[modeller_usage] Python Modeller Script

[Ricardo Nicoluci <nicoluci AT gmail.com>]

Hi,

We used to have a script for modeller in the old type way. Now we
translated it to python mode, but the function
automodel.generate_method and automodel.rand_method are not working
properly. The following error occurs:

when a.generate_method is activated:

Traceback (most recent call last):
  File "mod.py", line 75, in ?
   
a.make()                           
# do the actual homology modelling
  File "/usr/local/modeller8v1/modlib/modeller/automodel/loopmodel.py", line 28, in make
    automodel.make(self, exit_stage)
  File "/usr/local/modeller8v1/modlib/modeller/automodel/automodel.py", line 100, in make
    self.homcsr(exit_stage)
  File "/usr/local/modeller8v1/modlib/modeller/automodel/automodel.py", line 334, in homcsr
    self.generate_method(self, aln)
TypeError: 'str' object is not callable


when a.rand_method is activated:

 File "mod.py", line 75, in ?
   
a.make()                           
# do the actual homology modelling
  File "/usr/local/modeller8v1/modlib/modeller/automodel/loopmodel.py", line 28, in make
    automodel.make(self, exit_stage)
  File "/usr/local/modeller8v1/modlib/modeller/automodel/automodel.py", line 110, in make
    self.multiple_models()
  File "/usr/local/modeller8v1/modlib/modeller/automodel/loopmodel.py", line 32, in multiple_models
    automodel.multiple_models(self)
  File "/usr/local/modeller8v1/modlib/modeller/automodel/automodel.py", line 197, in multiple_models
    self.single_model(num)
  File "/usr/local/modeller8v1/modlib/modeller/automodel/automodel.py", line 210, in single_model
    self.rand_method(self)
TypeError: 'str' object is not callable


Also I would like suggestions to the script file that is attached.

Thanks,

-- 
Ricardo de Paula Nicoluci
PhD Student
Medicinal Chemistry Laboratory
IFSC - University of Sao Paulo
Sao Carlos - SP - Brazil