trying to fix docs

protein_design_tools/core/protein_structure.py

@@ -62,6 +62,7 @@ def get_coordinates(
         -------
         np.ndarray
             Array of coordinates.
+
         """
 
         # 1) Merge chain(s) info into a selection dictionary if needed
@@ -149,6 +150,7 @@ def remove_residues_by_name(self, residue_name: str) -> None:
         ----------
         residue_name : str
             Residue name to be removed (e.g. 'HOH' for water).
+            
         """
         for chain in self.chains:
             # Keep only residues whose name != residue_name

protein_design_tools/io/pdb.py

@@ -34,6 +34,7 @@ def fetch_pdb(
     -------
     ProteinStructure
         The parsed protein structure.
+
     """
     structure = ProteinStructure(name=name)
 
@@ -72,6 +73,7 @@ def read_pdb(
     -------
     ProteinStructure
         The parsed protein structure.
+
     """
     structure = ProteinStructure(name=name)
 
@@ -110,6 +112,7 @@ def _parse_pdb_content(
     -------
     ProteinStructure
         The populated ProteinStructure object.
+        
     """
     for line in content:
         if line.startswith("ATOM") or line.startswith("HETATM"):

protein_design_tools/metrics/tmscore.py

@@ -5,7 +5,7 @@
 
 
 @jit
-def compute_tm_score_jax(P: jnp.ndarray, Q: jnp.ndarray) -> jnp.ndarray:
+def compute_tmscore_jax(P: jnp.ndarray, Q: jnp.ndarray) -> jnp.ndarray:
     """
     Compute TM-score between two NxD JAX arrays using JIT compilation.
 
@@ -30,7 +30,7 @@ def compute_tm_score_jax(P: jnp.ndarray, Q: jnp.ndarray) -> jnp.ndarray:
     return tm_score
 
 
-def compute_tm_score_numpy(P: np.ndarray, Q: np.ndarray) -> float:
+def compute_tmscore_numpy(P: np.ndarray, Q: np.ndarray) -> float:
     """
     Compute TM-score between two NxD NumPy arrays.
 
@@ -55,7 +55,7 @@ def compute_tm_score_numpy(P: np.ndarray, Q: np.ndarray) -> float:
     return tm_score
 
 
-def compute_tm_score_pytorch(P: torch.Tensor, Q: torch.Tensor) -> torch.Tensor:
+def compute_tmscore_pytorch(P: torch.Tensor, Q: torch.Tensor) -> torch.Tensor:
     """
     Compute TM-score between two NxD PyTorch tensors.