This command reads the sequence(s) and/or their alignment from a text file. Only sequences with the specified codes are read in; align_codes = 'all' can be used to read all sequences. The sequences are added to any currently in the alignment.
There are several alignment formats:
If remove_gaps = True, positions with gaps in all selected sequences are removed from the alignment.
The io argument is required since PIR files can contain empty sequences; in this case, the sequence is read from the corresponding PDB file.
For 'PIR' and 'FASTA' files, the end_of_file variable is set to 1 if MODELLER reached the end of the file during the read, or 0 otherwise.
This command can raise a FileFormatError if the alignment file format is invalid.
# Example for: alignment.append(), alignment.write(), # alignment.check() # Read an alignment, write it out in the 'PAP' format, and # check the alignment of the N-1 structures as well as the # alignment of the N-th sequence with each of the N-1 structures. from modeller import * log.level(output=1, notes=1, warnings=1, errors=1, memory=0) env = environ() env.io.atom_files_directory = ['../atom_files'] aln = alignment(env) aln.append(file='toxin.ali', align_codes='all') aln.write(file='toxin.pap', alignment_format='PAP') aln.write(file='toxin.fasta', alignment_format='FASTA') aln.check()