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.
file can be either a file name or a readable file handle (see modfile.File()).
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 or ranges; in this case, the sequence or range is read from the corresponding PDB file.
If allow_alternates = True, and reading a 'PIR' file where ‘.’ is used to force MODELLER to read the sequence range from the corresponding PDB file (see Section B.1), then the search for matches between the alignment sequence and PDB is made a little more flexible. Not only will an exact equivalence of one-letter codes be considered a match, but each residue's alternate (as defined by the STD column in 'modlib/restyp.lib') will also count as a match; for example, B (ASX) in the alignment will be considered a match for N (ASN) in the PDB, while G (GLY) in the alignment will match any non-standard residue in the PDB for which an explicit equivalence has not been defined (the DEFATM behavior in 'modlib/restyp.lib'). The alignment sequence will be modified to match the exact sequence from the PDB. This is useful if the alignment sequence is extracted from a database containing 'cleaned' sequences, e.g. that created by sequence_db.read().
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, or a SequenceMismatchError if a 'PIR' sequence does not match that read from PDB (when an empty range is given).
# 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()
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