User 1c25459954
29-10-2010 09:49:20
Hello,
I followed the tutorial for importing sdf files in InstantJChem. It was able to import all the other information except the ZINC identifier when it imports using JChemBase table. However, when it imports using new database table, it imports only the ZINC identifier.
Please can you suggest a way using which I can import the ZINC identifier and all the structure information in one table as I need to query using the ZINC identifier.
Thanks,
Saumya
ChemAxon fa971619eb
29-10-2010 09:57:29
Could you describe how the zinc code is defined in the SD file?
IJC should import all normal data fields, and if the code is there then it should be imported. IJC cannot currently handle the identifier that comes at the top of the entry (before the connection table), only normal fields that come after the conenction table.
Tim
User 1c25459954
29-10-2010 10:05:08
A sample of my sdf file is as follows:
ZINC36124575
-OEChem-10201010543D
49 50 0 1 0 0 0 0 0999 V2000
-0.0187 1.5258 0.0104 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0021 -0.0041 0.0020 C 0 0 1 0 0 0 0 0 0 0 0 0
-1.0205 -0.3815 0.0098 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7196 -0.4984 -1.2584 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8426 -1.9623 -1.1812 N 0 0 0 0 0 0 0 0 0 0 0 0
1.3963 -2.5474 0.0497 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6469 -1.9564 1.2484 C 0 0 1 0 0 0 0 0 0 0 0 0
1.1072 -2.3052 2.1728 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7126 -0.4906 1.1914 N 0 3 0 0 0 0 0 0 0 0 0 0
0.0896 0.0730 2.3964 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9027 -0.3316 3.6277 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2540 0.2555 4.8828 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0347 -0.1330 6.0650 N 0 0 0 0 0 0 0 0 0 0 0 0
2.3684 0.4823 6.0406 C 0 0 0 0 0 0 0 0 0 0 0 0
0.3204 0.2075 7.3027 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8157 -2.4036 1.2065 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4585 -2.7452 -2.2088 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0037 -2.2446 -3.2155 O 0 0 0 0 0 0 0 0 0 0 0 0
0.5939 -4.2426 -2.1068 C 0 0 0 0 0 0 0 0 0 0 0 0
1.6318 -4.9207 -3.0034 C 0 0 0 0 0 0 0 0 0 0 0 0
0.1403 -5.0763 -3.3069 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0039 1.9031 0.0027 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.5459 1.8868 -0.8726 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.5289 1.8773 0.9072 H 0 0 0 0 0 0 0 0 0 0 0 0
0.1403 -0.2255 -2.1405 H 0 0 0 0 0 0 0 0 0 0 0 0
1.7115 -0.0499 -1.3149 H 0 0 0 0 0 0 0 0 0 0 0 0
1.2645 -3.6293 0.0325 H 0 0 0 0 0 0 0 0 0 0 0 0
2.4566 -2.3059 0.1253 H 0 0 0 0 0 0 0 0 0 0 0 0
0.0652 1.1600 2.3183 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.9274 -0.3074 2.4916 H 0 0 0 0 0 0 0 0 0 0 0 0
0.9272 -1.4185 3.7059 H 0 0 0 0 0 0 0 0 0 0 0 0
1.9198 0.0489 3.5326 H 0 0 0 0 0 0 0 0 0 0 0 0
0.2295 1.3424 4.8047 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.7631 -0.1249 4.9779 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2677 1.5676 6.0294 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9251 0.1782 6.9270 H 0 0 0 0 0 0 0 0 0 0 0 0
2.9019 0.1578 5.1473 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.6348 -0.3169 7.3269 H 0 0 0 0 0 0 0 0 0 0 0 0
0.9206 -0.0908 8.1623 H 0 0 0 0 0 0 0 0 0 0 0 0
0.1455 1.2828 7.3373 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.8643 -3.4917 1.2483 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.3488 -1.9831 2.0592 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.2761 -2.0545 0.2822 H 0 0 0 0 0 0 0 0 0 0 0 0
0.4353 -4.6625 -1.1135 H 0 0 0 0 0 0 0 0 0 0 0 0
2.2167 -4.2837 -3.6670 H 0 0 0 0 0 0 0 0 0 0 0 0
2.1564 -5.7868 -2.5999 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.3164 -6.0448 -3.1031 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.2561 -4.5417 -4.1701 H 0 0 0 0 0 0 0 0 0 0 0 0
1.6778 -0.2000 1.1474 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 22 1 0 0 0 0
1 23 1 0 0 0 0
1 24 1 0 0 0 0
2 3 1 0 0 0 0
2 9 1 0 0 0 0
2 4 1 0 0 0 0
4 5 1 0 0 0 0
4 25 1 0 0 0 0
4 26 1 0 0 0 0
5 6 1 0 0 0 0
5 17 1 0 0 0 0
6 7 1 0 0 0 0
6 27 1 0 0 0 0
6 28 1 0 0 0 0
7 8 1 0 0 0 0
7 9 1 0 0 0 0
7 16 1 0 0 0 0
9 10 1 0 0 0 0
9 49 1 0 0 0 0
10 11 1 0 0 0 0
10 29 1 0 0 0 0
10 30 1 0 0 0 0
11 12 1 0 0 0 0
11 31 1 0 0 0 0
11 32 1 0 0 0 0
12 13 1 0 0 0 0
12 33 1 0 0 0 0
12 34 1 0 0 0 0
13 14 1 0 0 0 0
13 15 1 0 0 0 0
14 35 1 0 0 0 0
14 36 1 0 0 0 0
14 37 1 0 0 0 0
15 38 1 0 0 0 0
15 39 1 0 0 0 0
15 40 1 0 0 0 0
16 41 1 0 0 0 0
16 42 1 0 0 0 0
16 43 1 0 0 0 0
17 18 2 0 0 0 0
17 19 1 0 0 0 0
19 21 1 0 0 0 0
19 20 1 0 0 0 0
19 44 1 0 0 0 0
20 21 1 0 0 0 0
20 45 1 0 0 0 0
20 46 1 0 0 0 0
21 47 1 0 0 0 0
21 48 1 0 0 0 0
M CHG 1 9 1
M END
$$$$
ChemAxon fa971619eb
29-10-2010 10:26:59
Yes, so if its the ZINC36124575 bit that you are wanting then IJC does not currently handle this, only proper fields that come after the conenction table. We do hope to support reading this extra info at some stage, but currenly its not possible.
