use separate radius and max_edge_dist in tests and notebooks

tests/data/hdf5/_generate_testdata.ipynb

@@ -102,7 +102,8 @@
     "models_folder_name = 'exp_nmers_all_HLA_quantitative'\n",
     "data = 'pMHCI'\n",
     "resolution = 'residue' # either 'residue' or 'atom'\n",
-    "distance_cutoff = 15 # max distance in Å between two interacting residues/atoms of two proteins\n",
+    "interaction_radius = 15 # max distance in Å between two interacting residues/atoms of two proteins\n",
+    "max_edge_distance = 15 # max distance in Å between to create an edge\n",
     "\n",
     "csv_file_path = f'{project_folder}data/external/processed/I/{csv_file_name}'\n",
     "models_folder_path = f'{project_folder}data/{data}/features_input_folder/{models_folder_name}'\n",
@@ -130,7 +131,8 @@
     "            pdb_path = pdb_files[i],\n",
     "            resolution = \"residue\",\n",
     "            chain_ids = [\"M\", \"P\"],\n",
-    "            distance_cutoff = distance_cutoff,\n",
+    "            interaction_radius = interaction_radius,\n",
+    "            max_edge_distance = max_edge_distance,\n",
     "            targets = {\n",
     "                'binary': int(float(bas[i]) <= 500), # binary target value\n",
     "                'BA': bas[i], # continuous target value\n",

tests/features/__init__.py

@@ -1,5 +1,5 @@
 from pathlib import Path
-from typing import Optional, Tuple, Union
+from typing import Literal, Optional, Tuple, Union
 
 from pdb2sql import pdb2sql
 
@@ -25,19 +25,21 @@ def _get_residue(chain: Chain, number: int) -> Residue:
 
 def build_testgraph( # pylint: disable=too-many-locals, too-many-arguments # noqa:MC0001
     pdb_path: str,
-    cutoff: float,
-    detail: str,
+    detail: Literal['atomic', 'residue'],
+    interaction_radius: float,
+    max_edge_distance: float,
     central_res: Optional[int] = None,
     variant: Optional[AminoAcid] = None,
     chain_ids: Optional[Union[str, Tuple[str, str]]] = None,
-    ) -> Union[Graph, Tuple[Graph, SingleResidueVariant]]:
+    ) -> Tuple[Graph, Union[SingleResidueVariant, None]]:
 
     """ Creates a Graph object for feature tests.
 
     Args:
         pdb_path (str): Path of pdb file.
-        cutoff (float): Cutoff distance of the graph (also used as radius for single-chain graphs).
-        detail (str): Level of detail. Accepted values are: 'residue' or 'atom'.
+        detail (Literal['atomic', 'residue']): Level of detail.
+        interaction_radius (float): max distance to include in graph.
+        max_edge_distance (float): max distance to create an edge.
         central_res (Optional[int], optional): Residue to center a single-chain graph around.
             Use None to create a 2-chain graph, or any value for a single-chain graph
             Defaults to None.
@@ -51,7 +53,7 @@ def build_testgraph( # pylint: disable=too-many-locals, too-many-arguments # noq
 
     Returns:
         Graph: As generated by build_residue_graph or build_atomic_graph
-        SingleResidueVariant: Only resturned if central_res is not None
+        SingleResidueVariant: returns None if central_res is None
     """
 
     pdb = pdb2sql(pdb_path)
@@ -69,7 +71,7 @@ def build_testgraph( # pylint: disable=too-many-locals, too-many-arguments # noq
         for residue1, residue2 in get_residue_contact_pairs(
             pdb_path, structure,
             chains[0], chains[1],
-            cutoff
+            interaction_radius
         ):
             if detail == 'residue':
                 nodes.add(residue1)
@@ -82,9 +84,9 @@ def build_testgraph( # pylint: disable=too-many-locals, too-many-arguments # noq
                     nodes.add(atom)
 
