Python AmberPDBFixer.add_missing_atoms Examples

Example #1

File: test_unit.py Project: mmagithub/pdb4amber

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

Example #2

File: test_unit.py Project: IAlibay/pdb4amber

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'])