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