         if detail == 'residue':
-            return build_residue_graph(list(nodes), structure.id, cutoff)
+            return build_residue_graph(list(nodes), structure.id, max_edge_distance), None
         if detail == 'atom':
-            return build_atomic_graph(list(nodes), structure.id, cutoff)
+            return build_atomic_graph(list(nodes), structure.id, max_edge_distance), None
         raise TypeError('detail must be "atom" or "residue"')
 
     else:
@@ -93,7 +95,7 @@ def build_testgraph( # pylint: disable=too-many-locals, too-many-arguments # noq
         else:
             chain = structure.get_chain(chain_ids)
         residue = _get_residue(chain, central_res)
-        surrounding_residues = list(get_surrounding_residues(structure, residue, cutoff))
+        surrounding_residues = list(get_surrounding_residues(structure, residue, interaction_radius))
 
         try:
             with open(f"tests/data/pssm/{structure.id}/{structure.id}.{chain.id}.pdb.pssm", "rt", encoding="utf-8") as f:
@@ -102,8 +104,8 @@ def build_testgraph( # pylint: disable=too-many-locals, too-many-arguments # noq
             pass
 
         if detail == 'residue':
-            return build_residue_graph(surrounding_residues, structure.id, cutoff), SingleResidueVariant(residue, variant)
+            return build_residue_graph(surrounding_residues, structure.id, max_edge_distance), SingleResidueVariant(residue, variant)
         if detail == 'atom':
             atoms = set(atom for residue in surrounding_residues for atom in residue.atoms)
-            return build_atomic_graph(list(atoms), structure.id, cutoff), SingleResidueVariant(residue, variant)
+            return build_atomic_graph(list(atoms), structure.id, max_edge_distance), SingleResidueVariant(residue, variant)
         raise TypeError('detail must be "atom" or "residue"')

tests/features/test_components.py

@@ -1,28 +1,39 @@
 import numpy as np
-from deeprank2.domain.aminoacidlist import glycine, serine
-from deeprank2.features.components import add_features
 
 from deeprank2.domain import nodestorage as Nfeat
+from deeprank2.domain.aminoacidlist import glycine, serine
+from deeprank2.features.components import add_features
 
 from . import build_testgraph
 
 
 def test_atom_features():
     pdb_path = "tests/data/pdb/101M/101M.pdb"
-    graph, _ = build_testgraph(pdb_path, 10, 'atom', 25)
-
+    graph, _ = build_testgraph(
+        pdb_path=pdb_path,
+        detail='atom',
+        interaction_radius=10,
+        max_edge_distance=10,
+        central_res=25,
+    )
     add_features(pdb_path, graph)
-
     assert not any(np.isnan(node.features[Nfeat.ATOMCHARGE]) for node in graph.nodes)
     assert not any(np.isnan(node.features[Nfeat.PDBOCCUPANCY]) for node in graph.nodes)
 
 
 def test_aminoacid_features():
     pdb_path = "tests/data/pdb/101M/101M.pdb"
-    graph, variant = build_testgraph(pdb_path, 10, 'residue', 25, serine)
+    graph, variant = build_testgraph(
+        pdb_path=pdb_path,
+        detail='residue',
+        interaction_radius=10,
+        max_edge_distance=10,
+        central_res=25,
+        variant=serine,
+    )
     add_features(pdb_path, graph, variant)
-
     node = graph.nodes[25].id
+
     for node in graph.nodes:
         if node.id == variant.residue:  # GLY -> SER
             assert sum(node.features[Nfeat.RESTYPE]) == 1

tests/features/test_conservation.py

@@ -1,16 +1,23 @@
 import numpy as np
 import pytest
-from deeprank2.domain.aminoacidlist import alanine
-from deeprank2.features.conservation import add_features
 
 from deeprank2.domain import nodestorage as Nfeat
+from deeprank2.domain.aminoacidlist import alanine
+from deeprank2.features.conservation import add_features
 
 from . import build_testgraph
 
 
 def test_conservation_residue():
     pdb_path = "tests/data/pdb/101M/101M.pdb"
-    graph, variant = build_testgraph(pdb_path, 10, 'residue', 25, alanine)
+    graph, variant = build_testgraph(
+        pdb_path=pdb_path,
+        detail='residue',
+        interaction_radius=10,
+        max_edge_distance=10,
+        central_res=25,
+        variant=alanine,
+    )
     add_features(pdb_path, graph, variant)
 
