clarify docstring for chain_ids

deeprank2/query.py

@@ -47,7 +47,8 @@ class Query:
     Args:
         pdb_path (str): the path to the PDB file to query.
         resolution (Literal['residue', 'atom']): sets whether each node is a residue or atom.
-        chain_ids (list[str] | str): the chain identifier(s) in the pdb file (generally a single capital letter).
+        chain_ids (list[str] | str): the chain identifier(s) of the variant residue or interacting interfaces.
+            Note that this does not limit the structure to residues from this/these chain(s).
         pssm_paths (dict[str, str]): the name of the chain(s) (key) and path to the pssm file(s) (value).
         distance_cutoff (float): the maximum distance between two nodes to generate an edge connecting them.
         targets (dict[str, float]) = Name(s) (key) and target value(s) (value) associated with this query.
@@ -222,7 +223,8 @@ class SingleResidueVariantQuery(Query):
     Args (common for `Query`):
         pdb_path (str): the path to the PDB file to query.
         resolution (Literal['residue', 'atom']): sets whether each node is a residue or atom.
-        chain_ids (list[str] | str): the chain identifier(s) in the pdb file (generally a single capital letter).
+        chain_ids (list[str] | str): the chain identifier of the variant residue (generally a single capital letter).
+            Note that this does not limit the structure to residues from this chain.
         pssm_paths (dict[str, str]): the name of the chain(s) (key) and path to the pssm file(s) (value).
         distance_cutoff (float): the maximum distance between two nodes to generate an edge connecting them.
         targets (dict[str, float]) = Name(s) (key) and target value(s) (value) associated with this query.
@@ -320,7 +322,8 @@ class ProteinProteinInterfaceQuery(Query):
     Args:
         pdb_path (str): the path to the PDB file to query.
         resolution (Literal['residue', 'atom']): sets whether each node is a residue or atom.
-        chain_ids (list[str] | str): the chain identifier(s) in the pdb file (generally a single capital letter).
+        chain_ids (list[str] | str): the chain identifiers of the interacting interfaces (generally a single capital letter each).
+            Note that this does not limit the structure to residues from these chains.
         pssm_paths (dict[str, str]): the name of the chain(s) (key) and path to the pssm file(s) (value).
         distance_cutoff (float): the maximum distance between two nodes to generate an edge connecting them.
         targets (dict[str, float]) = Name(s) (key) and target value(s) (value) associated with this query.