SMARTS queries?? How to read SMARTS

Hello,

    I want use KNIME to turn SMARTS to structure. I used "molecule  to indigo" and "query molecule to indigo", but these nodes can not turn all the SMARTS to structure. It said " fragments are only allowed in SMARTS queries". But I don't find the node of SMARTS queries, can you tell me how to get the extention of SMARTS queries or how to turn SMARTS to structure?

  Thanks

Hello, maybe the Molecule Type Cast node may help you.

Hello, thank you very much. Molecule Type Cast node is much better than "molecule to indigo". But Molecule Type Cast node can not recognize C and c. And I want to out the substructure of SMARTS. Can you help me ??

Thank you very much~

sun

In my case, the node correctly manages c1ccccc1 and C1CCCCC1 which are correclty rendered as benzene and cyclohexane. Could you attach an example?

Hello, thank you very much for your reply. The SMARTS file is substructure fingerprint. The follwing is the file. Can you help me ?

Thank you very much.

 

SMARTS
[CX4H3][#6]
[CX4H2]([#6])[#6]
[CX4H1]([#6])([#6])[#6]
[CX4]([#6])([#6])([#6])[#6]
"[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]=[CX3;$([H2]),$([H1][#6]),$(C([#6])[#6])]"
[CX2]#[CX2]
[CX3]=[CX2]=[CX3]
[ClX1][CX4]
[FX1][CX4]
[BrX1][CX4]
[IX1][CX4]
"[OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])]"
"[OX2H][CX4H2;!$(C([OX2H])[O,S,#7,#15])]"
"[OX2H][CX4H;!$(C([OX2H])[O,S,#7,#15])]"
"[OX2H][CX4D4;!$(C([OX2H])[O,S,#7,#15])]"
"[OX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]"
"[SX2]([CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([OX2])[O,S,#7,#15])]"
"[OX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]"
[c][OX2][c]
"[SX2](c)[CX4;!$(C([OX2])[O,S,#7,#15,F,Cl,Br,I])]"
[c][SX2][c]
"[O+;!$([O]~[!#6]);!$([S]*~[#7,#8,#15,#16])]"
"[NX3+0,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])]"
"[NX3H2+0,NX4H3+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]"
"[NX3H1+0,NX4H2+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]"
"[NX3H0+0,NX4H1+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]"
"[NX4H0+;!$([N][!C]);!$([N]*~[#7,#8,#15,#16])]"
"[NX3H2+0,NX4H3+]c"
"[NX3H1+0,NX4H2+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]"
"[NX3H0+0,NX4H1+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]"
"[NX4H0+;!$([N][!c]);!$([N]*~[#7,#8,#15,#16])]"
"[NX3H1+0,NX4H2+;$([N]([c])[C]);!$([N]*~[#7,#8,#15,#16])]"
"[NX3H0+0,NX4H1+;$([N]([c])([C])[#6]);!$([N]*~[#7,#8,#15,#16])]"
"[NX4H0+;$([N]([c])([C])[#6][#6]);!$([N]*~[#7,#8,#15,#16])]"
"[N+;!$([N]~[!#6]);!$(N=*);!$([N]*~[#7,#8,#15,#16])]"
"[SX2H][CX4;!$(C([SX2H])~[O,S,#7,#15])]"
"[SX2]([CX4;!$(C([SX2])[O,S,#7,#15,F,Cl,Br,I])])[CX4;!$(C([SX2])[O,S,#7,#15])]"
"[SX2](c)[CX4;!$(C([SX2])[O,S,#7,#15])]"
[SX2D2][SX2D2]
