On Dec 15, 2006, at 1:07 PM, Randy Heiland wrote:
> Eric,
> Need a bit more help on this... how can I invoke this reader
> programmatically from my plugin and display the model in the viewer
> window? Til now, with PDB formatted files, I've done:
>
> fp = open(tmpfile.name, 'w')
> fp.write(pdbstr)
> fp.close()
> self.model = chimera.openModels.open(tmpfile.name, type='PDB',
> identifyAs=id[0])
If your temp file's name ends in '.sdf' then you don't have to supply
a 'type' keyword to openModels.open(). If not, then with the code I
gave you the 'type' would be "Structure Data Format" (it's the
"fileType" variable in ReadSDF/fileInfo.py). You might want to
import that variable and use it instead of a fixed string, because in
the next release of Chimera the string will be "MDL MOL/SDF" since I
enhanced the reader to handle MOL files as well.
Also, openModels.open() always returns a _list_ of models, even if
the input only creates one model.
> Now I have a 'pdbstr' that's really an sdf format, and when I try to
> substitue type='PDB' w/ 'SDF', it doesn't recognize it.
>
> And when I try the following, it doesn't complain, however no model is
> displayed:
> import ReadSDF
>
> fp = open(tmpfile.name, 'w')
> fp.write(sdfstr)
> fp.close()
> self.model = ReadSDF.readSDF(tmpfile.name)
The readSDF() function returns a list of models. To add them to the
list of open models, use chimera.openModels.add(), probably like this:
self.models = ReadSDF.readSDF(tmpfile.name)
chimera.openModels.add(self.models)
--Eric
