model.to_iupac() -- standardize certain dihedral angles

Description:

This routine swaps specific pairs of atoms within some residues of MODEL so that certain dihedral angles are within $\pm 90$${}^{o}$, 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); $\chi_2$;
• Asp: (OD1, OD2); $\chi_2$;
• Glu: (OE1, OE2); $\chi_3$;
• Arg: (NH1, NH2); $\chi_4$.

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.

env = environ()
log.level(1, 1, 1, 1, 0)

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