"[OX2H][CX4;!$(C([OX2H])[O,S,#7,#15,F,Cl,Br,I])][CX4;!$(C([N])[O,S,#7,#15])][NX3;!$(NC=[O,S,N])]"
"[OX2H][CX4;!$(C([OX2H])[O,S,#7,#15])][CX4;!$(C([OX2H])[O,S,#7,#15])][OX2H]"
"[OX2H][CX4;!$(C([OX2H])([OX2H])[O,S,#7,#15])][OX2H]"
[OX2H][OX2]
[OX2D2][OX2D2]
"[LiX1][#6,#14]"
"[MgX2][#6,#14]"
[!#1;!#5;!#6;!#7;!#8;!#9;!#14;!#15;!#16;!#17;!#33;!#34;!#35;!#52;!#53;!#85]~[#6;!-]
"[$([CX3H][#6]),$([CX3H2])]=[OX1]"
[#6][CX3](=[OX1])[#6]
"[$([CX3H][#6]),$([CX3H2])]=[SX1]"
[#6][CX3](=[SX1])[#6]
"[NX2;$([N][#6]),$([NH]);!$([N][CX3]=[#7,#8,#15,#16])]=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])]"
"[NX3+;!$([N][!#6]);!$([N][CX3]=[#7,#8,#15,#16])]"
"[NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2H]"
"[NX2](=[CX3;$([CH2]),$([CH][#6]),$([C]([#6])[#6])])[OX2][#6;!$(C=[#7,#8])]"
"[OX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]"
"[OX2H][CX4;!$(C(O)(O)[!#6])][OX2][#6;!$(C=[O,S,N])]"
"[NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][NX3v3;!$(NC=[#7,#8,#15,#16])][#6]"
"[NX3v3;!$(NC=[#7,#8,#15,#16])]([#6])[CX4;!$(C(N)(N)[!#6])][OX2H]"
"[SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][SX2][#6;!$(C=[O,S,N])]"
"[SX2]([#6;!$(C=[O,S,N])])[CX4;!$(C(S)(S)[!#6])][OX2H]"
"[NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]"
"[NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]"
"[NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1]"
"[NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]"
"[NX3v3,SX2,OX2;$(**=[#7,#8,#15,#16])][CX4;!$(C([N,S,O])([N,S,O])[!#6])][FX1,ClX1,BrX1,IX1,NX3v3,SX2,OX2;!$(*C=[#7,#8,#15,#16])]"
"[NX1]#[CX2][CX4;$([CH2]),$([CH]([CX2])[#6]),$(C([CX2])([#6])[#6])][OX2H]"
[ClX1][CX3]=[CX3]
[FX1][CX3]=[CX3]
[BrX1][CX3]=[CX3]
[IX1][CX3]=[CX3]
"[OX2H][CX3;$([H1]),$(C[#6])]=[CX3]"
"[OX2H][CX3;$([H1]),$(C[#6])]=[CX3;$([H1]),$(C[#6])][OX2H]"
"[OX2]([#6;!$(C=[N,O,S])])[CX3;$([H0][#6]),$([H1])]=[CX3]"
"[OX2]([CX3]=[OX1])[#6X3;$([#6][#6]),$([H1])]=[#6X3;!$(C[OX2H])]"
"[NX3;$([NH2][CX3]),$([NH1]([CX3])[#6]),$([N]([CX3])([#6])[#6]);!$([N]*=[#7,#8,#15,#16])][CX3;$([CH]),$([C][#6])]=[CX3]"
"[SX2H][CX3;$([H1]),$(C[#6])]=[CX3]"
"[SX2]([#6;!$(C=[N,O,S])])[CX3;$(C[#6]),$([CH])]=[CX3]"
"[CX3;$([R0][#6]),$([H1R0])](=[OX1])[ClX1]"
"[CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1]"
"[CX3;$([R0][#6]),$([H1R0])](=[OX1])[BrX1]"
"[CX3;$([R0][#6]),$([H1R0])](=[OX1])[IX1]"
"[CX3;$([R0][#6]),$([H1R0])](=[OX1])[FX1,ClX1,BrX1,IX1]"
"[CX3;$([R0][#6]),$([H1R0])](=[OX1])[$([OX2H]),$([OX1-])]"
"[CX3;$([R0][#6]),$([H1R0])](=[OX1])[OX2][#6;!$(C=[O,N,S])]"
"[#6][#6X3R](=[OX1])[#8X2][#6;!$(C=[O,N,S])]"
"[CX3;$([H0][#6]),$([H1])](=[OX1])[#8X2][CX3;$([H0][#6]),$([H1])](=[OX1])"
"[$([#6X3H0][#6]),$([#6X3H])](=[!#6])[!#6]"
"[CX3;!R;$([C][#6]),$([CH]);$([C](=[OX1])[$([SX2H]),$([SX1-])]),$([C](=[SX1])[$([OX2H]),$([OX1-])])]"
"[CX3;$([R0][#6]),$([H1R0])](=[OX1])[SX2][#6;!$(C=[O,N,S])]"
