alignment.describe() — describe proteins

describe(io=None)

This command outputs basic data about the proteins in the current alignment (e.g.as read in by alignment.append()). This command is useful for preparation before comparative modeling because it summarizes disulfides, cis-prolines, charges, chain breaks, etc. Results which depend only on the amino acid sequences are still written out even if some atom files do not exist.

Example: examples/commands/describe.py

# Example for: alignment.describe()

# Describe the sequences and structures in the alignment.

from modeller import *

env = environ()
env.io.atom_files_directory = ['../atom_files']
aln = alignment(env, file='toxin.ali', align_codes=('2ctx', '2abx'))
aln.describe()