original_docstring: Place a sequence of amino acids into a peptide with specified
  	backbone dihedral angles. The argument AA_chain holds the
  	sequence of amino acids to be used. The arguments phi and psi_im1 hold
  	lists of backbone angles, one for each amino acid, *starting from
  	the second amino acid in the chain*. The argument 
  	omega (optional) holds a list of omega angles, also starting from
  	the second amino acid in the chain.
docstring: Place a sequence of amino acids into a peptide with specified
  backbone dihedral angles. The argument AA_chain holds the
  sequence of amino acids to be used. The arguments phi and psi_im1 hold
  lists of backbone angles, one for each amino acid, *starting from
  the second amino acid in the chain*. The argument
  omega (optional) holds a list of omega angles, also starting from
  the second amino acid in the chain.
docstring_tokens: Place a sequence of amino acids into a peptide with specified backbone dihedral angles . The argument AA_chain holds the sequence of amino acids to be used . The arguments phi and psi_im1 hold lists of backbone angles one for each amino acid * starting from the second amino acid in the chain * . The argument omega ( optional ) holds a list of omega angles also starting from the second amino acid in the chain .
code: def make_structure(AA_chain,phi,psi_im1,omega=[]):
  	'''Place a sequence of amino acids into a peptide with specified
  	backbone dihedral angles. The argument AA_chain holds the
  	sequence of amino acids to be used. The arguments phi and psi_im1 hold
  	lists of backbone angles, one for each amino acid, *starting from
  	the second amino acid in the chain*. The argument 
  	omega (optional) holds a list of omega angles, also starting from
  	the second amino acid in the chain.'''
  	geo = geometry(AA_chain[0])
  	struc=initialize_res(geo)
  	
  	if len(omega)==0:
  		for i in range(1,len(AA_chain)): 
  			AA = AA_chain[i]
  			add_residue(struc, AA, phi[i-1], psi_im1[i-1])
  	else:
  		for i in range(1,len(AA_chain)): 
  			AA = AA_chain[i]
  			add_residue(struc, AA, phi[i-1], psi_im1[i-1], omega[i-1])
  	return struc
code_tokens: def make_structure ( AA_chain , phi , psi_im1 , omega = [ ] ) : geo = geometry ( AA_chain [ 0 ] ) struc = initialize_res ( geo ) if len ( omega ) == 0 : for i in range ( 1 , len ( AA_chain ) ) : AA = AA_chain [ i ] add_residue ( struc , AA , phi [ i - 1 ] , psi_im1 [ i - 1 ] ) else : for i in range ( 1 , len ( AA_chain ) ) : AA = AA_chain [ i ] add_residue ( struc , AA , phi [ i - 1 ] , psi_im1 [ i - 1 ] , omega [ i - 1 ] ) return struc
short_docstring: Place a sequence of amino acids into a peptide with specified
  backbone dihedral angles.
short_docstring_tokens: Place a sequence of amino acids into a peptide with specified backbone dihedral angles .
comment: '''Place a sequence of amino acids into a peptide with specified
  	backbone dihedral angles. The argument AA_chain holds the
  	sequence of amino acids to be used. The arguments phi and psi_im1 hold
  	lists of backbone angles, one for each amino acid, *starting from
  	the second amino acid in the chain*. The argument 
  	omega (optional) holds a list of omega angles, also starting from
  	the second amino acid in the chain.'''