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Re: [modeller_usage] modeller_usage Digest, Vol 19, Issue 52

Nevermind.  I just created a new function reset_defaults() to rewrite self.set_defaults() in automodel and I can get it.  Thanks for your help.

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From: modeller_usage <> On Behalf Of 
Sent: Friday, August 7, 2020 6:47 PM
To: 
Subject: modeller_usage Digest, Vol 19, Issue 52


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Today's Topics:

   1. Re: Change ROOT_NAME for automodel.make() (Modeller Caretaker)
   2. Re: Change ROOT_NAME for automodel.make() (Brian Wiley)


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Message: 1
Date: Fri, 7 Aug 2020 15:33:39 -0700
From: Modeller Caretaker <>
To: Brian Wiley <>, ""
        <>
Subject: Re: [modeller_usage] Change ROOT_NAME for automodel.make()
Message-ID: <>
Content-Type: text/plain; charset=windows-1252; format=flowed

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://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalilab.org%2Fmodeller%2F9.24%2Fmanual%2Fnode76.html&amp;data=02%7C01%7Cbwiley4%40jhu.edu%7C283a9b9ef68145537d9308d83b2404e8%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637324373239714284&amp;sdata=G4e1TN3OZEKxZVV4XxVA7ZW0s1EEto%2FRJr1fFNO0G6U%3D&amp;reserved=0

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
--
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------------------------------

Message: 2
Date: Fri, 7 Aug 2020 22:47:13 +0000
From: Brian Wiley <>
To: Modeller Caretaker <>,
        "" <>
Subject: Re: [modeller_usage] Change ROOT_NAME for automodel.make()
Message-ID:
        <>

Content-Type: text/plain; charset="us-ascii"

Thanks,

I would like to change the root_name for all the output file.  It's kind of silly there is not class root_name attribute in automodel.  Then you could just name that.  I am having trouble overriding the __init__ in automodel because it calls self.set_defaults().

Brian

-----Original Message-----
From: Modeller Caretaker <>
Sent: Friday, August 7, 2020 6:34 PM
To: Brian Wiley <>; 
Subject: Re: [modeller_usage] Change ROOT_NAME for automodel.make()


      External Email - Use Caution



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://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalilab.org%2Fmodeller%2F9.24%2Fmanual%2Fnode76.html&amp;data=02%7C01%7Cbwiley4%40jhu.edu%7C283a9b9ef68145537d9308d83b2404e8%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637324373239719269&amp;sdata=o%2F19FFGDWr7vqGpqh2wg%2BsHls6NEPookE0Ik9EbB3Tk%3D&amp;reserved=0

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
--
             https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsalilab.org%2Fmodeller%2F&amp;data=02%7C01%7Cbwiley4%40jhu.edu%7C283a9b9ef68145537d9308d83b2404e8%7C9fa4f438b1e6473b803f86f8aedf0dec%7C0%7C0%7C637324373239719269&amp;sdata=iR0Z9D5QCFHkMlLVdxlCLoRnA1t92GsPFWVKyECqqjk%3D&amp;reserved=0
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