similarity_->matchSmarts(usmile,rules_[i].first,matches);
logP += matches*rules_[i].second;
match_sum += matches;
// if(matches>0) cout<<rules_[i].first<<" : "<<matches<<endl;
}
else
{
Size no_atoms;
String smarts = rules_[i].first.after("remaining");
smarts.trim();
molecular_similarity_->matchSmarts(usmile,smarts,no_atoms);
if(no_atoms>match_sum)
{
logP += (no_atoms-match_sum)*rules_[i].second;
}
// if(match_sum>no_atoms)
// {
// cout<<"Error: Atoms "<<smarts<<" were matches mulitple times!!"<<endl;
// cout<<match_sum<<" "<<no_atoms<<endl;
// }
match_sum=0;
}
}
return logP;
}
}
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