build: bump rnapolis from 0.1.4 to 0.2.0 (#81)

requirements.txt

@@ -1,4 +1,4 @@
 mmcif==0.81
 numpy==1.26.2
 orjson==3.9.10
-rnapolis==0.1.4
+rnapolis==0.2.0

src/eltetrado/analysis.py

@@ -12,7 +12,7 @@
 
 import numpy
 import numpy.typing
-from rnapolis.common import GlycosidicBond, Structure2D
+from rnapolis.common import BaseInteractions, GlycosidicBond
 from rnapolis.tertiary import Atom, BasePair3D, Mapping2D3D, Residue3D, Structure3D
 
 from eltetrado.model import (
@@ -729,7 +729,7 @@ def __str__(self):
 
 @dataclass
 class Analysis:
-    structure2d: Structure2D
+    base_interactions: BaseInteractions
     structure3d: Structure3D
     strict: bool
     no_reorder: bool
@@ -752,8 +752,8 @@ def __post_init__(self):
         self.global_index = self.__prepare_global_index()
         self.mapping = Mapping2D3D(
             self.structure3d,
-            self.structure2d.basePairs,
-            self.structure2d.stackings,
+            self.base_interactions.basePairs,
+            self.base_interactions.stackings,
             False,
         )
         self.tetrads = self.__find_tetrads(self.no_reorder)
@@ -1409,9 +1409,9 @@ def __to_helix(
 
 
 class AnalysisSimple:
-    def __init__(self, structure2d: Structure2D, structure3d: Structure3D):
+    def __init__(self, base_interactions: BaseInteractions, structure3d: Structure3D):
         self.mapping = Mapping2D3D(
-            structure3d, structure2d.basePairs, structure2d.stackings, False
+            structure3d, base_interactions.basePairs, base_interactions.stackings, False
         )
 
     def has_tetrads(self) -> bool:
@@ -1444,15 +1444,17 @@ def center_of_mass(atoms: List[Atom]) -> numpy.typing.NDArray[numpy.floating]:
 
 
 def eltetrado(
-    structure2d: Structure2D,
+    base_interactions: BaseInteractions,
     structure3d: Structure3D,
     strict: bool,
     no_reorder: bool,
     stacking_mismatch: int,
 ) -> Analysis:
-    return Analysis(structure2d, structure3d, strict, no_reorder, stacking_mismatch)
+    return Analysis(
+        base_interactions, structure3d, strict, no_reorder, stacking_mismatch
+    )
 
 
-def has_tetrad(structure2d: Structure2D, structure3d: Structure3D) -> bool:
-    structure = AnalysisSimple(structure2d, structure3d)
+def has_tetrad(base_interactions: BaseInteractions, structure3d: Structure3D) -> bool:
+    structure = AnalysisSimple(base_interactions, structure3d)
     return structure.has_tetrads()

src/eltetrado/cli.py

@@ -9,7 +9,7 @@
 import orjson
 import rnapolis.annotator
 import rnapolis.parser
-from rnapolis.annotator import LeontisWesthof, Structure2D
+from rnapolis.annotator import BaseInteractions, LeontisWesthof
 from rnapolis.common import BasePair, Residue, Stacking
 from rnapolis.tertiary import Structure3D
 
@@ -76,7 +76,7 @@ def eltetrado_cli(args=sys.argv[1:]):
         cif_or_pdb, args.model, nucleic_acid_only=False
     )
     structure2d = (
-        rnapolis.annotator.extract_secondary_structure(structure3d, args.model)
+        rnapolis.annotator.extract_base_interactions(structure3d, args.model)
         if args.dssr_json is None
         else read_secondary_structure_from_dssr(structure3d, args.model, args.dssr_json)
     )
@@ -154,12 +154,12 @@ def has_tetrad_cli(args=sys.argv[1:]):
     structure3d = rnapolis.parser.read_3d_structure(
         cif_or_pdb, args.model, nucleic_acid_only=False
     )
-    structure2d = (
-        rnapolis.annotator.extract_secondary_structure(structure3d, args.model)
+    base_interactions = (
+        rnapolis.annotator.extract_base_interactions(structure3d, args.model)
         if args.dssr_json is None
         else read_secondary_structure_from_dssr(structure3d, args.model, args.dssr_json)
     )
-    print(has_tetrad(structure2d, structure3d))
+    print(has_tetrad(base_interactions, structure3d))
 
