RNApolis 0.8.2__py3-none-any.whl → 0.8.3__py3-none-any.whl

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.dist-info → rnapolis-0.8.3.dist-info}/METADATA

@@ -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.dist-info → rnapolis-0.8.3.dist-info}/RECORD

@@ -16,13 +16,13 @@ rnapolis/parser_v2.py,sha256=qG6CO3or7zmuJu368g9Nzokiqdeip4yjD14F163uH6w,40618
 rnapolis/rfam_folder.py,sha256=SjiiyML_T1__saruFwSMJEoQ7Y55GIU8ktS8ZUn5-fw,11111
 rnapolis/splitter.py,sha256=x-Zn21mkiMgvYPptUFD9BbdNIvoaM6b8GzGf6uYXEwE,4052
 rnapolis/tertiary.py,sha256=mTVpz8rz5Q9s5_QVSMdEMXSooCce0rAD5RQMh00bHm4,39200
-rnapolis/tertiary_v2.py,sha256=I1uyHWIUePNGO5m-suoL4ibtz02qAJUMvYm0BUKUygY,22480
+rnapolis/tertiary_v2.py,sha256=y7Rh43Jzt9QU6wCa1wAHIcO3BcNQY83PbbWNTmqI8zM,23424
 rnapolis/transformer.py,sha256=aC0nBmHHJf5TyLvBIV57Jj3tlwpvHbPo347opfAOlQA,3844
 rnapolis/unifier.py,sha256=2ge7IB9FdRgzSAiVD39U_ciwtdDJ2fGzf8mUIudbrqY,5820
 rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
-rnapolis-0.8.2.dist-info/licenses/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
-rnapolis-0.8.2.dist-info/METADATA,sha256=1_ITZKV6JF324k9MawJIQCYH1VI8fQffIp9IRquKwnE,54537
-rnapolis-0.8.2.dist-info/WHEEL,sha256=CmyFI0kx5cdEMTLiONQRbGQwjIoR1aIYB7eCAQ4KPJ0,91
-rnapolis-0.8.2.dist-info/entry_points.txt,sha256=H00KoN54wU3dFOofAu3H_3PADmZOBTB1hXf5TUU2uzo,438
-rnapolis-0.8.2.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
-rnapolis-0.8.2.dist-info/RECORD,,
+rnapolis-0.8.3.dist-info/licenses/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
+rnapolis-0.8.3.dist-info/METADATA,sha256=qdVlCdQ9zj6-qb8EXVVnhbCD7TJEUtF51LZN7VIx658,54537
+rnapolis-0.8.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+rnapolis-0.8.3.dist-info/entry_points.txt,sha256=H00KoN54wU3dFOofAu3H_3PADmZOBTB1hXf5TUU2uzo,438
+rnapolis-0.8.3.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
+rnapolis-0.8.3.dist-info/RECORD,,

{rnapolis-0.8.2.dist-info → rnapolis-0.8.3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (78.1.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any