Hello guys,
i think i have a problem with my syntax.
I have an sdf-File then i make an mol-File with: babel input.sdf -omol query.mol
and then i want to search with the query-File against one fs-File:
babel Compound_000000001_000025000.fs babelresult.sdf -sbabelsearch.mol -at0.85
But i became he following error:
==============================
*** Open Babel Warning in ParseSimple
Illegal aromatic element b
==============================
*** Open Babel Error in ObtainTarget
Could not make a molecule from babelsearch.mol
This needs to be valid SMILES when using fastsearch.You can use the more
versatile SMARTS in a normal substructure search.
0 molecules converted
1 errors 1 warnings 5 audit log messages
What is my Problem?
The query.mol looks like this:
1
OpenBabel12161108573D
31 30 0 0 0 0 0 0 0 0999 V2000
0.3387 0.9262 0.4600 O 0 0 0 0 0
3.4786 -1.7069 -0.3119 O 0 0 0 0 0
1.8428 -1.4073 1.2523 O 0 0 0 0 0
0.4166 2.5213 -1.2091 O 0 0 0 0 0
-2.2359 -0.7251 0.0270 N 0 0 0 0 0
-0.7783 -1.1579 0.0914 C 0 0 0 0 0
0.1368 -0.0961 -0.5161 C 0 0 0 0 0
-3.1119 -1.7972 0.6590 C 0 0 0 0 0
-2.4103 0.5837 0.7840 C 0 0 0 0 0
-2.6433 -0.5289 -1.4260 C 0 0 0 0 0
1.4879 -0.6438 -0.9795 C 0 0 0 0 0
2.3478 -1.3163 0.1002 C 0 0 0 0 0
0.4627 2.1935 -0.0312 C 0 0 0 0 0
0.6678 3.1549 1.1001 C 0 0 0 0 0
-0.7073 -2.1051 -0.4563 H 0 0 0 0 0
-0.5669 -1.3392 1.1503 H 0 0 0 0 0
-0.3089 0.3239 -1.4193 H 0 0 0 0 0
-2.9705 -2.7295 0.1044 H 0 0 0 0 0
-2.8083 -1.9210 1.7028 H 0 0 0 0 0
-4.1563 -1.4762 0.6031 H 0 0 0 0 0
-2.0398 1.4170 0.1863 H 0 0 0 0 0
-3.4837 0.7378 0.9384 H 0 0 0 0 0
-1.9129 0.5071 1.7551 H 0 0 0 0 0
-2.2450 0.4089 -1.8190 H 0 0 0 0 0
-2.3000 -1.3879 -2.0100 H 0 0 0 0 0
-3.7365 -0.4723 -1.4630 H 0 0 0 0 0
1.3299 -1.3744 -1.7823 H 0 0 0 0 0
2.0900 0.1756 -1.3923 H 0 0 0 0 0
-0.1953 3.1280 1.7699 H 0 0 0 0 0
0.7681 4.1684 0.7012 H 0 0 0 0 0
1.5832 2.9010 1.6404 H 0 0 0 0 0
1 7 1 0 0 0
1 13 1 0 0 0
2 12 1 0 0 0
3 12 2 0 0 0
4 13 2 0 0 0
5 6 1 0 0 0
5 8 1 0 0 0
5 9 1 0 0 0
5 10 1 0 0 0
6 7 1 0 0 0
6 15 1 0 0 0
6 16 1 0 0 0
7 11 1 0 0 0
7 17 1 0 0 0
8 18 1 0 0 0
8 19 1 0 0 0
8 20 1 0 0 0
9 21 1 0 0 0
9 22 1 0 0 0
9 23 1 0 0 0
10 24 1 0 0 0
10 25 1 0 0 0
10 26 1 0 0 0
11 12 1 0 0 0
11 27 1 0 0 0
11 28 1 0 0 0
13 14 1 0 0 0
14 29 1 0 0 0
14 30 1 0 0 0
14 31 1 0 0 0
M CHG 2 2 -1 5 1
M END
Regards,
Jochen
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