This command will write a profile to a specified file, together with a number of variables that are associated with the profile in the memory. Two formats are supported: TEXT and BINARY.
For TEXT files, file can be either a file name or a writeable file handle (see modfile.File()). For BINARY files, it must be a file name.
from modeller import * env = environ() # Read in the alignment file aln = alignment(env) aln.append(file='toxin.ali', alignment_format='PIR', align_codes='ALL') # Convert the alignment to profile format prf = aln.to_profile() # Write out the profile # in text file prf.write(file='alntoprof.prf', profile_format='TEXT') # in binary format prf.write(file='alntoprof.bin', profile_format='BINARY')