Add support for DSSP version and add rsa node features to residues with insertion codes

graphein/protein/features/nodes/dssp.py

@@ -107,7 +107,13 @@ def add_dssp_df(
 
     # Check for existence of pdb file. If not, reconstructs it from the raw df.
     if pdb_file:
-        dssp_dict = dssp_dict_from_pdb_file(pdb_file, DSSP=executable)
+        # get dssp version string
+        dssp_version = (
+            os.popen(f"{executable} --version").read().strip().split()[-1]
+        )  # e.g. "4.0.4"
+        dssp_dict = dssp_dict_from_pdb_file(
+            pdb_file, DSSP=executable, dssp_version=dssp_version
+        )
     else:
         with tempfile.TemporaryDirectory() as tmpdirname:
             save_pdb_df_to_pdb(
@@ -143,6 +149,14 @@ def add_dssp_df(
         + ":"
         + dssp_dict["resnum"].astype(str)
     )
+    if G.graph["config"].insertions:
+        dssp_dict["node_id"] = (
+            dssp_dict["node_id"] + ":" + dssp_dict["icode"].apply(str)
+        )
+        # Replace trailing : for non insertions
+        dssp_dict["node_id"] = dssp_dict["node_id"].str.replace(
+            r":\s*$", "", regex=True
+        )
 
     dssp_dict.set_index("node_id", inplace=True)
 

tests/protein/nodes/features/test_dssp.py

@@ -0,0 +1,65 @@
+# basic
+from functools import partial
+from pathlib import Path
+
+# test
+import pytest
+
+from graphein.protein.config import DSSPConfig, ProteinGraphConfig
+from graphein.protein.edges import distance as D
+from graphein.protein.features.nodes import rsa
+
+# graphein
+from graphein.protein.graphs import construct_graph
+from graphein.protein.subgraphs import extract_surface_subgraph
+from graphein.protein.utils import ProteinGraphConfigurationError
+
+# ---------- input ----------
+pdb_path = "example_pdb_with_cryst1_insertions.pdb"
+dssp_exe = "/usr/bin/mkdssp"
+RSA_THRESHOLD = 0.2
+
+# ---------- graph config ----------
+params_to_change = {
+    "granularity": "centroids",  # "atom", "CA", "centroids"
+    "insertions": True,
+    "edge_construction_functions": [
+        # graphein.protein.edges.distance.add_peptide_bonds,
+        D.add_distance_to_edges,
+        D.add_hydrogen_bond_interactions,
+        D.add_ionic_interactions,
+        D.add_backbone_carbonyl_carbonyl_interactions,
+        D.add_salt_bridges,
+        # distance
+        partial(
+            D.add_distance_threshold,
+            long_interaction_threshold=4,
+            threshold=4.5,
+        ),
+    ],
+    "dssp_config": DSSPConfig(executable=dssp_exe),
+    "graph_metadata_functions": [rsa],
+}
+config = ProteinGraphConfig(**params_to_change)
+# ---------- construct graph ----------
+g = construct_graph(config=config, path=pdb_path, verbose=False)
+
+
+# ---------- test: dssp DataFrame ----------
+def test_assert_nonempty_dssp_df():
+    """if not provided dssp version to dssp.add_dssp_df, will output an empty DataFrame"""
+    if g.graph["dssp_df"].empty:
+        pytest.fail("DSSP dataframe is empty")
+
+
+# ---------- test: surface subgraph nodes with insertion code ----------
+def test_extract_surface_subgraph_insertion_node():
+    """if not added insertion codes, will raise ProteinGraphConfigurationError"""
+    try:
+        # without the modification, the following line will raise
+        # ProteinGraphConfigurationError RSA not defined for all nodes (H:TYR:52:A).
+        s_g = extract_surface_subgraph(g, RSA_THRESHOLD)
+    except ProteinGraphConfigurationError as e:
+        pytest.fail(
+            "extract_surface_subgraph raised ProteinGraphConfigurationError:\n{e}"
+        )