Skip to content

Commit

Permalink
update tests
Browse files Browse the repository at this point in the history
  • Loading branch information
@fgrunewald
fgrunewald committed Oct 14, 2024
1 parent d627ac2 commit 985500a
Show file tree
Hide file tree
Showing 2 changed files with 40 additions and 25 deletions.
64 changes: 39 additions & 25 deletions cgsmiles/tests/test_cgsmile_parsing.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -183,94 +183,108 @@ def test_read_cgsmiles(smile, nodes, edges, orders):
fragnames = nx.get_node_attributes(meta_mol, 'fragname')
assert nodes == list(fragnames.values())

@pytest.mark.parametrize('big_smile, smile, bonding, rs, ez',(
@pytest.mark.parametrize('big_smile, smile, bonding, rs, ez, weights',(
# smiple symmetric bonding
("[$]COC[$]",
"COC",
{0: ["$1"], 2: ["$1"]},
None,
None,
None),
# smiple symmetric bonding with more than one name
("[$1A]COC[$1A]",
"COC",
{0: ["$1A1"], 2: ["$1A1"]},
None,
None,
None),
# smiple bonding multiletter atom
("Clc[$]c[$]",
"Clcc",
{1: ["$1"], 2: ["$1"]},
None,
None,
None),
# simple symmetric but with explicit hydrogen
("[$][CH2]O[CH2][$]",
"[CH2]O[CH2]",
{0: ["$1"], 2: ["$1"]},
None,
None,
None),
# smiple symmetric bonding; multiple descript
("[$]COC[$][$1]",
"COC",
{0: ["$1"], 2: ["$1", "$11"]},
None,
None,
None),
# named different bonding descriptors
("[$1]CCCC[$2]",
"CCCC",
{0: ["$11"], 3: ["$21"]},
None,
None,
None),
# ring and bonding descriptors
("[$1]CC[$2]C1CCCCC1",
"CCC1CCCCC1",
{0: ["$11"], 1: ["$21"]},
None,
None,
None),
# bonding descript. after branch
("C(COC[$1])[$2]CCC[$3]",
"C(COC)CCC",
{0: ["$21"], 3: ["$11"], 6: ["$31"]},
None,
None,
None),
# left rigth bonding desciptors
("[>]COC[<]",
"COC",
{0: [">1"], 2: ["<1"]},
None,
None,
None),
# simple chirality in residue
("[>]C[C@](F)(B)N[<]",
"C[C](F)(B)N",
{0: [">1"], 4: ["<1"]},
{1: ('@', [])},
None,
None),
# simple chirality inverse in residue
("[>]C[C@@](F)(B)N[<]",
"C[C](F)(B)N",
{0: [">1"], 4: ["<1"]},
{1: ('@@', [])},
None,
None),
# \ fragment split
("[>]CC(\F)=[<]",
"CC(F)",
{0: [">1"], 1: ["<2"]},
None,
{2: (2, 1, '\\')}),
{2: (2, 1, '\\')},
None),
# / fragment split
("[>]CC(/F)=[<]",
"CC(F)",
{0: [">1"], 1: ["<2"]},
None,
{2: (2, 1, '/')}),
{2: (2, 1, '/')},
None),
# both in one fragment
("[>]CC(/F)=C(\F)C[<]",
"CC(F)=C(F)C",
{0: [">1"], 5: ["<1"]},
None,
{2: (2, 1, '/'), 4: (4, 3, '\\')}),
{2: (2, 1, '/'), 4: (4, 3, '\\')},
None),
))
def test_strip_bonding_descriptors(big_smile, smile, bonding, rs, ez):
new_smile, new_bonding, rs_isomers, ez_isomers = strip_bonding_descriptors(big_smile)
def test_strip_bonding_descriptors(big_smile, smile, bonding, rs, ez, weights):
new_smile, new_bonding, rs_isomers, ez_isomers, weights = strip_bonding_descriptors(big_smile)
assert new_smile == smile
assert new_bonding == bonding
if rs:
Expand All @@ -281,50 +295,50 @@ def test_strip_bonding_descriptors(big_smile, smile, bonding, rs, ez):
@pytest.mark.parametrize('fragment_str, nodes, edges',(
# single fragment
("{#PEO=[$]COC[$]}",
{"PEO": ((0, {"atomname": "C0", "fragname": "PEO", "bonding": ["$1"], "element": "C", "hcount": 3}),
(1, {"atomname": "O1", "fragname": "PEO", "element": "O", "hcount": 0}),
(2, {"atomname": "C2", "fragname": "PEO", "bonding": ["$1"], "element": "C", "hcount": 3}),
{"PEO": ((0, {"atomname": "C0", "fragname": "PEO", "bonding": ["$1"], "element": "C", "hcount": 3, "weight": 1}),
(1, {"atomname": "O1", "fragname": "PEO", "element": "O", "hcount": 0, "weight": 1}),
(2, {"atomname": "C2", "fragname": "PEO", "bonding": ["$1"], "element": "C", "hcount": 3, "weight": 1}),
)},
{"PEO": [(0, 1), (1, 2)]}),
# single fragment but with explicit hydrogen in smiles
("{#PEO=[$][CH2]O[CH2][$]}",
{"PEO": ((0, {"atomname": "C0", "fragname": "PEO", "bonding": ["$1"], "element": "C", "hcount": 2}),
(1, {"atomname": "O1", "fragname": "PEO", "element": "O", "hcount": 0}),
(2, {"atomname": "C2", "fragname": "PEO", "bonding": ["$1"], "element": "C", "hcount": 2}),
{"PEO": ((0, {"atomname": "C0", "fragname": "PEO", "bonding": ["$1"], "element": "C", "hcount": 2, "weight": 1}),
