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Replace hard-coded attribute keys #110

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merged 13 commits into from
Jan 4, 2024
Merged

Replace hard-coded attribute keys #110

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7f510e9
replace hard-coded node attribute "atom_number"
flange-ipb Nov 10, 2023
ddad063
replace hard-coded node attribute "element_symbol"
flange-ipb Nov 10, 2023
1464f6f
replace hard-coded node attributes of the coordinates
flange-ipb Nov 10, 2023
c221ece
replace hard-coded node attribute "partition"
flange-ipb Nov 14, 2023
3c64635
forgot one replacement of "element_symbol"
flange-ipb Nov 14, 2023
d6cdc23
replace hard-coded node attribute "chg"
flange-ipb Nov 14, 2023
e4a2f1c
replace hard-coded node attribute "rad"
flange-ipb Nov 15, 2023
604922f
add test for V2000 Molfile charge mechanics (implemented via MOLFILE_…
flange-ipb Nov 15, 2023
c594405
replace hard-coded node attribute "mass"
flange-ipb Nov 15, 2023
4c73490
replace hard-coded node attribute "explored"
flange-ipb Nov 15, 2023
8354070
replace hard-coded node attribute "invariant_code"
flange-ipb Nov 15, 2023
0890e4e
replace hard-coded edge attribute "bond_type"
flange-ipb Nov 15, 2023
5128b07
cleanup, add/correct type hints
flange-ipb Nov 15, 2023
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6 changes: 4 additions & 2 deletions tests/conftest.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@
import networkx as nx
from pathlib import Path
from networkx.algorithms.components import is_connected

from tucan.graph_attributes import ATOMIC_NUMBER, ELEMENT_SYMBOL
from tucan.io import graph_from_file


Expand All @@ -25,8 +27,8 @@ def graph_from_dimacs(filepath):

graph = nx.Graph()
graph.add_nodes_from(node_labels)
nx.set_node_attributes(graph, "C", "element_symbol")
nx.set_node_attributes(graph, 6, "atomic_number")
nx.set_node_attributes(graph, "C", ELEMENT_SYMBOL)
nx.set_node_attributes(graph, 6, ATOMIC_NUMBER)
graph.add_edges_from(bonds)

return graph
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82 changes: 76 additions & 6 deletions tests/io/test_molfile_v2000_reader.py
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Original file line number Diff line number Diff line change
@@ -1,9 +1,22 @@
import pytest
from pathlib import Path

from tucan.graph_attributes import (
ATOMIC_NUMBER,
CHG,
ELEMENT_SYMBOL,
MASS,
PARTITION,
RAD,
X_COORD,
Y_COORD,
Z_COORD,
)
from tucan.io import graph_from_file
from tucan.io.exception import MolfileParserException
from tucan.io.molfile_v2000_reader import (
_merge_tuples_into_additional_attributes,
_parse_atom_line,
_parse_atom_value_assignments,
_to_int,
_to_float,
Expand All @@ -27,6 +40,63 @@ def test_graphs_from_v2000_and_v3000_molfiles_match(mol):
assert e1 == e2


@pytest.mark.parametrize(
"line, expected_additional_attr",
[
(
" 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0",
{},
),
(
" 0.0000 0.0000 0.0000 C 0 1 0 0 0 0 0 0 0 0 0 0",
{CHG: 3},
),
(
" 0.0000 0.0000 0.0000 C 0 2 0 0 0 0 0 0 0 0 0 0",
{CHG: 2},
),
(
" 0.0000 0.0000 0.0000 C 0 3 0 0 0 0 0 0 0 0 0 0",
{CHG: 1},
),
(
" 0.0000 0.0000 0.0000 C 0 4 0 0 0 0 0 0 0 0 0 0",
{RAD: 2},
),
(
" 0.0000 0.0000 0.0000 C 0 5 0 0 0 0 0 0 0 0 0 0",
{CHG: -1},
),
(
" 0.0000 0.0000 0.0000 C 0 6 0 0 0 0 0 0 0 0 0 0",
{CHG: -2},
),
(
" 0.0000 0.0000 0.0000 C 0 7 0 0 0 0 0 0 0 0 0 0",
{CHG: -3},
),
(
" 0.0000 0.0000 0.0000 C 0 8 0 0 0 0 0 0 0 0 0 0",
{}, # ignored
),
],
)
def test_parse_atom_line_charge_field(line, expected_additional_attr):
expected_attrs = {
ELEMENT_SYMBOL: "C",
ATOMIC_NUMBER: 6,
PARTITION: 0,
X_COORD: 0,
Y_COORD: 0,
Z_COORD: 0,
}
expected_attrs.update(expected_additional_attr)

atom_attrs = _parse_atom_line(line)

assert atom_attrs == expected_attrs


@pytest.mark.parametrize(
"tuples, additional_attrs, expected_additional_attrs_after_merge",
[
Expand All @@ -37,21 +107,21 @@ def test_graphs_from_v2000_and_v3000_molfiles_match(mol):
(2, 3), # atom index is not in additional_attrs yet
],
{
0: {"chg": 2}, # will add new key
1: {"mass": 1}, # will overwrite value
0: {CHG: 2}, # will add new key
1: {MASS: 1}, # will overwrite value
},
{
0: {"chg": 2, "mass": 2},
1: {"mass": 13},
2: {"mass": 3},
0: {CHG: 2, MASS: 2},
1: {MASS: 13},
2: {MASS: 3},
},
),
],
)
def test_merge_tuples_into_additional_attributes(
tuples, additional_attrs, expected_additional_attrs_after_merge
):
_merge_tuples_into_additional_attributes(tuples, "mass", additional_attrs)
_merge_tuples_into_additional_attributes(tuples, MASS, additional_attrs)
assert additional_attrs == expected_additional_attrs_after_merge


Expand Down
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