stuff

deeprank2/query.py

@@ -150,14 +150,7 @@ def _load_structure(self, load_pssms: bool) -> PDBStructure:
 
         # read the pssm
         if load_pssms:
-            _check_pssm(self.pdb_path, self.pssm_paths, suppress = self.suppress_pssm_errors)
-            for chain in structure.chains:
-                chain: Chain
-                if chain.id in self.pssm_paths:
-                    pssm_path = self.pssm_paths[chain.id]
-
-                    with open(pssm_path, "rt", encoding="utf-8") as f:
-                        chain.pssm = parse_pssm(f, chain)
+            _load_ppi_pssms(self.pssm_paths, structure, self.pdb_path, self.suppress_pssm_errors)
 
         return structure
 
@@ -191,6 +184,7 @@ def __repr__(self) -> str:
         return f"{type(self)}({self.get_query_id()})"
 
     def build(self, feature_modules: List[ModuleType]) -> Graph:
+        #TODO: convert feature_modules to list of not already the case
         raise NotImplementedError("Must be defined in child classes.")
     def get_query_id(self) -> str:
         raise NotImplementedError("Must be defined in child classes.")
@@ -436,7 +430,7 @@ def build(
             feature_modules = [feature_modules]
         structure: PDBStructure = self._load_structure(load_pssms)
 
-        # find the variant residue
+        # find the variant residue and its surroundings
         variant_residue = None
         for residue in structure.get_chain(self.variant_chain_id).residues:
             residue: Residue
@@ -456,7 +450,6 @@ def build(
         # build the graph
         if self.resolution == 'residue':
             graph = build_residue_graph(residues, self.get_query_id(), self.distance_cutoff)
-
         elif self.resolution == 'atomic':
             residues.append(variant_residue)
             atoms = set([])
@@ -473,12 +466,10 @@ def build(
 
         else:
             raise NotImplementedError(f"No function exists to build graphs with resolution of {self.resolution}.")
-
         graph.center = get_residue_center(variant_residue)
 
         # add data to the graph
         self._set_graph_targets(graph)
-
         for feature_module in feature_modules:
             feature_module.add_features(self.pdb_path, graph, variant)
 
@@ -487,19 +478,21 @@ def build(
 
 def _load_ppi_pssms(
     pssm_paths: Optional[Dict[str, str]],
-    chain_ids: List[str],
     structure: PDBStructure,
     pdb_path: str,
     suppress_error: bool,
 ):
     _check_pssm(pdb_path, pssm_paths, suppress_error, verbosity = 0)
-    for chain_id in chain_ids:
-        if chain_id in pssm_paths:
-            chain = structure.get_chain(chain_id)
-            pssm_path = pssm_paths[chain_id]
+    for chain in structure.chains:
+        chain: Chain
+        if chain.id in pssm_paths:
+            pssm_path = pssm_paths[chain.id]
+
             with open(pssm_path, "rt", encoding="utf-8") as f:
                 chain.pssm = parse_pssm(f, chain)
 
+
+
 @dataclass(kw_only=True)
 class ProteinProteinInterfaceQuery(DeepRankQuery):
     """A query that builds a protein-protein interface graph."""
@@ -525,7 +518,6 @@ def get_query_id(self) -> str:
             + f"{self.chain_ids[0]}-{self.chain_ids[1]}:{self.model_id}"
         )
 
-
     def build(
         self,
         feature_modules: List[ModuleType] | ModuleType,
@@ -544,13 +536,16 @@ def build(
         if len(contact_atoms) == 0:
             raise ValueError("no contact atoms found")
 
+        # build the graph
         if self.resolution == 'atomic':
             graph = build_atomic_graph(contact_atoms, self.get_query_id(), self.distance_cutoff)
-
         elif self.resolution == 'residue':
             residues_selected = {atom.residue for atom in contact_atoms}
             graph = build_residue_graph(list(residues_selected), self.get_query_id(), self.distance_cutoff)
             #TODO: check whether this works with a set instead of a list
+        else:
+            raise NotImplementedError(f"No function exists to build graphs with resolution of {self.resolution}.")
+        graph.center = np.mean([atom.position for atom in contact_atoms], axis=0)
 
         # add data to the graph
         self._set_graph_targets(graph)
@@ -563,7 +558,6 @@ def build(
             feature_modules = [feature_modules]
         if conservation in feature_modules:
             _load_ppi_pssms(self.pssm_paths,
-                            [self.chain_ids[0], self.chain_ids[1]],
                             structure, self.pdb_path,
                             suppress_error=self.suppress_pssm_errors)