def test_add_missing_atoms(): fname = get_fn('dna.pdb') parm = pmd.load_file(fname) parm = parm['!@H='] assert len(parm['@H='].atoms) == 0 fixer = AmberPDBFixer(parm) fixer.add_missing_atoms() assert len(fixer.parm['@H='].atoms) > 0
def test_mutate(): pdb_fh = get_fn('ala3_alpha.pdb') parm = pmd.load_file(pdb_fh) assert set(res.name for res in parm.residues) == {'ALA'} pdbfixer = AmberPDBFixer(parm) pdbfixer.mutate([ (1, 'ARG'), ]) pdbfixer.add_missing_atoms() assert [res.name for res in pdbfixer.parm.residues] == ['ALA', 'ARG', 'ALA'] assert ([ atom.name for atom in pdbfixer.parm.residues[1] if atom.atomic_number == 6 ] == ['CA', 'CB', 'CG', 'CD', 'CZ', 'C'])