RNApolis 0.4.6__tar.gz → 0.4.7__tar.gz

{rnapolis-0.4.6/src/RNApolis.egg-info → rnapolis-0.4.7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.4.6
+Version: 0.4.7
 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 → rnapolis-0.4.7}/setup.py

@@ -5,7 +5,7 @@ with open("README.md") as f:
 
 setup(
     name="RNApolis",
-    version="0.4.6",
+    version="0.4.7",
     packages=["rnapolis"],
     package_dir={"": "src"},
     author="Tomasz Zok",

{rnapolis-0.4.6 → rnapolis-0.4.7/src/RNApolis.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.4.6
+Version: 0.4.7
 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 → rnapolis-0.4.7}/src/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
 
@@ -838,7 +841,7 @@ 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-0.4.6 → rnapolis-0.4.7}/src/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)

{rnapolis-0.4.6 → rnapolis-0.4.7}/tests/test_bugfixes.py

@@ -42,7 +42,7 @@ def test_4WTI():
     mapping = Mapping2D3D(
         structure3d, base_interactions.basePairs, base_interactions.stackings, True
     )
-    assert mapping.dot_bracket == ">strand_T\nACGG\n..((\n>strand_P\nCC\n))"
+    assert mapping.dot_bracket == ">strand_T\nCGG\n.((\n>strand_P\nCC\n))"
 
 
 # in 1HMH the bases are oriented in 45 degrees and it caused the program to identify invalid base pair

{rnapolis-0.4.6 → rnapolis-0.4.7}/tests/test_common.py

@@ -1,3 +1,4 @@
+import string
 from collections import Counter
 
 import orjson
@@ -11,6 +12,7 @@ from rnapolis.common import (
     BaseRibose,
     BpSeq,
     DotBracket,
+    Entry,
     Interaction,
     LeontisWesthof,
     MultiStrandDotBracket,
@@ -180,3 +182,20 @@ def test_conflicted_base_pairs():
     assert (
         mapping.dot_bracket == ">strand_B\nGGACUAGCGGAGGCUAGUCC\n((((((((....))))))))"
     )
+
+
+def test_high_level_pseudoknot():
+    entries = []
+    brackets = "([{<" + string.ascii_uppercase
+
+    for i in range(len(brackets)):
+        entries.append(Entry(i + 1, "C", i + len(brackets) + 1))
+        entries.append(Entry(i + len(brackets) + 1, "G", i + 1))
+
+    bpseq = BpSeq(sorted(entries))
+    dot_bracket = bpseq.fcfs
+    assert dot_bracket.sequence == "C" * len(brackets) + "G" * len(brackets)
+    assert (
+        dot_bracket.structure
+        == "([{<" + string.ascii_uppercase + ")]}>" + string.ascii_lowercase
+    )