RNApolis 0.4.6__py3-none-any.whl → 0.4.8__py3-none-any.whl

{RNApolis-0.4.6.dist-info → RNApolis-0.4.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.4.6
+Version: 0.4.8
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{RNApolis-0.4.6.dist-info → RNApolis-0.4.8.dist-info}/RECORD

@@ -1,17 +1,17 @@
 rnapolis/annotator.py,sha256=7U3f0gchKdIGc6FwJx0UAc_95HJI5SgECj-b7-1yBhc,22086
 rnapolis/clashfinder.py,sha256=i95kp0o6OWNqmJDBr-PbsZd7RY2iJtBDr7QqolJSuAQ,8513
-rnapolis/common.py,sha256=PUYF01P2vevhyImhZjGYE0jJlsxWHX6GQmsxI4W7S-E,30255
+rnapolis/common.py,sha256=7KSWZzqR7ntpaS6VRDYgpP2pC1dnBttOzYB06hQzWEI,30499
 rnapolis/metareader.py,sha256=I1-cXc2YNBPwa3zihAnMTjEsAo79tEKzSmWu5yvN1Pk,2071
 rnapolis/molecule_filter.py,sha256=hB6-nXgjmw7FAsQ3bj0cZ2FvuW2I1PXunEfcdwEUB1o,7389
 rnapolis/motif_extractor.py,sha256=duHvpi9Ulcny9K60E6VBpz5RpJZw-KdTB4_Ph0iP478,774
 rnapolis/parser.py,sha256=2pQYy0sh8TCpeluMmmSJ7C5dudK_bsfstTWCdpwwpNU,15193
 rnapolis/rfam_folder.py,sha256=SjiiyML_T1__saruFwSMJEoQ7Y55GIU8ktS8ZUn5-fw,11111
-rnapolis/tertiary.py,sha256=SQyiYWA0RJhAK70f88CKZvS4EzGKHQ2RoL1s4MueEDQ,21657
+rnapolis/tertiary.py,sha256=6t9ZB4w33-5n_M3sns1RoFXCOTgVAgGH4WDNG5OG9Kg,23426
 rnapolis/transformer.py,sha256=V9nOQvdq4-p7yUWo0vQg0CDQMpmyxz9t4TMSRVEKHnw,1817
 rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
-RNApolis-0.4.6.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
-RNApolis-0.4.6.dist-info/METADATA,sha256=1Zd34oJFXeLnKDzG7HG-6jSjsAnIimsiWPbTlvDerO4,54322
-RNApolis-0.4.6.dist-info/WHEEL,sha256=GV9aMThwP_4oNCtvEC2ec3qUYutgWeAzklro_0m4WJQ,91
-RNApolis-0.4.6.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
-RNApolis-0.4.6.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
-RNApolis-0.4.6.dist-info/RECORD,,
+RNApolis-0.4.8.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
+RNApolis-0.4.8.dist-info/METADATA,sha256=FZsizaaGYKRz7ndlAySWt8mPfpjjHUoP-OzXaO3LBv8,54322
+RNApolis-0.4.8.dist-info/WHEEL,sha256=PZUExdf71Ui_so67QXpySuHtCi3-J3wvF4ORK6k_S8U,91
+RNApolis-0.4.8.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
+RNApolis-0.4.8.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
+RNApolis-0.4.8.dist-info/RECORD,,

{RNApolis-0.4.6.dist-info → RNApolis-0.4.8.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (75.1.0)
+Generator: setuptools (75.6.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

rnapolis/common.py

@@ -338,6 +338,9 @@ class Entry(Sequence):
             return self.pair
         raise IndexError()
 
+    def __lt__(self, other):
+        return self.index_ < other.index_
+
     def __len__(self) -> int:
         return 3
 
@@ -701,12 +704,17 @@ class BpSeq:
 
     @cached_property
     def dot_bracket(self):
-        pulp.LpSolverDefault.msg = False
-        return self.convert_to_dot_bracket(pulp.LpSolverDefault)
+        if pulp.HiGHS_CMD().available():
+            solver = pulp.HiGHS_CMD()  # much faster than default
+        else:
+            solver = pulp.LpSolverDefault
+        if solver is not None:
+            solver.msg = False
+        return self.convert_to_dot_bracket(solver)
 
     def convert_to_dot_bracket(self, solver: pulp.LpSolver):
         # if PuLP solvers are not installed, use FCFS
-        if len(pulp.listSolvers(onlyAvailable=True)) == 0:
+        if solver is None:
             return self.fcfs()
 
