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Atom name nomenclature

ARIA 2 follows the IUPAC convention for naming the atoms of the standard amino acids and nucleotides. It can deal with CNS or DYANA atom names for conformer generation of conformer import from another program. In ARIA's conversion facility the atom names of the input data are translated to the IUPAC convention.

The definition of the IUPAC atom names and CNS/DYANA atom names can be found respectively in the files iupac.xml  and atomnames.xml  contained in the directory src/py/data of the ARIA distribution.

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