[Open Babel] error in MOL2 -> HIN conversion?

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

[Open Babel] error in MOL2 -> HIN conversion?

Rajarshi Guha
Hi, I have a MOL2 file for naphthalene (attached to this mail). When I
convert it to HIN (also attached to this mail) by

babel -imol2 naphthalene.mol2 -ohin naphthalene.hin

the C-C bonds are marked as alternating double and single rather than
'a'.

The mol2 version has the C-C bonds marked as 'ar'

(I'm using 1.100.2)

Thanks,
 
-------------------------------------------------------------------
Rajarshi Guha <[hidden email]> <http://jijo.cjb.net>
GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE
-------------------------------------------------------------------
Every nonzero finite dimensional inner product
space has an orthonormal basis.
It makes sense, when you don't think about it.


naphthalene.hin (1K) Download Attachment
naphthalene.mol2 (1K) Download Attachment
Reply | Threaded
Open this post in threaded view
|

Re: [Open Babel] error in MOL2 -> HIN conversion?

Mathias W.
Rajarshi Guha wrote:

>Hi, I have a MOL2 file for naphthalene (attached to this mail). When I
>convert it to HIN (also attached to this mail) by
>
>babel -imol2 naphthalene.mol2 -ohin naphthalene.hin
>
>the C-C bonds are marked as alternating double and single rather than
>'a'.
>
>The mol2 version has the C-C bonds marked as 'ar'
>  
>
Yes, but in your naphthalene the C-Atoms are typed C.2 not C.ar
First I thought this could be the reason so I corrected it and
 I tried both with SYBYL naphthalene (from fragment library) and with a
modified naphthalene from Rajarshi using Open Babel 2.0.0b5-20051001.

I've never seen HIN files before, but the result seems to be the same
(no 'a's there)

Mathias

mol 1 naphthalene
atom 1 - C   **  - -0.05403  1.21580   1.39550   0.00000 3 2 d 9 s 11 s
atom 2 - C   **  - -0.06117  2.42700   0.69840   0.00000 3 1 d 3 s 12 s
atom 3 - C   **  - -0.06117  2.42700  -0.69840   0.00000 3 2 s 4 d 13 s
atom 4 - C   **  - -0.05403  1.21580  -1.39550   0.00000 3 3 d 10 s 14 s
atom 5 - C   **  - -0.05403 -1.21580  -1.39550   0.00000 3 6 s 10 d 15 s
atom 6 - C   **  - -0.06117 -2.42700  -0.69840   0.00000 3 5 s 7 d 16 s
atom 7 - C   **  - -0.06117 -2.42700   0.69840   0.00000 3 6 d 8 s 17 s
atom 8 - C   **  - -0.05403 -1.21580   1.39550   0.00000 3 7 s 9 d 18 s
atom 9 - C   **  - -0.01788  0.00000   0.70090   0.00000 3 1 s 8 d 10 s
atom 10 - C   **  - -0.01788  0.00000  -0.70090   0.00000 3 4 s 5 d 9 s
atom 11 - H   **  -  0.06236  1.23060   2.48120   0.00000 1 1 s
atom 12 - H   **  -  0.06178  3.36720   1.24140   0.00000 1 2 s
atom 13 - H   **  -  0.06178  3.36720  -1.24140   0.00000 1 3 s
atom 14 - H   **  -  0.06236  1.23060  -2.48120   0.00000 1 4 s
atom 15 - H   **  -  0.06236 -1.23060  -2.48120   0.00000 1 5 s
atom 16 - H   **  -  0.06178 -3.36720  -1.24140   0.00000 1 6 s
atom 17 - H   **  -  0.06178 -3.36720   1.24140   0.00000 1 7 s
atom 18 - H   **  -  0.06236 -1.23060   2.48120   0.00000 1 8 s
endmol 1

mol 1 naphthalene.csf
atom 1 - C   **  - -0.05403 -0.00000   0.00000   0.00000 3 2 d 6 s 11 s
atom 2 - C   **  - -0.06117 -1.15280  -0.74600   0.00040 3 1 d 3 s 12 s
atom 3 - C   **  - -0.06117 -1.08950  -2.16080   0.00000 3 2 s 4 d 13 s
atom 4 - C   **  - -0.05403  0.12520  -2.80100   0.00040 3 3 d 5 s 14 s
atom 5 - C   **  - -0.01788  1.33500  -2.05370   0.00000 3 4 s 6 d 10 s
atom 6 - C   **  - -0.01788  1.27170  -0.63630   0.00050 3 5 d 1 s 7 s
atom 7 - C   **  - -0.05403  2.48150   0.11100   0.00010 3 6 s 8 d 15 s
atom 8 - C   **  - -0.06117  3.69600  -0.52930   0.00020 3 7 d 9 s 16 s
atom 9 - C   **  - -0.06117  3.75930  -1.94400   0.00030 3 8 s 10 d 17 s
atom 10 - C   **  - -0.05403  2.60670  -2.69000   0.00020 3 9 d 5 s 18 s
atom 11 - H   **  -  0.06236 -0.03850   1.08330   0.00030 1 1 s
atom 12 - H   **  -  0.06178 -2.12350  -0.26360   0.00020 1 2 s
atom 13 - H   **  -  0.06178 -2.01330  -2.72800   0.00020 1 3 s
atom 14 - H   **  -  0.06236  0.18360  -3.88340   0.00020 1 4 s
atom 15 - H   **  -  0.06236  2.42290   1.19340   0.00020 1 7 s
atom 16 - H   **  -  0.06178  4.61970   0.03800   0.00020 1 8 s
atom 17 - H   **  -  0.06178  4.72980  -2.42670   0.00020 1 9 s
atom 18 - H   **  -  0.06236  2.64490  -3.77330   0.00020 1 10 s
endmol 1

