Replace hard-coded attribute keys (#110)

* replace hard-coded node attribute "atom_number"

* replace hard-coded node attribute "element_symbol"

* replace hard-coded node attributes of the coordinates

* replace hard-coded node attribute "partition"

* forgot one replacement of "element_symbol"

* replace hard-coded node attribute "chg"

* replace hard-coded node attribute "rad"
intoduce a mapping in the (de-)serialization of TUCAN strings

* add test for V2000 Molfile charge mechanics (implemented via MOLFILE_V2000_CHARGES)

* replace hard-coded node attribute "mass"

* replace hard-coded node attribute "explored"

* replace hard-coded node attribute "invariant_code"

* replace hard-coded edge attribute "bond_type"

* cleanup, add/correct type hints

tests/conftest.py

@@ -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
 
 
@@ -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

tests/io/test_molfile_v2000_reader.py

@@ -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,
@@ -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",
     [
@@ -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