Hello,
I have a mol2 file:
###########
@<TRIPOS>MOLECULE
CHEMBL11635_frag_1
13 14 0 0 0
SMALL
GASTEIGER
Energy = 0
@<TRIPOS>ATOM
1 C11 1.3913 1.3016 1.1119 C.ar 1 UNNAMED1411
0.2272
2 C9 -0.6008 1.3104 0.2794 C.ar 14
UNNAMED141414 0.1335
3 C12 2.5674 1.2512 1.8692 C.ar 14
UNNAMED141414 0.6770
4 N18 2.6619 0.5252 -0.8633 N.ar 14
UNNAMED141414 -0.4811
5 N10 0.0675 1.5811 1.3901 N.ar 14
UNNAMED141414 -0.5653
6 O13 2.5306 1.4983 3.0409 O.2 14
UNNAMED141414 -0.5600
7 N14 3.7935 0.8764 1.2941 N.ar 14
UNNAMED141414 -0.5341
8 C15 4.9609 0.6794 2.0987 C.3 14
UNNAMED141414 0.3001
9 C16 3.8108 0.4728 -0.0439 C.ar 14
UNNAMED141414 0.7940
10 O17 4.8344 0.0650 -0.5104 O.2 14
UNNAMED141414 -0.5600
11 C19 2.7929 0.1203 -2.2395 C.3 14
UNNAMED141414 0.3001
12 C20 1.5249 0.9487 -0.2151 C.ar 14
UNNAMED141414 -0.0876
13 N21 0.2793 1.0645 -0.7541 N.ar 14
UNNAMED141414 0.0332
@<TRIPOS>BOND
1 5 2 ar
2 1 5 ar
3 3 1 ar
4 6 3 2
5 7 3 ar
6 8 7 1
7 9 7 ar
8 10 9 2
9 4 9 ar
10 11 4 1
11 12 1 ar
12 13 12 ar
13 13 2 ar
14 12 4 ar
###############
and I would like to convert it to canonical smile format.
Using version 2.2.0 I get:
babel -imol2 tt.mol2 -ocan
Cn1c(=O)n(C)c2nc[nH]c2c1=O CHEMBL11635_frag_1
1 molecule converted
25 audit log messages
That seems good.
Using version 2.3.1 I get:
/home/luisa/openbabel-2.3.1/bin/babel -imol2 tt.mol2 -ocan
CN1[C@H]2NCN[C@H]2C(=O)N(C1=O)C CHEMBL11635_frag_1
1 molecule converted
1 info messages 41 audit log messages 2 debugging messages
That is wrong because arimatic atoms are missed.
Anybody knows what could be the problem?
Thank you and best regards
Luisa
--
Luisa Pugliese, Ph.D.
luisa.pugli...@safan-bioinformatics.it
S.A.F.AN. BIOINFORMATICS
via Fulvio Croce 23/B
10136 Torino -Italy
www.safan-bioinformatics.it
tel/fax +390112767365
cell. 333-6130644
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