RNApolis 0.3.14__py3-none-any.whl → 0.3.16__py3-none-any.whl

{RNApolis-0.3.14.dist-info → RNApolis-0.3.16.dist-info}/METADATA

@@ -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.dist-info → RNApolis-0.3.16.dist-info}/RECORD

@@ -1,17 +1,17 @@
 rnapolis/annotator.py,sha256=XnjFBeu3P_2UMdkD4Ao7m7K6JfeqYa-13xRzghrLvt8,22086
 rnapolis/clashfinder.py,sha256=jD3s_UovygWi01NUbQNeAeRRFkARTSRraLXUV43UbAA,8514
-rnapolis/common.py,sha256=mgn9psuBcgJVGPRxsxilVedPygqfwFz9wn5Z0vTU6SY,30107
+rnapolis/common.py,sha256=tbmKV64nLClmzNN0HyKnvWA0-5aSyf4x8CGpBjpIJ4M,30290
 rnapolis/metareader.py,sha256=4qtMKRvww2sUStLeV8WVrLEt-ScydHUv4Gxx96tnf-M,1683
 rnapolis/molecule_filter.py,sha256=NhjuqdCRnXgPefWZPeTq77tifmnAzamQtA0ODqPPG9k,6918
 rnapolis/motif_extractor.py,sha256=duHvpi9Ulcny9K60E6VBpz5RpJZw-KdTB4_Ph0iP478,774
-rnapolis/parser.py,sha256=Cmjt7p8UkiSNhSQDjc6I7BRqtuIIHs23Fp-Glb8Zikw,12216
+rnapolis/parser.py,sha256=6xEeQghil0eXIzi0bNUkebknfqIxx9EfOfT9q33eN4A,12666
 rnapolis/rfam_folder.py,sha256=3rgXEJR16uPFy_BOo8qkdClOAOQDVOkidnLE-yoRbeI,11112
 rnapolis/tertiary.py,sha256=VuATTN2SD7lBL9iUgT-doDwuEYsLodgV2u-SwQsyQcU,19658
 rnapolis/transformer.py,sha256=V9nOQvdq4-p7yUWo0vQg0CDQMpmyxz9t4TMSRVEKHnw,1817
 rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
-RNApolis-0.3.14.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
-RNApolis-0.3.14.dist-info/METADATA,sha256=Yrp600ac6KI9zfglV3wf4bY9-dOHO32YgWwwKzYzo94,54301
-RNApolis-0.3.14.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-RNApolis-0.3.14.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
-RNApolis-0.3.14.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
-RNApolis-0.3.14.dist-info/RECORD,,
+RNApolis-0.3.16.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
+RNApolis-0.3.16.dist-info/METADATA,sha256=k4D9WCUq94R1lGhWmYJqTjfh9ww8RPRjxg_IOHiPEcg,54301
+RNApolis-0.3.16.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+RNApolis-0.3.16.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
+RNApolis-0.3.16.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
+RNApolis-0.3.16.dist-info/RECORD,,

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/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"])