Re: [modeller_usage] Using an alignment object in automodel
To: Will Dampier <>
Subject: Re: [modeller_usage] Using an alignment object in automodel
From: Modeller Caretaker <>
Date: Tue, 16 Feb 2010 11:37:51 -0800
Cc:
On 02/15/2010 09:56 AM, Will Dampier wrote:
I was wondering if there was a trick to using an alignment object
produced by alingment.salign() in an automodel.
My current method writes the alignment to a file and then re-reads it
with automodel. This is extremely clunky but based on the docs it
seems the only way to go.
Yes, unfortunately that is currently the only way to do it. There are
various parts of the automodel code that read in part or all of the
alignment file (e.g. auto_align, final_malign3d). It wouldn't be
impossible to make them work with alignment objects instead, but it
would be hard to do it without breaking existing code. I'll add it as a
wishlist item.
As I expand this using the parrellel toolbox it becomes difficult to
manage filenames, etc.
True, although you can use Python's tempfile module to handle this for
you automatically.