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Methods defined here:
- __init__(self, pdbfile)
- Wrapper class for Bio.PDB which makes it convenient to
read phi/psi/omega/chi torsion angles from a PDB-file.
Arguments:
pdbfile -- The PDB file you wish to read.
- get_bb_angles(self, resnum)
- Returns a list of [phi, psi, omega] angles for a residue.
Arguments:
resnum -- The number of the residue.
- get_chi_angles(self, resnum)
- Returns a list of chi angles for a residue.
Arguments:
resnum -- The number of the residue.
NOTE: Also corrects for incorrect naming of CG1/CG2 in
valine residues and CD1/CD2 in leucine residues.
Will display an error if .pdb file is incorrect.
- get_length(self)
- Returns the length of the protein.
- get_residue_numbers(self)
- Returns a list with indexes of all amino acids in the chain.
Can be used for iterating over residues, e.g.:
>>> for i in pdbfile.get_residue_numbers():
... print i, pdbfile.get_residue_bb_angles(i)
- get_resname(self, resnum)
- Returns the three letter code for a residue in the PDB file.
E.g. "VAL", "ALA", etc.
Arguments:
resnum -- The number of the residue
- get_sequence(self)
- Returns the amino acid sequence from the PDB structure.
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