Here's the doxygen docs. I'll check it in once I've checked the HTML.
Note that I've changed the method to return a bool (this method will
be new in 2.3).
/**
* Convert a molecule's Tetrahedral Stereo objects to a series of hash or
* wedge bonds. Note that the molecule itself is not modified; the result
* is returned in the maps @param updown and @param from, which indicate
* the origin and direction of each hash or wedge bond.
*
* When converting, the following guidelines are followed when trying to
* find the best candidate bond to set up/down for each tetrahedral stereo
* object:
* 1. **Should not already be set**
* 2. Should not be connected to a 2nd tet center
* (this is acceptable in theory, as the wedge is only at one end but
* it may cause confusion and thus we avoid it)
* 3. Preferably is not in a cycle
* 4. Preferably is a terminal H
*
* If no bond can be found that matches all of these rules (and there is
* a slim possibility of this at the moment) then an error message is logged
* and the function returns false.
*
* @param mol The molecule.
* @param updown A map of OBStereo::BondDirection for each hash/wedge bond
* @param from A map of OBStereo::Ref indicate the origin of each
hash/wedge bond
*
* @since version 2.3
*/
OBAPI bool TetStereoTo0D(OBMol &mol,
std::map<OBBond*, enum OBStereo::BondDirection> &updown,
std::map<OBBond*, OBStereo::Ref> &from);
This function is called from inchiformat and mdlformat.
- Noel
On 23 August 2010 18:11, Noel O'Boyle <baoille...@gmail.com> wrote:
> On 23 August 2010 15:43, Chris Morley <c.mor...@gaseq.co.uk> wrote:
>> I'm trying to get wedge and hash bonds displayed in SVGFormat,
>> starting with a 0D molecule. (Note the new SMILES input.)
>>
>> This doesn't:
>> obabel -:b...@h](F)I --gen2D -O out.svg
>>
>> This does:
>> obabel -:b...@h](F)I -omol --gen2D -xw | obabel -imol -O out.svg
>>
>> This doesn't:
>> obabel -:b...@h](F)I -omol --gen2D | obabel -imol -O out.svg
>>
>> So presumably calling TetStereoTo0D() does the job and it really
>> should be called in --gen2D. There is a lack of documentation "(HASSLE
>> NOEL ABOUT THIS!!)" and I don't understand where the parameter
>> std::map<OBBond*, OBStereo::Ref> &from should come from.
>>
>> Can anybody help?
>
> Consider me hassled. I'll write these docs in the next few minutes
> once I figure it out.
>
>> I also guess we could talk about why it is necessary for
>>
>> obabel -:b...@h](F)I -omol | obabel -imol -osmi
>>
>> to drop the stereo information.
>
> Discussed at
> http://baoilleach.blogspot.com/2010/02/how-to-store-stereochemistry-in-mol.html.
> I don't think it's neccessary to drop the stereo but the spec says to
> do it. I added the "s" option to MDL to enable the atom stereo parity
> to be optionally retained. Hopefully this works for you.
>
>> Chris
>>
>>
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