Fix sphinx doc string layout issues

kripodb/db.py

@@ -215,7 +215,7 @@ def add_molecules(self, mols):
         """Adds molecules to to molecules table.
 
         Args:
-            mols (List[rdkit.Chem.Mol]): List of molecules
+            mols (list[rdkit.Chem.Mol]): List of molecules
         """
         with FastInserter(self.cursor):
             for mol in mols:
@@ -258,8 +258,6 @@ def add_molecule(self, mol):
         Args:
             mol (rdkit.Chem.AllChem.Mol): the rdkit molecule
 
-        Returns:
-
         """
         sql = '''INSERT OR REPLACE INTO molecules (frag_id, smiles, mol) VALUES (?, ?, ?)'''
 
@@ -392,7 +390,7 @@ def by_pdb_code(self, pdb_code):
             pdb_code (str): PDB code
 
         Returns:
-            List[Fragment]
+            List[Fragment]: List of fragments
 
         Raises:
             LookupError: When pdb_code could not be found

kripodb/frozen.py

@@ -97,7 +97,7 @@ def find(self, query, cutoff, limit=None):
             limit (int): Maximum number of hits. Default is None for no limit.
 
         Returns:
-            Tuple[(str, float)]: Hit fragment idenfier and similarity score
+            list[tuple[str,float]]: Hit fragment identifier and similarity score
         """
         precision = float(self.score_precision)
         precision10 = float(10**(floor(log10(precision))))
@@ -121,7 +121,7 @@ def __getitem__(self, item):
             item (STR): Label of a fragment
 
         Returns:
-            List((str, float)): list of (fragment_label, score)
+            list[tuple[str, float]]: list of (fragment_label, score)
 
         """
         precision = float(self.score_precision)

kripodb/hdf5.py

@@ -88,8 +88,8 @@ def update(self, similarities_iter, label2id):
         """Store pairs of fragment identifier with their similarity score and label 2 id lookup
 
         Args:
-            similarities_iter (Iterator): Iterator which yields (label1, label2, similarity_score)
-            label2id (Dict): Dictionary with fragment label as key and fragment identifier as value.
+            similarities_iter (iterator): Iterator which yields (label1, label2, similarity_score)
+            label2id (dict): Dictionary with fragment label as key and fragment identifier as value.
 
         """
         self.pairs.update(similarities_iter, label2id)
@@ -104,7 +104,7 @@ def find(self, query, cutoff, limit=None):
             limit (int): Maximum number of hits. Default is None for no limit.
 
         Yields:
-            Tuple[(str, float)]: Hit fragment idenfier and similarity score
+            (str, float): Hit fragment idenfier and similarity score
         """
         if self.cache_l2i:
             frag_id = self.cache_l2i[query]
@@ -122,7 +122,7 @@ def count(self, frame_size):
             frame_size (int): Size of matrix loaded each time. Larger requires more memory and smaller is slower.
 
         Returns:
-            Tuple[(str, int)]: Score and number of occurrences
+            (str, int): Score and number of occurrences
         """
         return self.pairs.count(frame_size)
 
@@ -393,7 +393,7 @@ def label2ids(self):
         """Return whole table as a dictionary
 
         Returns:
-            Dict: Dictionary with label as key and frag_id as value.
+            dict: Dictionary with label as key and frag_id as value.
 
         """
         return {r['label'].decode(): r['frag_id'] for r in self.table}
@@ -402,7 +402,7 @@ def update(self, label2id):
         """Update labels lookup by adding labels in label2id.
 
         Args:
-            label2id (Dict): Dictionary with fragment label as key and fragment identifier as value.
+            label2id (dict): Dictionary with fragment label as key and fragment identifier as value.
 
         """
         for label, frag_id in six.iteritems(label2id):
@@ -432,10 +432,10 @@ def merge(self, label2id):
         When label does exist the id of the label in self is kept.
 
         Args:
-            label2id (Dict): Dictionary with fragment label as key and fragment identifier as value.
+            label2id (dict]): Dictionary with fragment label as key and fragment identifier as value.
 
