## model.to_iupac() — standardize certain dihedral angles

`to_iupac()`

> This routine swaps specific pairs of atoms within some residues of MODEL so that certain dihedral angles are within ± 90°, satisfying the IUPAC convention [IUPAC-IUB, 1970,Kendrew et al., 1970]. These residues, pairs of atoms, and dihedral angles are:

- Phe, Tyr: (CD1, CD2), (CE1, CE2); χ2;
- Asp: (OD1, OD2); χ2;
- Glu: (OE1, OE2); χ3;
- Arg: (NH1, NH2); χ4.

> It is possible that for distorted sidechains, neither of the two possibilities satisfies the IUPAC convention. In such a case, a warning message is written to the `log` file.

Example: examples/commands/iupac_model.py

      # This will swap certain atom names in some planar sidechains to satisfy
      # the IUPAC convention.

      from modeller import *

      env = environ()
      env.io.atom_files_directory = ['../atom_files']
      log.level(1, 1, 1, 1, 0)

      mdl = model(env, file='2abx')
      mdl.to_iupac()
      mdl.write(file='2abx.iup')