Viewing Highlighted results of substructure search with bingo server

[Karl Harrison]

Dear Support,

I have the Bingo server running nicely with my MSSQL server and substructure searches are working and I can get the output of a highlighting search generated too. 

So get a table with

id smiles and highlighting and the contents of the highlighting column are Molv V3000 files. e.g.

   -INDIGO-04101710292D    0  0  0  0  0  0  0  0  0  0  0 V3000 M  V30 BEGIN CTAB M  V30 COUNTS 24 24 0 0 0 M  V30 BEGIN ATOM M  V30 1 C 4.330127 1.500000 0.000000 0 M  V30 2 C 4.330127 0.500000 0.000000 0 M  V30 3 O 3.464101 0.000000 0.000000 0 M  V30 4 C 2.598076 0.500000 0.000000 0 M  V30 5 C 1.732051 0.000000 0.000000 0 M  V30 6 C 0.866025 0.500000 0.000000 0 M  V30 7 O 0.866026 1.500000 0.000000 0 M  V30 8 C 1.732051 2.000000 0.000000 0 M  V30 9 C 2.598076 1.500000 0.000000 0 M  V30 10 O 1.732051 3.000000 0.000000 0 M  V30 11 C 0.000000 0.000000 0.000000 0 M  V30 12 O -0.866025 0.500000 0.000000 0 M  V30 13 C -1.732051 -0.000000 0.000000 0 M  V30 14 C -1.732051 -1.000000 0.000000 0 M  V30 15 O -2.598076 0.500000 0.000000 0 M  V30 16 C 0.000000 -1.000000 0.000000 0 M  V30 17 O -0.866025 -1.500000 0.000000 0 M  V30 18 C -0.866026 -2.500000 0.000000 0 M  V30 19 C -0.000000 -3.000000 0.000000 0 M  V30 20 O -1.732051 -3.000000 0.000000 0 M  V30 21 C 0.866025 -1.500000 0.000000 0 M  V30 22 O 0.866026 -2.500000 0.000000 0 M  V30 23 O 1.732051 -1.000000 0.000000 0 M  V30 24 O 5.196153 0.000000 0.000000 0 M  V30 END ATOM M  V30 BEGIN BOND M  V30 1 1 1 2 M  V30 2 1 2 3 M  V30 3 1 3 4 M  V30 4 1 4 5 M  V30 5 1 5 6 M  V30 6 1 6 7 M  V30 7 1 7 8 M  V30 8 1 8 9 M  V30 9 2 8 10 M  V30 10 1 6 11 M  V30 11 1 11 12 M  V30 12 1 12 13 M  V30 13 1 13 14 M  V30 14 2 13 15 M  V30 15 1 11 16 M  V30 16 1 16 17 M  V30 17 1 17 18 M  V30 18 1 18 19 M  V30 19 2 18 20 M  V30 20 1 16 21 M  V30 21 1 21 22 M  V30 22 1 21 23 M  V30 23 1 23 5 M  V30 24 2 2 24 M  V30 END BOND M  V30 BEGIN COLLECTION M  V30 MDLV30/HILITE BONDS=(4 2 3 4 5) M  V30 MDLV30/HILITE ATOMS=(5 2 3 4 5 6) M  V30 END COLLECTION M  V30 END CTAB M  END 

The question I have is there are web .js rendered which can display this MOL V3000 file and show the hlighlighted substructure ? Ketcher v1.x and v2.x does seem to. So I am wondering what to use. 

I can see that there might be a couple of issues, since the exmple above doesn't have line breaks so when I converted to look like this, I get parsing errors.

