Tim,
Thanks - this is what I need! I am going to save wavy bonds in sd file for
structures recognized by osra. Having setWavy() wrapper would be great too.
By the way I am at the ACS meeting, are you here as well?
Igor
On Aug 20, 2012 10:23 AM, "Tim Vandermeersch" <tim.vandermeer...@gmail.com>
wrote:
> On Mon, Aug 20, 2012 at 4:12 PM, Tim Vandermeersch
> <tim.vandermeer...@gmail.com> wrote:
> > On Mon, Aug 20, 2012 at 4:08 PM, Tim Vandermeersch
> > <tim.vandermeer...@gmail.com> wrote:
> >> On Mon, Aug 20, 2012 at 3:18 PM, Igor Filippov
> >> <igor.v.filip...@gmail.com> wrote:
> >>> Noel,
> >>>
> >>> Thank you - could you give just a few lines example how to do this?
> >>> I looked at the suggested header file and I'm still stumped :(
> >>
> >> The code to set an atom's tetrahedral stereochemistry to unknown goes
> >> something like this:
> >>
> >> #include <openbabel/stereo/tetrahedral.h>
> >>
> >> void SetTetrahedtalUnknown(OBAtom *atom)
> >> {
> >> OBStereoFacade facade(atom->GetParent());
> >> OBTetrahedralStereo *stereo;
> >> if (facade.HasTetrahedralStereo(atom->GetId())
> >> stereo = facade.GetTetrahedralStereo(atom->GetId());
> >> else
> >> stereo = new OBTetrahedralStereo(atom->GetParent());
> >>
> >> OBTetrahedralStereo::Config config = stereo->GetConfig();
> >> config.center = atom->GetId();
> >> config.specified = true;
> >> config.winding = OBStereo::UnknownWinding;
> >> stereo->SetConfig(config);
> >>
> >> if (!facade.HasTetrahedralStereo(atom->GetId())
> >> atom->GetParent()->SetData(stereo);
> >> }
> >>
> >> To set the stereochemistry unspecified, change true to false in the
> >> code above and remove the winding line. However, for many purposes
> >> this would be the same as not having an OBTetrahedralStereo object for
> >> that atom. Where needed, OpenBabel has algorithms to find which atoms
> >> are stereogenic and does not rely on the user specifying which atoms
> >> are stereogenic.
> >>
> >> Could you tell me a bit more on why you would need wavy bonds? The
> >> only application I can think of is for 2D depiction. OpenBabel's 2D
> >> depiction only draws wavy bonds when the stereochemistry is specified
> >> as unknown (could be RS, R or S). Another use of wavy bonds could be
> >> to inform the reader that the atom is stereogenic and is a RS mixture
> >> (or unknown) but this is not used by OpenBabel. This could easily be
> >> achieved by calling SetTetrahedralUnknown() though and interpret the
> >> depiction differently.
> >>
> >> There is the TetStereoToWedgeHash() function in
> >> src/stereo/perception.cpp that selects the optimal bond to be the
> >> wavy.
> >
> > Hmm, I just though of the use case where you need to write a wavy bond
> > to a file format.I don't know what file formats support wavy bond
> > output but if they do the same applies.
>
> Perhaps it's better to wait a few minutes before sending a mail but... :)
>
> We could add SetSpecified(unsigned long atomId), IsSpecified(unsigned
> int atomId), SetUnknown(...), IsUnknown(...) functions to stereo.h to
> make it easier for users. Additionally we could add SetWavy(...) and
> IsWavy(...) wrapper functions around [Set,Is]Unknown(...) for library
> users that want to interpret wavy bonds differently. In any case,
> OpenBabel selects which bond should be wavy and there is no way of
> explicitly specifying the wavy bonds but this can be seen as positive
> since this would be error-prone. Think of this as a feature :) If we
> add these functions, we should probably also check if the atom is
> stereogenic or not and allow for an override as in SetWavy(unsigned
> long atomId, bool force = false). Any ideas?
>
> Tim
>
> > Tim
> >
> >> Tim
> >>
> >>>
> >>> Igor
> >>>
> >>> On Sun, 2012-08-19 at 05:48 -0400, Noel O'Boyle wrote:
> >>>> You can set the corresponding stereo config to defined=false.
> >>>> Internally stereo is not stored as an attribute of a bond.
> >>>>
> >>>> - Noel
> >>>>
> >>>> On 17 August 2012 19:12, Igor Filippov [Contr] <
> filipp...@mail.nih.gov> wrote:
> >>>> > Dear colleagues,
> >>>> >
> >>>> > Is it possible to set a bond as "wavy" or to check if it has "wavy"
> >>>> > attribute in OB similar to SetWedge() and IsWedge()?
> >>>> >
> >>>> >
> >>>> > Best regards,
> >>>> > Igor
> >>>> >
> >>>> >
> >>>> >
> >>>> >
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