         Returns:
-            Dict: Dictionary of label/id which where in label2id, but missing in self
+            dict: Dictionary of label/id which where in label2id, but missing in self
         """
         id_offset = max([r['frag_id'] for r in self.table]) + 1
 

kripodb/modifiedtanimoto.py

@@ -45,7 +45,7 @@ def corrections(mean_onbit_density):
         mean_onbit_density (float): Mean on bit density
 
     Returns:
-        S\ :sub:`T` correction, S\ :sub:`T0` correction
+        float: S\ :sub:`T` correction, S\ :sub:`T0` correction
     """
     p0 = mean_onbit_density
     corr_st = (2 - p0) / 3

kripodb/pairs.py

@@ -196,7 +196,7 @@ def open_similarity_matrix(fn):
         fn (str): Filename of similarity matrix
 
     Returns:
-        SimilarityMatrix|FrozenSimilarityMatrix: A read-only similarity matrix object
+        SimilarityMatrix | FrozenSimilarityMatrix: A read-only similarity matrix object
 
     """
     # peek in file to detect format

kripodb/script/dive.py

@@ -54,7 +54,7 @@ def dive_sphere(inputfile, outputfile, onlyfrag1):
     Args:
         inputfile (str): fragments db input file
         outputfile (file): fragments dive output file
-        onlyfrag1 (bool):O nly *_frag1
+        onlyfrag1 (bool): Only \*_frag1
 
     """
     frags_db = FragmentsDb(inputfile)

kripodb/webservice/client.py

@@ -40,7 +40,7 @@ def similar_fragments(self, fragment_id, cutoff, limit=1000):
             limit (int): Maximum number of hits. Default is None for no limit.
 
         Returns:
-            List(Dict()): Query fragment identifier, hit fragment identifier and similarity score
+            list[dict]: Query fragment identifier, hit fragment identifier and similarity score
         """
         url = self.base_url + '/fragments/{fragment_id}/similar'.format(fragment_id=fragment_id)
         params = {'cutoff': cutoff, 'limit': limit}
@@ -56,7 +56,7 @@ def fragments_by_pdb_codes(self, pdb_codes, chunk_size=450):
             chunk_size (int): Number of PDB codes to retrieve in a single http request
 
         Returns:
-            List(Dict()): List of fragment information
+            list[dict]: List of fragment information
 
         Raises:
             requests.HTTPError: When one of the PDB codes could not be found.
@@ -71,7 +71,7 @@ def fragments_by_id(self, fragment_ids, chunk_size=100):
             chunk_size (int): Number of PDB codes to retrieve in a single http request
 
         Returns:
-            List(Dict()): List of fragment information
+            list[dict]: List of fragment information
 
         Raises:
             requests.HTTPError: When one of the identifiers could not be found.

kripodb/webservice/server.py

@@ -58,7 +58,7 @@ def get_similar_fragments(fragment_id, cutoff, limit):
         limit (int): Maximum number of hits. Default is None for no limit.
 
     Returns:
-        List(Dict()): Query fragment identifier, hit fragment identifier and similarity score
+        list[dict]: List of dict with query fragment identifier, hit fragment identifier and similarity score
 
     Raises:
         werkzeug.exceptions.NotFound: When the fragments_id could not be found
@@ -72,7 +72,7 @@ def get_similar_fragments(fragment_id, cutoff, limit):
         # add query column
         for hit_id, score in raw_hits:
             hits.append({'query_frag_id': query_id, 'hit_frag_id': hit_id, 'score': score})
-    except LookupError as e:
+    except LookupError:
         abort(404, 'Fragment with identifier \'{0}\' not found'.format(fragment_id))
     return hits
 
@@ -85,7 +85,7 @@ def get_fragments(fragment_ids=None, pdb_codes=None):
         pdb_codes (List[str]): List of PDB codes
 
     Returns:
-        List(Dict()): List of fragment information
+        list[dict]: List of fragment information
 
     Raises:
         werkzeug.exceptions.NotFound: When one of the fragments_ids or pdb_code could not be found
@@ -119,6 +119,16 @@ def mol2svg(mol, width, height):
 
 
 def get_fragment_svg(fragment_id, width, height):
+    """2D drawing of fragment in SVG format
+
+    Args:
+        fragment_id (str): Fragment identifier
+        width (int): Width of SVG in pixels
+        height (int): Height of SVG in pixels
+
+    Returns:
+        str: SVG document
+    """
     fragments_db_filename = current_app.config['db_fn']
     with FragmentsDb(fragments_db_filename) as fragmentsdb:
         try:
@@ -133,7 +143,7 @@ def get_fragment_svg(fragment_id, width, height):
 def get_version():
     """
     Returns:
-        Dict: Version of web service
+        dict[version]: Version of web service
     """
     # TODO check if matrix is usable
     return {'version': __version__}