The Sequence class: a single sequence within an alignment
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The `Sequence` class: a single sequence within an alignment

The `Sequence` class contains a single sequence, in a model (see Section 6.6) or in an alignment (see Section 6.15).

For alignment template structures (i.e., sequences for which a structure is also available) see the `Structure` class in Section 6.17.

Example: examples/python/alnsequence.py

      # Example for alnsequence objects

      from modeller import *

      env = environ()

      aln = alignment(env, file='../commands/toxin.ali')
      print "Alignment contains %d sequences:" % len(aln)
      for seq in aln:
          print "   Sequence %s from %s contains %d residues" \
                % (seq.code, seq.source, len(seq))

Subsections

- Sequence.range -- residue range
- Sequence.code -- alignment code
- Sequence.atom_file -- PDB file name
- Sequence.source -- source organism
- Sequence.name -- protein name
- Sequence.prottyp -- protein sequence type
- Sequence.resolution -- structure resolution
- Sequence.rfactor -- R factor
- Sequence.residues -- list of all residues in the sequence
- Sequence.chains -- list of all chains in the sequence
- Sequence.transfer_res_prop() -- transfer residue properties
- Sequence.get_num_equiv() -- get number of equivalences
- Sequence.get_sequence_identity() -- get sequence identity