Dear Fredrik and Pascal,
Thank you for your time very much !
Thank you Pascal for your knowledgeable analysis !!
Could you help to comment on how to obtain OpenBabel v2.2.3 binaries on the
latest CentOS 5 and 6 ?
It would be great if you would comment on the procedure how to get a full
static build on linux for the v2.2.3 version ! I mean, the “static build”
options appeard after 2010, while v2.2.3 was from 2009.
http://ehc.ac/p/openbabel/mailman/message/26441509/
http://openbabel.org/wiki/CMake#Static_builds
Best wishes,
Xichen Li
From: Pascal Muller-3 [via Open Babel]
Sent: Thursday, May 15, 2014 10:32 AM
To: Jiaguo
Subject: Re: The SMILES of Hip (protonated Histine) is wrong ?
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 <[hidden email]>:
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 <[hidden email]>:
> <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
>
>
>
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