"[#6][#6X3R](=[OX1])[#16X2][#6;!$(C=[O,N,S])]"
"[CX3;$([H0][#6]),$([H1])](=[SX1])[OX2][#6;!$(C=[O,N,S])]"
"[#6][#6X3R](=[SX1])[#8X2][#6;!$(C=[O,N,S])]"
"[CX3;$([H0][#6]),$([H1])](=[SX1])[FX1,ClX1,BrX1,IX1]"
"[CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2H])]"
"[CX3;!R;$([C][#6]),$([CH]);$([C](=[SX1])[SX2][#6;!$(C=[O,N,S])])]"
"[#6][#6X3R](=[SX1])[#16X2][#6;!$(C=[O,N,S])]"
"[CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]"
"[CX3;$([R0][#6]),$([H1R0])](=[OX1])[NX3H2]"
"[CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H1][#6;!$(C=[O,N,S])]"
"[CX3;$([R0][#6]),$([H1R0])](=[OX1])[#7X3H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])]"
"[#6R][#6X3R](=[OX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]"
"[#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])"
"[#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H0]([!#6])[#6X3;$([H0][#6]),$([H1])](=[OX1])"
"[#6X3;$([H0][#6]),$([H1])](=[OX1])[#7X3H1][#6X3;$([H0][#6]),$([H1])](=[OX1])"
"[$([CX3;!R][#6]),$([CX3H;!R])](=[SX1])[#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]"
"[#6R][#6X3R](=[SX1])[#7X3;$([H1][#6;!$(C=[O,N,S])]),$([H0]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]"
"[#6X3;$([H0][#6]),$([H1])](=[OX1])[#8X2][#7X2]=,:[#6X3;$([H0]([#6])[#6]),$([H1][#6]),$([H2])]"
"[NX3;!$(NC=[O,S])][CX3;$([CH]),$([C][#6])]=[NX2;!$(NC=[O,S])]"
"[CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][$([OX2H]),$([OX1-])]"
"[CX3;$([H0][#6]),$([H1])](=[OX1])[#7X3;$([H1]),$([H0][#6;!$(C=[O,N,S])])][OX2][#6;!$(C=[O,N,S])]"
"[CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]"
"[#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([OX2H]),$([OX1-])]"
"[CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]"
"[#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[OX2][#6;!$(C=[O,N,S])]"
"[CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]"
"[#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[$([SX2H]),$([SX1-])]"
"[CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]"
"[#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[SX2][#6;!$(C=[O,N,S])]"
"[#7X3v3;!$(N([#6X3]=[#7X2])C=[O,S])][CX3R0;$([H1]),$([H0][#6])]=[NX2v3;!$(N(=[#6X3][#7X3])C=[O,S])]"
"[#6][#6X3R;$([H0](=[NX2;!$(N(=[#6X3][#7X3])C=[O,S])])[#7X3;!$(N([#6X3]=[#7X2])C=[O,S])]),$([H0](-[NX3;!$(N([#6X3]=[#7X2])C=[O,S])])=,:[#7X2;!$(N(=[#6X3][#7X3])C=[O,S])])]"
"[CX3R0;$([H0][#6]),$([H1])](=[NX2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]"
"[#6R][#6X3R](=,:[#7X2;$([H1]),$([H0][#6;!$(C=[O,N,S])])])[FX1,ClX1,BrX1,IX1]"
"[$([$([#6X3][#6]),$([#6X3H])](=[#7X2v3])[#7X3v3][#7X3v3]),$([$([#6X3][#6]),$([#6X3H])]([#7X3v3])=[#7X2v3][#7X3v3])]"
"[NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[OX2H,OX1-]"
"[OX2H][C][CX3](=[OX1])[OX2H,OX1-]"
"[NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]"
