RNApolis 0.3.14__tar.gz → 0.3.16__tar.gz

{rnapolis-0.3.14/src/RNApolis.egg-info → rnapolis-0.3.16}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.3.14
+Version: 0.3.16
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{rnapolis-0.3.14 → rnapolis-0.3.16}/setup.py

@@ -5,7 +5,7 @@ with open("README.md") as f:
 
 setup(
     name="RNApolis",
-    version="0.3.14",
+    version="0.3.16",
     packages=["rnapolis"],
     package_dir={"": "src"},
     author="Tomasz Zok",

{rnapolis-0.3.14 → rnapolis-0.3.16/src/RNApolis.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.3.14
+Version: 0.3.16
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{rnapolis-0.3.14 → rnapolis-0.3.16}/src/rnapolis/common.py

@@ -900,33 +900,37 @@ class BpSeq:
                     else:
                         stack.pop()
 
-        # permute order of every component
-        permutations = [
-            list(itertools.permutations(component)) for component in components
-        ]
-        solutions = set()
+        # find unique orders for each component
+        unique = []
+        for component in components:
+            unique.append(set())
 
-        for permutation in itertools.product(*permutations):
-            orders = [0 for _ in range(len(regions))]
+            for permutation in itertools.permutations(component):
+                orders = {region: 0 for region in component}
 
-            for component in permutation:
-                for i in range(1, len(component)):
-                    region_i = component[i]
-                    available = [True for _ in range(len(graph))]
+                for i in range(1, len(permutation)):
+                    available = [True for _ in range(len(component))]
 
                     for j in range(i):
-                        region_j = component[j]
-
-                        if region_j in graph[region_i]:
-                            available[orders[region_j]] = False
+                        if permutation[j] in graph[permutation[i]]:
+                            available[orders[permutation[j]]] = False
 
                     order = next(
-                        filter(lambda i: available[i] is True, range(len(available)))
+                        filter(lambda k: available[k] is True, range(len(available)))
                     )
-                    orders[region_i] = order
+                    orders[permutation[i]] = order
+
+                unique[-1].add(frozenset(orders.items()))
+
+        # generate all possible dot-brackets
+        solutions = set()
+        for assignment in itertools.product(*unique):
+            orders = {region: 0 for region in range(len(regions))}
 
-                solutions.add(self.__make_dot_bracket(regions, orders))
+            for order in assignment:
+                orders.update(order)
 
+            solutions.add(self.__make_dot_bracket(regions, orders))
         return list(solutions)
 
 

{rnapolis-0.3.14 → rnapolis-0.3.16}/src/rnapolis/parser.py

@@ -1,3 +1,4 @@
+import logging
 from typing import IO, Dict, List, Optional, Tuple, Union
 
 from mmcif.io.IoAdapterPy import IoAdapterPy
@@ -5,6 +6,9 @@ from mmcif.io.IoAdapterPy import IoAdapterPy
 from rnapolis.common import ResidueAuth, ResidueLabel
 from rnapolis.tertiary import BASE_ATOMS, Atom, Residue3D, Structure3D
 
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
 
 def read_3d_structure(
     cif_or_pdb: IO[str], model: Optional[int] = None, nucleic_acid_only: bool = False
@@ -104,6 +108,14 @@ def parse_cif(
                         auth_residue_name,
                     )
 
+                if label is None and auth is None:
+                    # this should not happen in a valid mmCIF file
+                    # skipping the line
+                    logger.debug(
+                        f"Cannot parse an atom line without chain name, residue number, and residue name: {row}"
+                    )
+                    continue
+
                 model = int(row_dict.get("pdbx_PDB_model_num", "1"))
                 atom_name = row_dict["label_atom_id"]
                 x = float(row_dict["Cartn_x"])

{rnapolis-0.3.14 → rnapolis-0.3.16}/tests/test_annotator.py

@@ -1,6 +1,6 @@
 from collections import Counter
 
-from rnapolis.annotator import extract_base_interactions
+from rnapolis.annotator import extract_base_interactions, extract_secondary_structure
 from rnapolis.parser import read_3d_structure
 
 
@@ -39,3 +39,9 @@ def test_1ehz():
                 assert (
                     False
                 ), f"Interaction {element} occurs {count} times among {labels[i]} type: {duplicates}"
+
+
+def test_8btk():
+    with open("tests/8btk_B7.cif") as f:
+        structure3d = read_3d_structure(f, 1)
+    assert extract_secondary_structure(structure3d, 1) is not None