  

   -INDIGO-04101710292D    

   

   0  0  0  0  0  0  0  0  0  0  0 V3000

M  V30 BEGIN CTAB

M  V30 COUNTS 24 24 0 0 0 

M  V30 BEGIN ATOM 

M  V30 1 C 4.330127 1.500000 0.000000 0 

M  V30 2 C 4.330127 0.500000 0.000000 0 

M  V30 3 O 3.464101 0.000000 0.000000 0 

M  V30 4 C 2.598076 0.500000 0.000000 0 

M  V30 5 C 1.732051 0.000000 0.000000 0 

M  V30 6 C 0.866025 0.500000 0.000000 0 

M  V30 7 O 0.866026 1.500000 0.000000 0

M  V30 8 C 1.732051 2.000000 0.000000 0 

M  V30 9 C 2.598076 1.500000 0.000000 0 

M  V30 10 O 1.732051 3.000000 0.000000 0 

M  V30 11 C 0.000000 0.000000 0.000000 0 

M  V30 12 O -0.866025 0.500000 0.000000 0 

M  V30 13 C -1.732051 -0.000000 0.000000 0 

M  V30 14 C -1.732051 -1.000000 0.000000 0 

M  V30 15 O -2.598076 0.500000 0.000000 0 

M  V30 16 C 0.000000 -1.000000 0.000000 0 

M  V30 17 O -0.866025 -1.500000 0.000000 0 

M  V30 18 C -0.866026 -2.500000 0.000000 0 

M  V30 19 C -0.000000 -3.000000 0.000000 0 

M  V30 20 O -1.732051 -3.000000 0.000000 0 

M  V30 21 C 0.866025 -1.500000 0.000000 0 

M  V30 22 O 0.866026 -2.500000 0.000000 0 

M  V30 23 O 1.732051 -1.000000 0.000000 0 

M  V30 24 O 5.196153 0.000000 0.000000 0 

M  V30 END ATOM 

M  V30 BEGIN BOND 

M  V30 1 1 1 2 

M  V30 2 1 2 3 

M  V30 3 1 3 4 

M  V30 4 1 4 5 

M  V30 5 1 5 6 

M  V30 6 1 6 7 

M  V30 7 1 7 8 

M  V30 8 1 8 9 

M  V30 9 2 8 10 

M  V30 10 1 6 11 

M  V30 11 1 11 12 

M  V30 12 1 12 13 

M  V30 13 1 13 14 

M  V30 14 2 13 15 

M  V30 15 1 11 16 

M  V30 16 1 16 17 

M  V30 17 1 17 18 

M  V30 18 1 18 19 

M  V30 19 2 18 20 

M  V30 20 1 16 21 

M  V30 21 1 21 22 

M  V30 22 1 21 23 

M  V30 23 1 23 5 

M  V30 24 2 2 24 

M  V30 END BOND 

M  V30 BEGIN COLLECTION 

M  V30 MDLV30/HILITE BONDS=(4 2 3 4 5) 

M  V30 MDLV30/HILITE ATOMS=(5 2 3 4 5 6) 

M  V30 END COLLECTION 

M  V30 END CTAB M  END 

When I tired to use your highlighting example from anohter thread this was loaded into Ketcher but this doesn't display highlights either c.f. 

https://groups.google.com/forum/m/#!topic/indigo-general/6KNXOKrBZz0

Many thanks. Karl

[Savelyev Alexander]

Dear Karl,

Unfortunately, Ketcher does not support highlighting of the structures. Also, Ketcher uses a backed server to read V3000 format.
In the thread you provided
https://groups.google.com/forum/m/#!topic/indigo-general/6KNXOKrBZz0
the suggestion is to use Indigo renderer. Indigo is a cheminformatics tookit which includes API for all general languages (python,java,C#). Using indigo render you can render the highlighted structures into different formats: PNG,JPG and even SVG

See render usage here
See some examples of highlighting here

Thanks
Alexander

[yingy...@gmail.com]

I have wrote a JSP file to show Mol V3000 result. It works no excellent, but it does can show Mol V3000 data ：-）

在 2017年4月10日星期一 UTC+8下午5:53:10，Karl Harrison写道：