Dear Ben,

 

I asked a similar question some time ago and unfortunately get_model_filename is not enough.

The problem is that the code has “file = self.sequence + '.xxx'” and “root_name=self.sequence”  and “root_name=sequence” sprinkled all over the place (and also loopmodel has a separate get_loop_model_filename).

 

I second the request to provide a nice get_root_name or get_job_name hook (defaulting to self.sequence) it would be very convenient because often one has to play with various model parameters for the same sequence and alignment.

 

Thank you

Eugene

 

-----Original Message-----

From: Modeller Caretaker

Sent: Saturday, August 8, 2020 1:33 AM

To: Brian Wiley ; modeller_usage@salilab.org

Subject: Re: [modeller_usage] Change ROOT_NAME for automodel.make()

 

On 8/7/20 2:21 PM, Brian Wiley wrote:

> a = automodel(env,

>                alnfile = 'TSC2_6ssh.ali',

>                knowns = ('6ssh'),

>                sequence = 'TSC2_HUMAN')

>

> a.make() # Here I want the prefix to be 'TSC2_6ssh' and not

> 'TSC2_HUMAN'  so all files and pdb file at end would be

> TSC2_6ssh.B99990001.pdb

 

automodel is written under the assumption that files are named for the sequence. If you want to name the output PDB files differently, that's straightforward; just override get_model_filename() as per https://salilab.org/modeller/9.24/manual/node76.html

 

If you want to name the other output files differently, there isn't currently a mechanism for that, but it would be easy enough to modify the Python code to do so.

 

Ben Webb, Modeller Caretaker

--

modeller-care@salilab.org             https://salilab.org/modeller/

Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage

_______________________________________________

modeller_usage mailing list

modeller_usage@salilab.org

https://salilab.org/mailman/listinfo/modeller_usage