     for feature_name in (
@@ -24,7 +31,14 @@ def test_conservation_residue():
 
 def test_conservation_atom():
     pdb_path = "tests/data/pdb/101M/101M.pdb"
-    graph, variant = build_testgraph(pdb_path, 10, 'atom', 25, alanine)
+    graph, variant = build_testgraph(
+        pdb_path=pdb_path,
+        detail='atom',
+        interaction_radius=10,
+        max_edge_distance=10,
+        central_res=25,
+        variant=alanine,
+    )
     add_features(pdb_path, graph, variant)
 
     for feature_name in (
@@ -38,6 +52,14 @@ def test_conservation_atom():
 
 def test_no_pssm_file_error():
     pdb_path = "tests/data/pdb/1CRN/1CRN.pdb"
-    graph, variant = build_testgraph(pdb_path, 10, 'residue', 17, alanine)
+    graph, variant = build_testgraph(
+        pdb_path=pdb_path,
+        detail='residue',
+        interaction_radius=10,
+        max_edge_distance=10,
+        central_res=17,
+        variant=alanine,
+    )
+
     with pytest.raises(FileNotFoundError):
         add_features(pdb_path, graph, variant)

tests/features/test_exposure.py

@@ -1,8 +1,8 @@
 import numpy as np
-from deeprank2.features.exposure import add_features
-from deeprank2.utils.graph import Graph
 
 from deeprank2.domain import nodestorage as Nfeat
+from deeprank2.features.exposure import add_features
+from deeprank2.utils.graph import Graph
 
 from . import build_testgraph
 
@@ -19,15 +19,23 @@ def _run_assertions(graph: Graph):
 
 def test_exposure_residue():
     pdb_path = "tests/data/pdb/1ATN/1ATN_1w.pdb"
-    graph = build_testgraph(pdb_path, 8.5, 'residue')
-
+    graph, _ = build_testgraph(
+        pdb_path=pdb_path,
+        detail='residue',
+        interaction_radius=8.5,
+        max_edge_distance=8.5,
+    )
     add_features(pdb_path, graph)
     _run_assertions(graph)
 
 
 def test_exposure_atom():
     pdb_path = "tests/data/pdb/1ak4/1ak4.pdb"
-    graph = build_testgraph(pdb_path, 4.5, 'atom')
-
+    graph, _ = build_testgraph(
+        pdb_path=pdb_path,
+        detail='atom',
+        interaction_radius=4.5,
+        max_edge_distance=4.5,
+    )
     add_features(pdb_path, graph)
     _run_assertions(graph)

tests/features/test_irc.py

@@ -1,8 +1,8 @@
 import numpy as np
-from deeprank2.features.irc import add_features
-from deeprank2.utils.graph import Graph
 
 from deeprank2.domain import nodestorage as Nfeat
+from deeprank2.features.irc import add_features
+from deeprank2.utils.graph import Graph
 
 from . import build_testgraph
 
@@ -25,15 +25,23 @@ def _run_assertions(graph: Graph):
 
 def test_irc_residue():
     pdb_path = "tests/data/pdb/1ATN/1ATN_1w.pdb"
-    graph = build_testgraph(pdb_path, 8.5, 'residue')
-
+    graph, _ = build_testgraph(
+        pdb_path=pdb_path,
+        detail='residue',
+        interaction_radius=8.5,
+        max_edge_distance=8.5,
+    )
     add_features(pdb_path, graph)
     _run_assertions(graph)
 
 
 def test_irc_atom():
     pdb_path = "tests/data/pdb/1A0Z/1A0Z.pdb"
-    graph = build_testgraph(pdb_path, 4.5, 'atom')
-
+    graph, _ = build_testgraph(
+        pdb_path=pdb_path,
+        detail='residue',
+        interaction_radius=4.5,
+        max_edge_distance=4.5,
+    )
     add_features(pdb_path, graph)
     _run_assertions(graph)

tests/features/test_secondary_structure.py

@@ -1,17 +1,22 @@
 import numpy as np
+
+from deeprank2.domain import nodestorage as Nfeat
 from deeprank2.features.secondary_structure import (SecondarySctructure,
                                                     _classify_secstructure,
                                                     add_features)
 
