Just use that Alignment file in right way. No need to change in automodel class python script.

Alignment will be like....

>P1;

target delimiters

Seq of Chain A

/

seq of chain B *

>P1;

1st template delimiters

Seq of 1st template with proper alignment*

>P1;

2nd template delimiters

Seq of 2nd template with alignment in first*

Under your python script simply define PDB codes with '" , "

Thats all.

You can also refer https://www.researchgate.net/post/How_to_model_Homodimers.

Wishes.

Thanks Mr. Rajnikant Namdeo