         # build conflict graph
@@ -838,7 +846,7 @@ class BpSeq:
 
         for i in range(1, len(regions)):
             k, l, _ = regions[i]
-            available = [True for i in range(10)]
+            available = [True for _ in range(len("([{<" + string.ascii_uppercase))]
 
             for j in range(i):
                 m, n, _ = regions[j]

rnapolis/tertiary.py

@@ -124,36 +124,17 @@ class Residue3D(Residue):
     outermost_atoms = {"A": "N9", "G": "N9", "C": "N1", "U": "N1", "T": "N1"}
     # Dist representing expected name of atom closest to the tetrad center
     innermost_atoms = {"A": "N6", "G": "O6", "C": "N4", "U": "O4", "T": "O4"}
+    # Heavy atoms in phosphate and ribose
+    phosphate_atoms = {"P", "OP1", "OP2", "O3'", "O5'"}
+    sugar_atoms = {"C1'", "C2'", "C3'", "C4'", "C5'", "O4'"}
     # Heavy atoms for each main nucleobase
     nucleobase_heavy_atoms = {
         "A": set(["N1", "C2", "N3", "C4", "C5", "C6", "N6", "N7", "C8", "N9"]),
         "G": set(["N1", "C2", "N2", "N3", "C4", "C5", "C6", "O6", "N7", "C8", "N9"]),
         "C": set(["N1", "C2", "O2", "N3", "C4", "N4", "C5", "C6"]),
         "U": set(["N1", "C2", "O2", "N3", "C4", "O4", "C5", "C6"]),
+        "T": set(["N1", "C2", "O2", "N3", "C4", "O4", "C5", "C5M", "C6"]),
     }
-    # Heavy atoms in nucleotide
-    nucleotide_heavy_atoms = (
-        set(
-            [
-                "P",
-                "OP1",
-                "OP2",
-                "O5'",
-                "C5'",
-                "C4'",
-                "O4'",
-                "C3'",
-                "O3'",
-                "C2'",
-                "O2'",
-                "C1'",
-            ]
-        )
-        .union(nucleobase_heavy_atoms["A"])
-        .union(nucleobase_heavy_atoms["G"])
-        .union(nucleobase_heavy_atoms["C"])
-        .union(nucleobase_heavy_atoms["U"])
-    )
 
     def __lt__(self, other):
         return (self.model, self.chain, self.number, self.icode or " ") < (
@@ -202,9 +183,59 @@ class Residue3D(Residue):
 
     @cached_property
     def is_nucleotide(self) -> bool:
-        return self.nucleotide_heavy_atoms.intersection(
-            set([atom.name for atom in self.atoms])
+        scores = {"phosphate": 0.0, "sugar": 0.0, "base": 0.0, "connections": 0.0}
+        weights = {"phosphate": 0.25, "sugar": 0.25, "base": 0.25, "connections": 0.25}
+
+        residue_atoms = {atom.name for atom in self.atoms}
+
+        phosphate_match = len(residue_atoms.intersection(self.phosphate_atoms))
+        scores["phosphate"] = phosphate_match / len(self.phosphate_atoms)
+
+        sugar_match = len(residue_atoms.intersection(self.sugar_atoms))
+        scores["sugar"] = sugar_match / len(self.sugar_atoms)
+
+        nucleobase_atoms = {
+            key: self.nucleobase_heavy_atoms[key] for key in self.nucleobase_heavy_atoms
+        }
+        matches = {
+            key: len(residue_atoms.intersection(nucleobase_atoms[key]))
+            / len(nucleobase_atoms[key])
+            for key in nucleobase_atoms
+        }
+        best_match = max(matches.items(), key=lambda x: x[1])
+        scores["base"] = best_match[1]
+
+        connection_score = 0.0
+        distance_threshold = 2.0
+
+        if "P" in residue_atoms and "O5'" in residue_atoms:
+            p_atom = next(atom for atom in self.atoms if atom.name == "P")
+            o5_atom = next(atom for atom in self.atoms if atom.name == "O5'")
+            if (
+                numpy.linalg.norm(p_atom.coordinates - o5_atom.coordinates)
+                <= distance_threshold
+            ):
+                connection_score += 0.5
+        if "C1'" in residue_atoms:
+            c1_atom = next(atom for atom in self.atoms if atom.name == "C1'")
+            for base_connection in ["N9", "N1"]:
+                if base_connection in residue_atoms:
+                    base_atom = next(
+                        atom for atom in self.atoms if atom.name == base_connection
+                    )
+                    if (
+                        numpy.linalg.norm(c1_atom.coordinates - base_atom.coordinates)
+                        <= distance_threshold
+                    ):
+                        connection_score += 0.5
+                        break
+
+        scores["connections"] = connection_score
+
+        probability = sum(
+            scores[component] * weights[component] for component in scores.keys()
         )
+        return probability > 0.5
 
     @cached_property
     def base_normal_vector(self) -> Optional[numpy.typing.NDArray[numpy.floating]]:
@@ -566,15 +597,14 @@ class Mapping2D3D:
         return self.__generate_bpseq(canonical)
 
     def __generate_bpseq(self, base_pairs):
+        nucleotides = list(filter(lambda r: r.is_nucleotide, self.structure3d.residues))
         result: Dict[int, List] = {}
         residue_map: Dict[Residue3D, int] = {}
         i = 1
 
-        for j, residue in enumerate(
-            filter(lambda r: r.is_nucleotide, self.structure3d.residues)
-        ):
+        for j, residue in enumerate(nucleotides):
             if self.find_gaps and j > 0:
-                previous = self.structure3d.residues[j - 1]
+                previous = nucleotides[j - 1]
 
                 if (
                     not previous.is_connected(residue)