Hi, Yes, I think there is something wrong. When I convert the smiles of protonated imidazole (the ring of histidine) in mol2, only one hydrogen is keeped:
[H][N+]1=CNC=C1 imidazole
obabel imidazole.smi -O imidazole.mol2 --gen2D
(see attached files)
@<TRIPOS>MOLECULE
imidazole
6 6 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 H 0.2788 -1.7601 0.0000 H 1 LIG1 0.3119
2 N -0.3090 -0.9511 0.0000 N.ar 1 LIG1 -0.2231
3 C -1.3090 -0.9511 0.0000 C.ar 1 LIG1 0.4189
4 N -1.6180 -0.0000 0.0000 N.ar 1 LIG1 -0.0230
5 C -0.8090 0.5878 0.0000 C.ar 1 LIG1 0.2817
6 C -0.0000 -0.0000 0.0000 C.ar 1 LIG1 0.2337
@<TRIPOS>BOND
1 1 2 1
2 2 3 ar
3 3 4 ar
4 4 5 ar
5 5 6 ar
6 2 6 ar
Using -h option:
obabel imidazole.smi -O imidazoleH.mol2 --gen2D -h
(I think that the -h option should be by default when outputting in mol2
format).
@<TRIPOS>MOLECULE
imidazole
10 10 0 0 0
SMALL
GASTEIGER
@<TRIPOS>ATOM
1 H 0.2788 -1.7601 0.0000 H 1 LIG1 0.3101
2 N -0.3090 -0.9511 0.0000 N.ar 1 LIG1 -0.2500
3 C -1.3090 -0.9511 0.0000 C.ar 1 LIG1 0.2423
4 N -1.6180 -0.0000 0.0000 N.ar 1 LIG1 -0.2500
5 C -0.8090 0.5878 0.0000 C.ar 1 LIG1 0.1280
6 C -0.0000 -0.0000 0.0000 C.ar 1 LIG1 0.1280
7 H -1.9156 -1.7860 0.0000 H 1 LIG1 0.1581
8 H -2.5543 0.3042 0.0000 H 1 LIG1 0.3101
9 H -0.8090 1.6198 0.0000 H 1 LIG1 0.1117
10 H 0.9815 0.3189 0.0000 H 1 LIG1 0.1117
@<TRIPOS>BOND
1 1 2 1
2 2 3 ar
3 3 4 ar
4 4 5 ar
5 5 6 ar
6 2 6 ar
7 3 7 1
8 4 8 1
9 5 9 1
10 6 10 1
And converting the mol2 in smiles
obabel imidazoleH.mol2 -O imidazole2.smi
with version 2.3.2, give a segmentation fault... (see my previous message
(C++ / segfault / "open file" change?), I think there is a bug in
mol2format.cpp. Do you have this segfault too?).
The smiles output with 2.3.1 and 2.3.90 is:
N1CNCC1 imidazole # wrong
(even the aromaticity or double bonds are lost).
Indeed, for 2.3.90, there is a modification in mol2format.cpp to exclude
5-membered ring - so there is no segfault (line 391) ; and in 2.3.1, the
patch is not yet present.
Going back to version 2.2.3, the smiles output is now OK:
[nH]1c[nH]cc1 imidazole
Perhaps not making things easier, sorry...
Regards,
Pascal
2014-05-15 9:45 GMT+02:00 Fredrik Wallner <fred...@wallner.nu>:
> Hi,
>
> I suppose you are talking about protonated Histidine, since that’s what is
> in the picture as far as I can tell. However, your coordinates are at most
> a fragment of HIP. My 3D vision isn’t good enough to see structure from
> coordinates, and I don’t know all of OpenBabel’s formats well enough to
> tell which one you have. So, I therefor can’t really tell what your
> coordinates are showing and hence I cannot say if the SMILE is a good
> representation or not. But I can say that it is a difficult problem to
> assign proper bondorders to molecules when only coordinates are given,
> especially with missing charges and even more so if we are talking about
> fragments. Further, I don’t really understand the part where you state that
> the coordinates back-converted are different. Since SMILES don’t carry any
> information about coordinates, it will obviously be lost in the conversion.
>
> If you provide your input file and the commands you use for the
> conversion, I could try to look at it again.
>
> Kind regards,
> Fredrik
>
> 14 maj 2014 kl. 20:00 skrev Jiaguo <comingn...@hotmail.com>:
>
> > <http://forums.openbabel.org/file/n4657433/GV_hip.png>
> >
> > The SMILES given by Open Babel for the Hip (protonated Histine),
> coordinates
> > shown below, is "CCC1=CNCN1".
> >
> >> From the coordinates, it should be easily seen that Hip (protonated
> Histine)
> > is +1 charge. However, from the SMILES, this information (and the
> > coordination pattern) is lost. In fact, the coordinates back-converted
> from
> > SMILES is quite different.
> >
> > I would think this is wrong, but I wonder whether this is be design ?
> >
> > 16
> > Hip (protonated Histine)
> > C -5.83770117 -1.72505544 0.00000000
> > H -6.46253417 -1.64825244 -0.88982300
> > C -6.72432417 -1.57893344 1.23214100
> > H -7.46855917 -2.37525544 1.24137300
> > H -6.11155117 -1.64458144 2.13119600
> > C -7.48375317 -0.27683644 1.32108500
> > N -8.33394317 0.00896456 2.38296700
> > C -7.52063117 0.80076756 0.49245500
> > H -8.52477017 -0.59484244 3.16979800
> > C -8.84813417 1.20805556 2.18249600
> > N -8.37444817 1.69329156 1.06166200
> > H -7.03093917 1.04067456 -0.45133900
> > H -9.54804417 1.62859556 2.90455700
> > H -8.60883517 2.59721956 0.67685400
> > H -5.14137252 -0.91263534 0.00000000
> > H -5.33042678 -2.66716620 0.00000000
> >
> >
> >
> > --
> > View this message in context:
> http://forums.openbabel.org/The-SMILES-of-Hip-protonated-Histine-is-wrong-tp4657433.html
> > Sent from the General discussion mailing list archive at Nabble.com.
> >
> >
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imidazole.smi
Description: application/smil
imidazoleH.mol2
Description: chemical/mol2
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