Hi,
The implementation of the new stereochimestry code is over. It works for
Pgchem and Mychem (== we have the same results as obgrep).
Here's a sample from the code:
Serialization:
vector<OBGenericData*>::iterator data;
vector<OBGenericData*> stereoData;
if (mol.HasData(OBGenericDataType::StereoData)) {
stereoData = mol.GetAllData(OBGenericDataType::StereoData);
}
unsigned int numstereo = stereoData.size();
for (data = stereoData.begin(); data != stereoData.end(); ++data) {
OBStereo::Type type;
type = ((OBStereoBase*)*data)->GetType();
if (type == OBStereo::Tetrahedral) {
OBTetrahedralStereo *ts =
dynamic_cast<OBTetrahedralStereo*>(*data);
OBTetrahedralStereo::Config config = ts->GetConfig();
stereoptr->type = type;
stereoptr->atomids[0] = config.center;
stereoptr->atomids[1] = config.towards;
stereoptr->refs[0] = config.refs[0];
stereoptr->refs[1] = config.refs[1];
stereoptr->refs[2] = config.refs[2];
stereoptr->winding = config.winding;
stereoptr->view = config.view;
} else if (type == OBStereo::SquarePlanar) {
OBSquarePlanarStereo *sp =
dynamic_cast<OBSquarePlanarStereo*>(*data);
OBSquarePlanarStereo::Config config = sp->GetConfig();
stereoptr->type = type;
stereoptr->atomids[0] = config.center;
stereoptr->refs[0] = config.refs[0];
stereoptr->refs[1] = config.refs[1];
stereoptr->refs[2] = config.refs[2];
stereoptr->refs[3] = config.refs[3];
stereoptr->shape = config.shape;
} else if (type == OBStereo::CisTrans) {
OBCisTransStereo *ct = dynamic_cast<OBCisTransStereo*>(*data);
OBCisTransStereo::Config config = ct->GetConfig();
stereoptr->type = type;
stereoptr->atomids[0] = config.begin;
stereoptr->atomids[1] = config.end;
stereoptr->refs[0] = config.refs[0];
stereoptr->refs[1] = config.refs[1];
stereoptr->refs[2] = config.refs[2];
stereoptr->refs[3] = config.refs[3];
stereoptr->shape = config.shape;
}
++stereoptr;
}
Unserialization:
for (i=0; i < nstereo; ++i) {
if (stereoptr->type == OBStereo::Tetrahedral) {
OBTetrahedralStereo::Config cfg;
cfg.center = stereoptr->atomids[0];
cfg.towards = stereoptr->atomids[1];
cfg.refs =
OBStereo::MakeRefs(stereoptr->refs[0],stereoptr->refs[1],stereoptr->refs[2]);
cfg.winding = stereoptr->winding;
cfg.view = stereoptr->view;
OBTetrahedralStereo *obts = new OBTetrahedralStereo(&mol);
obts->SetConfig(cfg);
mol.SetData(obts);
} else if (stereoptr->type == OBStereo::SquarePlanar) {
OBSquarePlanarStereo::Config cfg;
cfg.center = stereoptr->atomids[0];
cfg.refs =
OBStereo::MakeRefs(stereoptr->refs[0],stereoptr->refs[1],stereoptr->refs[2],stereoptr->refs[3]);
cfg.shape = stereoptr->shape;
OBSquarePlanarStereo *obsp = new OBSquarePlanarStereo(&mol);
obsp->SetConfig(cfg);
mol.SetData(obsp);
} else if (stereoptr->type == OBStereo::CisTrans) {
OBCisTransStereo::Config cfg;
cfg.begin = stereoptr->atomids[0];
cfg.end = stereoptr->atomids[1];
cfg.refs =
OBStereo::MakeRefs(stereoptr->refs[0],stereoptr->refs[1],stereoptr->refs[2],stereoptr->refs[3]);
cfg.shape = stereoptr->shape;
OBCisTransStereo *obct = new OBCisTransStereo(&mol);
obct->SetConfig(cfg);
mol.SetData(obct);
}
++stereoptr;
}
Should I add to the end of unserialization :
if (nstereo > 0) {
mol.SetChiralityPerceived();
}
Do not hesitate to send us any comments about this code.
Cheers,
Jerome
On ven., 2011-12-09 at 17:17 +0100, Jérôme Pansanel wrote:
> Hi,
>
> I will wait for the release of Mychem 0.9.0 (it is based on Open Babel
> 2.3.0).
>
> Ernst-Georg, I have started the serialization of the OBCisTransStereo
> and OBTetrahedralStereo objects. I will send you the code next week.
>
> Cheers,
>
> Jerome
>
> On ven., 2011-12-09 at 11:15 +0000, Ernst-Georg Schmid wrote:
> > Hi,
> >
> > >The OBChiralData isn't used anymore. Also the functions
> > >OBAtom::IsClockwise, and OBAtom::IsAntiClockwise are obsolate.
> > >Instead, you should serialize the OBCisTransStereo and
> > >OBTetrahedralStereo data objects.
> >
> > thank you. This was the missing link.
> >
> > Best regards,
> >
> > Ernst-Georg
> >
> >
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