Hi!
In the documentation https://salilab.org/modeller/9.15/manual/node75.html the signature for automodel.get_model_filename() is declared as
get_model_filename(sequence, id1, id2, file_ext)
But I got the following error: Traceback (most recent call last): File "d:/data/modeller/poly_modeller/ppmod/make_homology_model.py", line 97, in <module> a.make() File "c:\bin\Modeller\modlib\modeller\automodel\automodel.py", line 121, in make self.multiple_models(atmsel) File "c:\bin\Modeller\modlib\modeller\automodel\automodel.py", line 225, in multiple_models self.outputs.append(self.single_model(atmsel, num)) File "c:\bin\Modeller\modlib\modeller\automodel\automodel.py", line 308, in single_model self.pdb_ext) TypeError: get_model_filename() takes exactly 4 arguments (5 given)
Of course one must include self as well, so the following works:
def get_model_filename(self, sequence, id1, id2, file_ext):
Perhaps in the documentation the self could be included as well? It's obvious in hindsight, but still took me 15 minutes to figure out.
Or maybe a quick example could be added: How to move the pdb files into subfolder outdir
class MyModel(automodel): def get_model_filename(self, sequence, id1, id2, file_ext): print self, sequence, id1, id2, file_ext
return "outdir/test-prefix-{id1:02}-{id2:02}{file_ext}".format( id1=id1, id2=id2, file_ext=file_ext)
PS: Is there some way to move all the generated files (including traces and sch and rsr files) into a subfolder? Scanning the sourcecode I see that redefining modfile.default could work.
Thanks & All the best, Ajasja