From 23357f088887e666a8d9634e9d59a5189a4b407b Mon Sep 17 00:00:00 2001 From: Dani Bodor Date: Fri, 3 Nov 2023 11:11:50 +0100 Subject: [PATCH] clarify docstring for `chain_ids` --- deeprank2/query.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/deeprank2/query.py b/deeprank2/query.py index b88777537..324a8cc98 100644 --- a/deeprank2/query.py +++ b/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.