"[NX3;$([N][CX3](=[OX1])[C][NX3,NX4+])][C][CX3](=[OX1])[OX2H,OX1-]"
"[NX3,NX4+;!$([N]~[!#6]);!$([N]*~[#7,#8,#15,#16])][C][CX3](=[OX1])[NX3;$([N][C][CX3](=[OX1])[NX3,OX2,OX1-])]"
"[#6][OX2][CX4;$(C[#6]),$([CH])]([OX2][#6])[OX2][#6]"
[CX3]=[CX2]=[OX1]
"[#7X2,#8X3,#16X2;$(*[#6,#14])][#6X3]([#7X2,#8X3,#16X2;$(*[#6,#14])])=[#6X3]"
[NX1]#[CX2]
[CX1-]#[NX2+]
"[#6X3](=[OX1])[#6X3]=,:[#6X3][#7,#8,#16,F,Cl,Br,I]"
"[#6X3](=[OX1])[#6X3]=,:[#6X3][$([OX2H]),$([OX1-])]"
"[#6X3](=[OX1])[#6X3]=,:[#6X3][#6;!$(C=[O,N,S])]"
"[#6X3](=[OX1])[#6X3]=,:[#6X3][#7X3;$([H2]),$([H1][#6;!$(C=[O,N,S])]),$([#7]([#6;!$(C=[O,N,S])])[#6;!$(C=[O,N,S])])]"
"[#6X3](=[OX1])[#6X3]=,:[#6X3][FX1,ClX1,BrX1,IX1]"
"[#6;!$(C=[O,N,S])][#8X2][#6X3](=[OX1])[#8X2][#6;!$(C=[O,N,S])]"
"[#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[OX2][FX1,ClX1,BrX1,IX1]"
"[#6;!$(C=[O,N,S])][OX2;!R][CX3](=[OX1])[$([OX2H]),$([OX1-])]"
[!#6][#6X3](=[!#6])[!#6]
"[#6;!$(C=[O,N,S])][#8X2][#6X3](=[SX1])[#8X2][#6;!$(C=[O,N,S])]"
"[#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[OX2][FX1,ClX1,BrX1,IX1]"
"[#6;!$(C=[O,N,S])][OX2;!R][CX3](=[SX1])[$([OX2H]),$([OX1-])]"
[#7X3;!$([#7][!#6])][#6X3](=[OX1])[#7X3;!$([#7][!#6])]
[#7X3;!$([#7][!#6])][#6X3](=[SX1])[#7X3;!$([#7][!#6])]
"[#7X2;!$([#7][!#6])]=,:[#6X3]([#8X2&!$([#8][!#6]),OX1-])[#7X3;!$([#7][!#6])]"
"[#7X2;!$([#7][!#6])]=,:[#6X3]([#16X2&!$([#16][!#6]),SX1-])[#7X3;!$([#7][!#6])]"
"[N;v3X3,v4X4+][CX3](=[N;v3X2,v4X3+])[N;v3X3,v4X4+]"
"[NX3]C(=[OX1])[O;X2H,X1-]"
[#7X3][#6](=[OX1])[#8X2][#6]
[#7X3][#6](=[OX1])[#7X3][#6](=[OX1])[#7X3]
[#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]
[#7X3][#7X3][#6X3]([#7X3][#7X3])=[OX1]
[#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[OX1]
[#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[OX1]
[#7X3][#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]
[#7X3][#7X3][#6X3]([#7X3][#7X3])=[SX1]
[#7X2](=[#6])[#7X3][#6X3]([#7X3;!$([#7][#7])])=[SX1]
[#7X2](=[#6])[#7X3][#6X3]([#7X3][#7X3])=[SX1]
[NX2]=[CX2]=[OX1]
[OX2][CX2]#[NX1]
[NX2]=[CX2]=[SX1]
[SX2][CX2]#[NX1]
[NX2]=[CX2]=[NX2]
"[CX4H0]([O,S,#7])([O,S,#7])([O,S,#7])[O,S,#7,F,Cl,Br,I]"
[OX2H][c]
[OX2H][c][c][OX2H]
[Cl][c]
[F][c]
[Br][c]
[I][c]
[SX2H][c]
"[c]=[NX2;$([H1]),$([H0][#6;!$([C]=[N,S,O])])]"
[c]=[OX1]
[c]=[SX1]
[nX3H1+0]
[nX3H0+0]
"[nX2,nX3+]"
[o]
[sX2]
[a;!c]
"[NX2](=[OX1])[O;$([X2]),$([X1-])]"
[SX2][NX2]=[OX1]
"[$([NX3](=[OX1])(=[OX1])[O;$([X2]),$([X1-])]),$([NX3+]([OX1-])(=[OX1])[O;$([X2]),$([X1-])])]"
"[$([NX3](=O)=O),$([NX3+](=O)[O-])][!#8]"
[NX2](=[OX1])[!#7;!#8]
"[NX1]~[NX2]~[NX2,NX1]"
[CX3](=[OX1])[NX2]~[NX2]~[NX1]
"[$([#6]=[NX2+]=[NX1-]),$([#6-]-[NX2+]#[NX1])]"
[#6][NX2+]#[NX1]
[#7;!$(N*=O)][NX2]=[OX1]
[NX2](=[OX1])N-*=O
"[$([#7+][OX1-]),$([#7v5]=[OX1]);!$([#7](~[O])~[O]);!$([#7]=[#7])]"
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Hello,

