suggestion for atomtyp.txt and types.txt

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suggestion for atomtyp.txt and types.txt

Menno Deij
Hiya,

I'm working on getting Dreiding atom types from Babel and so far it's
working pretty good. I had to make some changes to the types defined and
the typing rules. At the end you can find a diff between atomtyp.txt and
types.txt

The following things have been added to atomtyp.txt
* typing of hydrogens capable of forming a hydrogen bond, e.g. O-H, N-H
and S-H
* typing of hydrogens bridging two borons, e.g. in B2H6
* typing of aromatic oxygen, e.g. in furan
* typing of sp hybridized oxygen and nitrogen

And to types.txt
* changed the DRE type for sodium from Xx to Na (Dreiding does support Na(+))
* added HS, HB, O1 and Oar INT types to accomodate for the types  defined
above.

Anyway, I hope this might end up in some form or another in OpenBabel. If
you have suggestions to do this typing better, I'd sure like to hear 'm!

Best wishes,

Menno Deij

diff atomtyp.txt_ORIG atomtyp.txt
156a157,169

> # hydrogens that can be involved in a hydrogen bond
> EXTTYP  [#1]~O                                  HO
> EXTTYP  [#1]~S                                  HS
> EXTTYP  [#1]~N                                  HN
> EXTTYP  [#1]~n                                  HN
> # hydrogens in a bridge between two borons, e.g. diborane
> EXTTYP  [#1]~B~B                                HB
> # aromatic oxygen, e.g. furan
> EXTTYP  [o]                                     Oar
> # sp oxygen, e.g. carbon monoxide
> EXTTYP  [O]#*                                   O1
> # sp nitrogen, e.g. acetonitrile
> EXTTYP  [N]#*
158c171
< ############################# End Extra Definitions
##########################
---
> ############################ End Extra Definitions
##########################

diff types.txt_ORIG types.txt
17c17
< 183   19
---
> 188   19
93c93
< Na    11      0       25      9       Na      Na      0       Z       9
     Na      21      NA      Xx      20      19      Na.6    74      21
---
> Na    11      0       25      9       Na      Na      0       Z       9
     Na      21      NA      Na      20      19      Na.6    74      21
203a204,207
> HS    1       0       42      21      H       H       0       H       11
     H       13      H       H_HB    15      25      H.1     185     26
> HB    1       0       42      21      H       H       0       H       11
     H       13      H       H_b     15      25      H.1     186     26
> Oar   8       2       15      7       O       O2      0       O       81
     O.2     9       O2      O_R     11      11      O.3     187     26
> O1    8       0       62      30      O       O       3       O       2
     O.      33      O       O_1     2       1       O.0     188     26



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