Standardizer

Hello





I have a short question concerning standardizer.





Using:





I would like to do the following transformation:





CNC(O)=N>>CNC(=O)N





I tried to use the following command (with a more generalized SMART representation of my transformation):

Code:

standardize -c "[#8H1:1][C:2]([*:5])=[N:3][*:4]>>[*:4][N;H1:3][C:2]([*:5])=[O:1]" "CNC(O)=N"

The result is not the one I'm trying to get but the same as the input.





What am I doing wrong?





Thanks a lot,





tobias

I just tried something very simple:

Code:

standardize -c "[N:1][N:2]>>[C:1][C:2]" "CNNC"

I expect CCCC as the result, but I don't get it. But I have no idea what am I doing wrong...

The problem is that you do not need the any-atoms in your reaction definition. The any atom does not match H atoms therefore the reactant side of your reaction does not match your input molecule: any-atom with map 4 has no matching atom. On the other hand, unspecified ligands match any ligand, including H atoms. Thus the solution is to remove the any-atoms from your equation:

Code:

standardize -c "[#8H1:1][C:2]=[N:3]>>[O:1]=[C:2][#7H1:3]" "CNC(O)=N" CNC(N)=O

If you require a non-H ligand attached to the carbon then you can write:

Code:

standardize -c "[#8H1:1][C:2](=[N:3])[*:5]>>[O:1]=[C:2]([#7H1:3])[*:5]" "CNC(O)=N" CNC(N)=O

Your second question: transform "CCCC" to "CNNC".


In the reaction equation you should sepcify at least one attachment point for each changing atom - otherwise the result molecule will split into separated fragments. You should map corresponding atoms with the same atom map in the reactant and the product sides. Here is a transformation that produces the required result:

Code:

standardize -c "[*:1][C:2][C:3][*:4]>>[*:1][N:5][N:6][*:4]" "CCCC" CNNC

The ligand any-atoms that are unchanged are mapped with the same atom maps in the reactant and the product sides (maps 1, 4) while the atoms to be removed (maps 2, 3) and the atoms to be added (maps 5, 6) have different atom maps.