 
 def handle_input_file(path) -> IO[str]:
@@ -181,7 +181,7 @@ def handle_input_file(path) -> IO[str]:
 
 def read_secondary_structure_from_dssr(
     structure3d: Structure3D, model: int, dssr_json_path: str
-) -> Structure2D:
+) -> BaseInteractions:
     base_pairs: List[BasePair] = []
     stackings: List[Stacking] = []
 
@@ -212,7 +212,7 @@ def read_secondary_structure_from_dssr(
             if nt1 is not None and nt2 is not None:
                 stackings.append(Stacking(nt1, nt2, None))
 
-    return Structure2D(base_pairs, stackings, [], [], [], "", "", "", [], [], [], [])
+    return BaseInteractions(base_pairs, stackings, [], [], [])
 
 
 def match_dssr_name_to_residue(

src/eltetrado/dto.py

@@ -3,7 +3,7 @@
 from dataclasses import dataclass
 from typing import List, Optional
 
-from eltetrado.analysis import Analysis, Helix, Quadruplex, TetradPair
+from eltetrado.analysis import Analysis, Quadruplex, TetradPair
 from eltetrado.model import Ion
 
 

src/eltetrado/model.py

@@ -1,12 +1,6 @@
 import logging
-import math
 import os
-from collections import Counter
-from dataclasses import dataclass
 from enum import Enum
-from typing import List, Optional
-
-import numpy.typing
 
 logging.basicConfig(level=os.environ.get("LOGLEVEL", "INFO"))
 

tests/test_dto.py

@@ -1,10 +1,8 @@
-from eltetrado.analysis import eltetrado
-
-from eltetrado.cli import handle_input_file
 import rnapolis.annotator
 import rnapolis.parser
 
-from eltetrado.cli import read_secondary_structure_from_dssr
+from eltetrado.analysis import eltetrado
+from eltetrado.cli import handle_input_file, read_secondary_structure_from_dssr
 from eltetrado.dto import convert_nucleotides, convert_tetrads, generate_dto
 
 
@@ -14,8 +12,8 @@ def test_convert_nucleotides():
     """
     cif = handle_input_file("tests/files/6fc9-assembly-1.cif.gz")
     structure3d = rnapolis.parser.read_3d_structure(cif, nucleic_acid_only=False)
-    structure2d = rnapolis.annotator.extract_secondary_structure(structure3d)
-    analysis = eltetrado(structure2d, structure3d, False, False, 2)
+    base_interactions = rnapolis.annotator.extract_base_interactions(structure3d)
+    analysis = eltetrado(base_interactions, structure3d, False, False, 2)
     nucleotides = convert_nucleotides(analysis)
     assert len(nucleotides) == 27
 
@@ -26,8 +24,8 @@ def test_ions():
     """
     cif = handle_input_file("tests/files/7dju-assembly-1.cif.gz")
     structure3d = rnapolis.parser.read_3d_structure(cif, nucleic_acid_only=False)
-    structure2d = rnapolis.annotator.extract_secondary_structure(structure3d)
-    analysis = eltetrado(structure2d, structure3d, False, False, 2)
+    base_interactions = rnapolis.annotator.extract_base_interactions(structure3d)
+    analysis = eltetrado(base_interactions, structure3d, False, False, 2)
     tetrads = convert_tetrads(analysis.helices[0].quadruplexes[0])
     assert len(tetrads) > 0
     assert len(tetrads[0].ionsChannel) > 0