You would need to process the file in some other tool to read the bit you want and add it as a normal field in the SD file.
Tim
User da00f5c453
29-10-2010 21:51:21
Hi Saum,
the easiest way to deal with this issue is to use molconvert command line tool from jchem package and run it with the following options:
> molconvert "smiles:n" zinc_file_name.sdf -o zinc.smiles
and import the resulting smiles file, IJC should read now the second field in SMILES file as text field which you can name ZINC ID.
Oleg.
| saum_kmr wrote: |
A sample of my sdf file is as follows:
ZINC36124575 -OEChem-10201010543D
49 50 0 1 0 0 0 0 0999 V2000 -0.0187 1.5258 0.0104 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0021 -0.0041 0.0020 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.0205 -0.3815 0.0098 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7196 -0.4984 -1.2584 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8426 -1.9623 -1.1812 N 0 0 0 0 0 0 0 0 0 0 0 0 1.3963 -2.5474 0.0497 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6469 -1.9564 1.2484 C 0 0 1 0 0 0 0 0 0 0 0 0 1.1072 -2.3052 2.1728 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7126 -0.4906 1.1914 N 0 3 0 0 0 0 0 0 0 0 0 0 0.0896 0.0730 2.3964 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9027 -0.3316 3.6277 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2540 0.2555 4.8828 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0347 -0.1330 6.0650 N 0 0 0 0 0 0 0 0 0 0 0 0 2.3684 0.4823 6.0406 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3204 0.2075 7.3027 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8157 -2.4036 1.2065 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4585 -2.7452 -2.2088 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0037 -2.2446 -3.2155 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5939 -4.2426 -2.1068 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6318 -4.9207 -3.0034 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1403 -5.0763 -3.3069 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0039 1.9031 0.0027 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5459 1.8868 -0.8726 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5289 1.8773 0.9072 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1403 -0.2255 -2.1405 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7115 -0.0499 -1.3149 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2645 -3.6293 0.0325 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4566 -2.3059 0.1253 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0652 1.1600 2.3183 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9274 -0.3074 2.4916 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9272 -1.4185 3.7059 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9198 0.0489 3.5326 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2295 1.3424 4.8047 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7631 -0.1249 4.9779 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2677 1.5676 6.0294 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9251 0.1782 6.9270 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9019 0.1578 5.1473 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6348 -0.3169 7.3269 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9206 -0.0908 8.1623 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1455 1.2828 7.3373 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8643 -3.4917 1.2483 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3488 -1.9831 2.0592 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2761 -2.0545 0.2822 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4353 -4.6625 -1.1135 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2167 -4.2837 -3.6670 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1564 -5.7868 -2.5999 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3164 -6.0448 -3.1031 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2561 -4.5417 -4.1701 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6778 -0.2000 1.1474 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 1 22 1 0 0 0 0 1 23 1 0 0 0 0 1 24 1 0 0 0 0 2 3 1 0 0 0 0 2 9 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 4 25 1 0 0 0 0 4 26 1 0 0 0 0 5 6 1 0 0 0 0 5 17 1 0 0 0 0 6 7 1 0 0 0 0 6 27 1 0 0 0 0 6 28 1 0 0 0 0 7 8 1 0 0 0 0 7 9 1 0 0 0 0 7 16 1 0 0 0 0 9 10 1 0 0 0 0 9 49 1 0 0 0 0 10 11 1 0 0 0 0 10 29 1 0 0 0 0 10 30 1 0 0 0 0 11 12 1 0 0 0 0 11 31 1 0 0 0 0 11 32 1 0 0 0 0 12 13 1 0 0 0 0 12 33 1 0 0 0 0 12 34 1 0 0 0 0 13 14 1 0 0 0 0 13 15 1 0 0 0 0 14 35 1 0 0 0 0 14 36 1 0 0 0 0 14 37 1 0 0 0 0 15 38 1 0 0 0 0 15 39 1 0 0 0 0 15 40 1 0 0 0 0 16 41 1 0 0 0 0 16 42 1 0 0 0 0 16 43 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 21 1 0 0 0 0 19 20 1 0 0 0 0 19 44 1 0 0 0 0 20 21 1 0 0 0 0 20 45 1 0 0 0 0 20 46 1 0 0 0 0 21 47 1 0 0 0 0 21 48 1 0 0 0 0 M CHG 1 9 1 M END $$$$
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