def test_with_quotation_mark_atom(self, mock_get_color):
'''Handle repeated atoms indicated by `{"}`.'''
mock_get_color.return_value = 'colorname'
inp = ['''{AAAABCCCDDDDEFF}colorname 'G' 0.0,1.0,2.0''',
'''{"}colorname 'G' -0.0,-1.0,-2.0''']
res = pt._parse_dotlist_body(inp)
self.assertEqual(res[0].atom, res[1].atom)
def test_with_quotation_mark_atom(self, mock_get_color):
'''Handle repeated atoms indicated by `{"}`.'''
mock_get_color.return_value = 'colorname'
inp = [
'''{AAAABCCCDDDDEFF}colorname 'G' 0.0,1.0,2.0''',
'''{"}colorname 'G' -0.0,-1.0,-2.0'''
]
res = pt._parse_dotlist_body(inp)
self.assertEqual(res[0].atom, res[1].atom)
def test_with_question_mark_in_atom_desc(self, mock_get_color):
'''Should handle ? in atom name e.g. "H?" for water hydrogen.'''
mock_get_color.return_value = 'colorname'
inp = ["{ H? HOH 293 A}colorname 'G' 0.0,1.0,2.0"]
ref_atom = {'name': 'H',
'alt': '',
'resn': 'HOH',
'resi': '293',
'chain': 'A'}
res = pt._parse_dotlist_body(inp)
self.assertEqual(res[0].atom, ref_atom)
def test_with_spaces_in_atom_desc(self, mock_get_color):
'''Should handle spaces in atom name, alt, resn, resi, and chain.'''
mock_get_color.return_value = 'colorname'
inp = ["{ CA SER 26 A}colorname 'G' 0.0,1.0,2.0"]
ref_atom = {'name': 'CA',
'alt': '',
'resn': 'SER',
'resi': '26',
'chain': 'A'}
res = pt._parse_dotlist_body(inp)
self.assertEqual(res[0].atom, ref_atom)
def test_general_form(self, mock_get_color):
mock_get_color.return_value = 'colorname'
inp = ["{AAAABCCCDDDDEFF}colorname 'G' 0.0,1.0,2.0"]
ref_atom = {'name': 'AAAA',
'alt': 'B',
'resn': 'CCC',
'resi': 'DDDDE',
'chain': 'FF'}
res = pt._parse_dotlist_body(inp)
self.assertEqual(res[0].atom, ref_atom)
self.assertEqual(res[0].color, 'colorname')
self.assertEqual(res[0].pm, 'G')
self.assertEqual(res[0].coords, [0.0, 1.0, 2.0])
def test_with_question_mark_in_atom_desc(self, mock_get_color):
'''Should handle ? in atom name e.g. "H?" for water hydrogen.'''
mock_get_color.return_value = 'colorname'
inp = ["{ H? HOH 293 A}colorname 'G' 0.0,1.0,2.0"]
ref_atom = {
'name': 'H',
'alt': '',
'resn': 'HOH',
'resi': '293',
'chain': 'A'
}
res = pt._parse_dotlist_body(inp)
self.assertEqual(res[0].atom, ref_atom)
def test_with_spaces_in_atom_desc(self, mock_get_color):
'''Should handle spaces in atom name, alt, resn, resi, and chain.'''
mock_get_color.return_value = 'colorname'
inp = ["{ CA SER 26 A}colorname 'G' 0.0,1.0,2.0"]
ref_atom = {
'name': 'CA',
'alt': '',
'resn': 'SER',
'resi': '26',
'chain': 'A'
}
res = pt._parse_dotlist_body(inp)
self.assertEqual(res[0].atom, ref_atom)
def test_general_form(self, mock_get_color):
mock_get_color.return_value = 'colorname'
inp = ["{AAAABCCCDDDDEFF}colorname 'G' 0.0,1.0,2.0"]
ref_atom = {
'name': 'AAAA',
'alt': 'B',
'resn': 'CCC',
'resi': 'DDDDE',
'chain': 'FF'
}
res = pt._parse_dotlist_body(inp)
self.assertEqual(res[0].atom, ref_atom)
self.assertEqual(res[0].color, 'colorname')
self.assertEqual(res[0].pm, 'G')
self.assertEqual(res[0].coords, [0.0, 1.0, 2.0])
def test_with_negative_coords(self, mock_get_color):
'''Handle negative coordinates.'''
mock_get_color.return_value = 'colorname'
inp = ["{AAAABCCCDDDDEFF}colorname 'G' -0.0,-1.0,-2.0"]
res = pt._parse_dotlist_body(inp)
self.assertEqual(res[0].coords, [-0.0, -1.0, -2.0])
def test_with_negative_coords(self, mock_get_color):
'''Handle negative coordinates.'''
mock_get_color.return_value = 'colorname'
inp = ["{AAAABCCCDDDDEFF}colorname 'G' -0.0,-1.0,-2.0"]
res = pt._parse_dotlist_body(inp)
self.assertEqual(res[0].coords, [-0.0, -1.0, -2.0])