(1, {"atomname": "O1", "fragname": "PEO", "element": "O", "hcount": 0, "weight": 1}),
(2, {"atomname": "C2", "fragname": "PEO", "bonding": ["$1"], "element": "C", "hcount": 2, "weight": 1}),
)},
{"PEO": [(0, 1), (1, 2)]}),
# test NH3 terminal
("{#AMM=N[$]}",
{"AMM": ((0, {"atomname": "N0", "fragname": "AMM", "bonding": ["$1"], "element": "N", "hcount": 3}),
{"AMM": ((0, {"atomname": "N0", "fragname": "AMM", "bonding": ["$1"], "element": "N", "hcount": 3, "weight": 1}),
)},
{"AMM": []}),
# single fragment + 1 terminal (i.e. only 1 bonding descrpt
("{#PEO=[$]COC[$],#OHter=[$][OH]}",
{"PEO": ((0, {"atomname": "C0", "fragname": "PEO", "bonding": ["$1"], "element": "C", "hcount": 3}),
(1, {"atomname": "O1", "fragname": "PEO", "element": "O", "hcount": 0}),
(2, {"atomname": "C2", "fragname": "PEO", "bonding": ["$1"], "element": "C", "hcount": 3}),
{"PEO": ((0, {"atomname": "C0", "fragname": "PEO", "bonding": ["$1"], "element": "C", "hcount": 3, "weight": 1}),
(1, {"atomname": "O1", "fragname": "PEO", "element": "O", "hcount": 0, "weight": 1}),
(2, {"atomname": "C2", "fragname": "PEO", "bonding": ["$1"], "element": "C", "hcount": 3, "weight": 1}),
),
"OHter": ((0, {"atomname": "O0", "fragname": "OHter", "bonding": ["$1"], "element": "O"}),)},
"OHter": ((0, {"atomname": "O0", "fragname": "OHter", "bonding": ["$1"], "element": "O", "weight": 1}),)},
{"PEO": [(0, 1), (1, 2)],
"OHter": []}),
# single fragment + 1 terminal but multiple bond descritp.
# this adjust the hydrogen count
("{#PEO=[$]COC[$][$1],#OHter=[$][OH]}",
{"PEO": ((0, {"atomname": "C0", "fragname": "PEO", "bonding": ["$1"], "element": "C", "hcount": 3}),
(1, {"atomname": "O1", "fragname": "PEO", "element": "O", "hcount": 0}),
(2, {"atomname": "C2", "fragname": "PEO", "bonding": ["$1", "$11"], "element": "C", "hcount": 3}),
{"PEO": ((0, {"atomname": "C0", "fragname": "PEO", "bonding": ["$1"], "element": "C", "hcount": 3, "weight": 1}),
(1, {"atomname": "O1", "fragname": "PEO", "element": "O", "hcount": 0, "weight": 1}),
(2, {"atomname": "C2", "fragname": "PEO", "bonding": ["$1", "$11"], "element": "C", "hcount": 3, "weight": 1}),
),
"OHter": ((0, {"atomname": "O0", "fragname": "OHter", "bonding": ["$1"], "element": "O", "hcount": 1}),)},
"OHter": ((0, {"atomname": "O0", "fragname": "OHter", "bonding": ["$1"], "element": "O", "hcount": 1, "weight": 1}),)},
{"PEO": [(0, 1), (1, 2)],
"OHter": []}),
# single fragment + 1 terminal but multiple bond descritp.
# but explicit hydrogen in the smiles string
("{#PEO=[$][CH2]O[CH2][$][$1],#OHter=[$][OH]}",
{"PEO": ((0, {"atomname": "C0", "fragname": "PEO", "bonding": ["$1"], "element": "C", "hcount": 2}),
(1, {"atomname": "O1", "fragname": "PEO", "element": "O", "hcount": 0}),
(2, {"atomname": "C2", "fragname": "PEO", "bonding": ["$1", "$11"], "element": "C", "hcount": 2}),
{"PEO": ((0, {"atomname": "C0", "fragname": "PEO", "bonding": ["$1"], "element": "C", "hcount": 2, "weight": 1}),
(1, {"atomname": "O1", "fragname": "PEO", "element": "O", "hcount": 0, "weight": 1}),
(2, {"atomname": "C2", "fragname": "PEO", "bonding": ["$1", "$11"], "element": "C", "hcount": 2, "weight": 1}),
),
"OHter": ((0, {"atomname": "O0", "fragname": "OHter", "bonding": ["$1"], "element": "O", "hcount": 1}),
"OHter": ((0, {"atomname": "O0", "fragname": "OHter", "bonding": ["$1"], "element": "O", "hcount": 1, "weight": 1}),
)},
{"PEO": [(0, 1), (1, 2),],
"OHter": []}),
Expand Down
1 change: 1 addition & 0 deletions cgsmiles/tests/test_sampler.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -104,6 +104,7 @@ def test_add_fragment(graph_str,
ref_graph = read_cgsmiles(ref_mol)
nx.set_node_attributes(ref_graph, bonding, 'bonding')
nx.set_node_attributes(ref_graph, fragid, 'fragid')
nx.set_node_attributes(ref_graph, 1, 'weight')
atomnames = nx.get_node_attributes(ref_graph, 'fragname')
nx.set_node_attributes(ref_graph, atomnames, 'atomname')
nx.set_node_attributes(ref_graph, resnames, 'fragname')
Expand Down

0 comments on commit 985500a

Please sign in to comment.