-from deeprank2.domain import nodestorage as Nfeat
-
 from . import build_testgraph
 
 
 def test_secondary_structure_residue():
     test_case = '9api' # properly formatted pdb file
     pdb_path = f"tests/data/pdb/{test_case}/{test_case}.pdb"
-    graph = build_testgraph(pdb_path, 10, 'residue')
+    graph, _ = build_testgraph(
+        pdb_path=pdb_path,
+        detail='residue',
+        interaction_radius=10,
+        max_edge_distance=10,
+    )
     add_features(pdb_path, graph)
 
     # Create a list of node information (residue number, chain ID, and secondary structure features)
@@ -53,7 +58,12 @@ def test_secondary_structure_residue():
 def test_secondary_structure_atom():
     test_case = '1ak4' # ATOM list
     pdb_path = f"tests/data/pdb/{test_case}/{test_case}.pdb"
-    graph = build_testgraph(pdb_path, 4.5, 'atom')
+    graph, _ = build_testgraph(
+        pdb_path=pdb_path,
+        detail='atom',
+        interaction_radius=4.5,
+        max_edge_distance=4.5,
+    )
     add_features(pdb_path, graph)
 
     # Create a list of node information (residue number, chain ID, and secondary structure features)

tests/features/test_surfacearea.py

@@ -1,7 +1,7 @@
 import numpy as np
-from deeprank2.features.surfacearea import add_features
 
 from deeprank2.domain import nodestorage as Nfeat
+from deeprank2.features.surfacearea import add_features
 
 from . import build_testgraph
 
@@ -28,7 +28,12 @@ def _find_atom_node(graph, chain_id, residue_number, atom_name):
 
 def test_bsa_residue():
     pdb_path = "tests/data/pdb/1ATN/1ATN_1w.pdb"
-    graph = build_testgraph(pdb_path, 8.5, 'residue')
+    graph, _ = build_testgraph(
+        pdb_path=pdb_path,
+        detail='residue',
+        interaction_radius=8.5,
+        max_edge_distance=8.5,
+    )
     add_features(pdb_path, graph)
 
     # chain B ASP 93, at interface
@@ -38,7 +43,12 @@ def test_bsa_residue():
 
 def test_bsa_atom():
     pdb_path = "tests/data/pdb/1ATN/1ATN_1w.pdb"
-    graph = build_testgraph(pdb_path, 4.5, 'atom')
+    graph, _ = build_testgraph(
+        pdb_path=pdb_path,
+        detail='atom',
+        interaction_radius=4.5,
+        max_edge_distance=4.5,
+    )
     add_features(pdb_path, graph)
 
     # chain B ASP 93, at interface
@@ -48,7 +58,13 @@ def test_bsa_atom():
 
 def test_sasa_residue():
     pdb_path = "tests/data/pdb/101M/101M.pdb"
-    graph, _ = build_testgraph(pdb_path, 10, 'residue', 108)
+    graph, _ = build_testgraph(
+        pdb_path=pdb_path,
+        detail='residue',
+        interaction_radius=10,
+        max_edge_distance=10,
+        central_res=108,
+    )
     add_features(pdb_path, graph)
 
     # check for NaN
@@ -67,7 +83,13 @@ def test_sasa_residue():
 
 def test_sasa_atom():
     pdb_path = "tests/data/pdb/101M/101M.pdb"
-    graph, _ = build_testgraph(pdb_path, 10, 'atom', 108)
+    graph, _ = build_testgraph(
+        pdb_path=pdb_path,
+        detail='atom',
+        interaction_radius=10,
+        max_edge_distance=10,
+        central_res=108,
+    )
     add_features(pdb_path, graph)
 
     # check for NaN