I am sorry, I am not familiar enough with SMARTS. Someone more competent will problably see your post.

Good luck

It is OK. Last time your reply are very useful. Thank you very much.

sun

Dear sun,

I have attached a simple workflow with two examples how can you use the smarts query ...of course depends which is your goal . The first is a very basic substructure matcher and the second is a loop and collect every smarts in the query.

 

i hope that this could help you

fab

It might be worth trying the RDKit substructure filter or counter nodes.  I think the error is suggesting that some of your SMARTS cannot be parsed by the Indigo toolkit. You can also use the SMARTSviewer node from the Vernalis community contribution to visualise the SMARTS strings to check that they are doing what you want them to.

Steve

Dear Sun,

I think that you can use the MolConverter node of ChemAxon.
For instance, File Reader (read as String) > Molecule Type Cast (to Smarts) > MolConverter

Best,
Taka
 

Hello, Steve

    Thank you for your advice. I think SMART Sviewer can help me. But I did not find the link to download the node of SMART Sviewer. Can you give the link to install the nodes and tell me how to use it?

thanks

Sun

Dear fab,

Thank you for your workflow. I learn a lot from your workflow. But it can not solve my problems.

Thank you for your help.

Best wishes

Sun

Hello, Taka

Thank you for your reply. If the SMARTS is short, your workflow can turn SMARTS to structure. But some SMARTS are very long so that MolConverter cann't recognize. 

Thank you for your help.

Sun

It is under the cheminformatics part of the community contributions - see http://tech.knime.org/community for installation instructions

Steve

Dear Steve,

Thank you very much. I install the nodes right now. It works ( sometimes maybe miss some SMARTS, but it's OK). Thank you. You are my angel.

Sun

Hello, Steve

I want to output the result of SMARTSViewer, but "Table to PDF" and "Table to HTML" only can show a part of the structure. Can you tell me which node can show all the structure?

Thank you 

Sun

I think you will need to use the Table to Report node, and then create the layout/scaling you want in the report designer