Regarding the PS: I solved the issue by a well placed os.chdir and some other minor tweaks.
Best, Ajasja
On 23 October 2015 at 16:07, Ajasja Ljubetič ajasja.ljubetic@gmail.com wrote:
> 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 >