# Name: naphthalene
# Creating user name: becker
# Creation time: Wed Jul  7 17:43:21 2004

# Modifying user name: becker
# Modification time: Wed Jul  7 17:43:21 2004

@<TRIPOS>MOLECULE
naphthalene
   18    19     1     1     0
SMALL
NO_CHARGES


@<TRIPOS>ATOM
      1 C1          1.2158    1.3955    0.0000 C.ar      1 NAPHTHALENE    0.0000
      2 C2          2.4270    0.6984    0.0000 C.ar      1 NAPHTHALENE    0.0000
      3 C3          2.4270   -0.6984    0.0000 C.ar      1 NAPHTHALENE    0.0000
      4 C4          1.2158   -1.3955    0.0000 C.ar      1 NAPHTHALENE    0.0000
      5 C5         -1.2158   -1.3955    0.0000 C.ar      1 NAPHTHALENE    0.0000
      6 C6         -2.4270   -0.6984    0.0000 C.ar      1 NAPHTHALENE    0.0000
      7 C7         -2.4270    0.6984    0.0000 C.ar      1 NAPHTHALENE    0.0000
      8 C8         -1.2158    1.3955    0.0000 C.ar      1 NAPHTHALENE    0.0000
      9 C9          0.0000    0.7009    0.0000 C.ar      1 NAPHTHALENE    0.0000
     10 C10         0.0000   -0.7009    0.0000 C.ar      1 NAPHTHALENE    0.0000
     11 H1          1.2306    2.4812    0.0000 H         1 NAPHTHALENE    0.0000
     12 H2          3.3672    1.2414    0.0000 H         1 NAPHTHALENE    0.0000
     13 H3          3.3672   -1.2414    0.0000 H         1 NAPHTHALENE    0.0000
     14 H4          1.2306   -2.4812    0.0000 H         1 NAPHTHALENE    0.0000
     15 H5         -1.2306   -2.4812    0.0000 H         1 NAPHTHALENE    0.0000
     16 H6         -3.3672   -1.2414    0.0000 H         1 NAPHTHALENE    0.0000
     17 H7         -3.3672    1.2414    0.0000 H         1 NAPHTHALENE    0.0000
     18 H8         -1.2306    2.4812    0.0000 H         1 NAPHTHALENE    0.0000
@<TRIPOS>BOND
     1    2    1 ar  
     2    1    9 ar  
     3    3    2 ar  
     4    4    3 ar  
     5   10    4 ar  
     6    5    6 ar  
     7    5   10 ar  
     8    6    7 ar  
     9    7    8 ar  
    10    8    9 ar  
    11    9   10 ar  
    12    1   11 1    
    13    2   12 1    
    14    3   13 1    
    15    4   14 1    
    16    5   15 1    
    17    6   16 1    
    18    7   17 1    
    19    8   18 1    
@<TRIPOS>SUBSTRUCTURE
     1 NAPHTHALENE     5 PERM              0 ****  ****    0 ROOT
@<TRIPOS>NORMAL
@<TRIPOS>FF_PBC
FORCE_FIELD_SETUP_FEATURE Force Field Setup information
v1.0  0 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 NONE 2 0 0 0 0 0 0 0 0 0 0 0 0
Reply | Threaded
Open this post in threaded view
|

Re: [Open Babel] error in MOL2 -> HIN conversion?

Geoffrey Hutchison

On Nov 1, 2005, at 1:15 PM, Mathias weigt wrote:

> Yes, but in your naphthalene the C-Atoms are typed C.2 not C.ar
> First I thought this could be the reason so I corrected it and
> I tried both with SYBYL naphthalene (from fragment library) and  
> with a modified naphthalene from Rajarshi using Open Babel  
> 2.0.0b5-20051001.

Right. The issue isn't so much the atom typing (in either case, the  
internal OBMol is the same after OBMol::Kekulize() is run).

The output for the HIN format has bond types. In this case, the code  
looked at the bond orders and wrote that. But until the change I put  
in CVS this morning, it did not check if the bond was aromatic as a  
special case. It does now.

Cheers,
-Geoff


nap.hin (1K) Download Attachment