The Residue class: a single residue in a model or alignment
Keywords: manual

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The `Residue` class: a single residue in a model or alignment

The `Residue` class holds information about a single residue in a sequence (see Sequence.residues).

Example: examples/python/residues.py

      # Example for 'residue' objects

      from modeller import *
      from modeller.scripts import complete_pdb

      def analyze_seq(description, seq):
          """Simple 'analysis' of a sequence of residues, from a model or alignment"""
          numcys = 0
          for res in seq:
              if res.pdb_name == 'CYS':
                  numcys += 1
          print "%s contains %d residues, of which %d are CYS" \
                % (description, len(seq), numcys)

      env = environ()
      env.io.atom_files_directory = ['../atom_files']
      env.libs.topology.read(file='$(LIB)/top_heav.lib')
      env.libs.parameters.read(file='$(LIB)/par.lib')

      mdl = complete_pdb(env, "1fas")

      # 'mdl.residues' is a list of all residues in the model
      print "1-letter code of 1st residue: ", mdl.residues[0].code
      print "PDB name of residue '10': ", mdl.residues['10:'].pdb_name

      # Get the first aligned sequence from a file
      aln = alignment(env, file='../commands/toxin.ali')
      firstseq = aln[0]

      # Analyze all residues in the model, a subset, and all residues in the
      # alignment sequence
      analyze_seq("Model 1fas", mdl.residues)
      analyze_seq("First 10 residues of 1fas", mdl.residue_range('1:', '10:'))
      analyze_seq("Aligned sequence %s" % firstseq.code, firstseq.residues)

Subsections

- Residue.name -- internal (CHARMM) residue type name
- Residue.pdb_name -- PDB (IUPAC) type name
- Residue.code -- One-letter residue type code
- Residue.hetatm -- HETATM indicator
- Residue.index -- internal integer index
- Residue.num -- PDB-style residue number
- Residue.curvature -- Mainchain curvature
- Residue.atoms -- all atoms in the residue
- Residue.chain -- chain object
- Residue.phi -- dihedral angle
- Residue.psi -- dihedral angle
- Residue.omega -- dihedral angle
- Residue.alpha -- dihedral angle
- Residue.chi1 -- dihedral angle
- Residue.chi2 -- dihedral angle
- Residue.chi3 -- dihedral angle
- Residue.chi4 -- dihedral angle
- Residue.chi5 -- dihedral angle
- Residue.get_aligned_residue() -- get aligned residue in another sequence
- Residue.add_leading_gaps() -- add gap(s) before this residue
- Residue.add_trailing_gaps() -- add gap(s) after this residue
- Residue.remove_leading_gaps() -- remove gap(s) before this residue
- Residue.remove_trailing_gaps() -- remove gap(s) after this residue
- Residue.get_leading_gaps() -- get number of gaps before this residue
- Residue.get_trailing_gaps() -- get number of gaps after this residue