RNApolis 0.8.2__tar.gz → 0.8.3__tar.gz

{rnapolis-0.8.2/src/RNApolis.egg-info → rnapolis-0.8.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: RNApolis
-Version: 0.8.2
+Version: 0.8.3
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{rnapolis-0.8.2 → rnapolis-0.8.3}/setup.py

@@ -5,7 +5,7 @@ with open("README.md") as f:
 
 setup(
     name="RNApolis",
-    version="0.8.2",
+    version="0.8.3",
     packages=["rnapolis"],
     package_dir={"": "src"},
     author="Tomasz Zok",

{rnapolis-0.8.2 → rnapolis-0.8.3/src/RNApolis.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: RNApolis
-Version: 0.8.2
+Version: 0.8.3
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{rnapolis-0.8.2 → rnapolis-0.8.3}/src/rnapolis/tertiary_v2.py

@@ -121,7 +121,9 @@ class Structure:
                     groupby_cols.append("pdbx_PDB_ins_code")
 
             # Group atoms by residue
-            grouped = self.atoms.groupby(groupby_cols, dropna=False, observed=False)
+            grouped = self.atoms.groupby(
+                groupby_cols, dropna=False, observed=False, sort=False
+            )
 
         else:
             # For unknown formats, return an empty list
@@ -495,6 +497,37 @@ class Residue:
                     return Atom(atoms_df.iloc[0], self.format)
         return None
 
+    @cached_property
+    def is_nucleotide(self) -> bool:
+        """
+        Check if this residue is a nucleotide.
+
+        A nucleotide is identified by the presence of specific atoms:
+        - Sugar atoms: C1', C2', C3', C4', O4'
+        - Base atoms: N1, C2, N3, C4, C5, C6
+
+        Returns:
+        --------
+        bool
+            True if the residue is a nucleotide, False otherwise
+        """
+        # Early check: if less than 11 atoms, can't be a nucleotide
+        if len(self.atoms) < 11:
+            return False
+
+        # Required sugar atoms
+        sugar_atoms = ["C1'", "C2'", "C3'", "C4'", "O4'"]
+
+        # Required base atoms
+        base_atoms = ["N1", "C2", "N3", "C4", "C5", "C6"]
+
+        # Check for all required atoms
+        for atom_name in sugar_atoms + base_atoms:
+            if self.find_atom(atom_name) is None:
+                return False
+
+        return True
+
     def is_connected(self, next_residue_candidate: "Residue") -> bool:
         """
         Check if this residue is connected to the next residue candidate.

{rnapolis-0.8.2 → rnapolis-0.8.3}/tests/test_v2.py

@@ -12,7 +12,7 @@ from rnapolis.parser_v2 import (
     write_cif,
     write_pdb,
 )
-from rnapolis.tertiary_v2 import Atom, Residue, Structure, calculate_torsion_angle
+from rnapolis.tertiary_v2 import Structure, calculate_torsion_angle
 
 
 def compare_structures(df1: pd.DataFrame, df2: pd.DataFrame, rtol=1e-5, atol=1e-8):
@@ -42,11 +42,13 @@ def compare_structures(df1: pd.DataFrame, df2: pd.DataFrame, rtol=1e-5, atol=1e-
     )
 
     # Sort residues for consistent comparison order
-    key_func = lambda r: (
-        r.chain_id,
-        r.residue_number,
-        r.insertion_code or "",
-    )
+    def key_func(r):
+        return (
+            r.chain_id,
+            r.residue_number,
+            r.insertion_code or "",
+        )
+
     residues1.sort(key=key_func)
     residues2.sort(key=key_func)
 
@@ -265,7 +267,6 @@ def test_torsion_angle_calculation():
     a4 = np.array([0.0, 1.0, 1.0])
 
     # Calculate the torsion angle
-    from rnapolis.tertiary_v2 import calculate_torsion_angle
 
     angle = calculate_torsion_angle(a1, a2, a3, a4)
 
@@ -414,3 +415,34 @@ def test_cif_pdb_cif_roundtrip(data_dir):
     # is preserved through the PDB intermediate representation, assuming
     # the PDB format could represent the original structure or its fitted version.
     compare_structures(df_to_write_pdb, df_final_cif)
+
+
+def test_groupby_order(data_dir):
+    cif_path = os.path.join(data_dir, "1ehz-assembly-1.cif")
+    if not os.path.exists(cif_path):
+        pytest.skip(f"Test file not found: {cif_path}")
+
+    # 1. Parse Original CIF
+    with open(cif_path, "r") as f:
+        df_atoms = parse_cif_atoms(f)
+    assert not df_atoms.empty, "Original CIF parsing failed"
+
+    # 2. Group by chain_id and residue_number
+    structure = Structure(df_atoms)  # Ensure Structure can be created
+    residues = structure.residues  # Access residues to trigger any necessary processing
+    assert str(residues[0]) == "A.G1"
+    assert str(residues[1]) == "A.C2"
+
+
+def test_is_nucleotide(data_dir):
+    cif_path = os.path.join(data_dir, "1ehz-assembly-1.cif")
+    if not os.path.exists(cif_path):
+        pytest.skip(f"Test file not found: {cif_path}")
+
+    with open(cif_path, "r") as f:
+        df_atoms = parse_cif_atoms(f)
+    assert not df_atoms.empty, "Original CIF parsing failed"
+
+    structure = Structure(df_atoms)
+    residues = [residue for residue in structure.residues if residue.is_nucleotide]
+    assert len(residues) == 76