RNApolis 0.1.5__tar.gz → 0.2.0__tar.gz

{RNApolis-0.1.5 → RNApolis-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.1.5
+Version: 0.2.0
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok
@@ -15,6 +15,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: graphviz
 Requires-Dist: mmcif
 Requires-Dist: numpy
 Requires-Dist: ordered-set

{RNApolis-0.1.5 → RNApolis-0.2.0}/setup.py

@@ -5,7 +5,7 @@ with open("README.md") as f:
 
 setup(
     name="RNApolis",
-    version="0.1.5",
+    version="0.2.0",
     packages=["rnapolis"],
     package_dir={"": "src"},
     author="Tomasz Zok",
@@ -33,5 +33,5 @@ setup(
             "motif-extractor=rnapolis.motif_extractor:main",
         ]
     },
-    install_requires=["mmcif", "numpy", "ordered-set", "orjson", "pulp", "scipy"],
+    install_requires=["graphviz", "mmcif", "numpy", "ordered-set", "orjson", "pulp", "scipy"],
 )

{RNApolis-0.1.5 → RNApolis-0.2.0}/src/RNApolis.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.1.5
+Version: 0.2.0
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok
@@ -15,6 +15,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Description-Content-Type: text/markdown
 License-File: LICENSE
+Requires-Dist: graphviz
 Requires-Dist: mmcif
 Requires-Dist: numpy
 Requires-Dist: ordered-set

{RNApolis-0.1.5 → RNApolis-0.2.0}/src/RNApolis.egg-info/requires.txt

@@ -1,3 +1,4 @@
+graphviz
 mmcif
 numpy
 ordered-set

{RNApolis-0.1.5 → RNApolis-0.2.0}/src/rnapolis/annotator.py

@@ -5,7 +5,7 @@ import logging
 import math
 import os
 from collections import Counter, defaultdict
-from typing import IO, Dict, List, Optional, Set, Tuple
+from typing import Dict, List, Optional, Set, Tuple
 
 import numpy
 import numpy.typing
@@ -15,6 +15,7 @@ from scipy.spatial import KDTree
 
 from rnapolis.common import (
     BR,
+    BaseInteractions,
     BasePair,
     BasePhosphate,
     BaseRibose,
@@ -471,19 +472,27 @@ def find_stackings(structure: Structure3D, model: int = 1) -> List[Stacking]:
     return stackings
 
 
-def extract_secondary_structure(
-    tertiary_structure: Structure3D, model: int = 1, find_gaps: bool = False
-) -> Structure2D:
+def extract_base_interactions(
+    tertiary_structure: Structure3D, model: int = 1
+) -> BaseInteractions:
     base_pairs, base_phosphate, base_ribose = find_pairs(tertiary_structure, model)
     stackings = find_stackings(tertiary_structure, model)
-    mapping = Mapping2D3D(tertiary_structure, base_pairs, stackings, find_gaps)
+    return BaseInteractions(base_pairs, stackings, base_ribose, base_phosphate, [])
+
+
+def extract_secondary_structure(
+    tertiary_structure: Structure3D, model: int = 1, find_gaps: bool = False
+) -> BaseInteractions:
+    base_interactions = extract_base_interactions(tertiary_structure, model)
+    mapping = Mapping2D3D(
+        tertiary_structure,
+        base_interactions.basePairs,
+        base_interactions.stackings,
+        find_gaps,
+    )
     stems, single_strands, hairpins, loops = mapping.bpseq.elements
     return Structure2D(
-        base_pairs,
-        stackings,
-        base_ribose,
-        base_phosphate,
-        [],
+        base_interactions,
         str(mapping.bpseq),
         mapping.dot_bracket,
         mapping.extended_dot_bracket,
@@ -494,12 +503,12 @@ def extract_secondary_structure(
     )
 
 
-def write_json(path: str, structure2d: Structure2D):
+def write_json(path: str, structure2d: BaseInteractions):
     with open(path, "wb") as f:
         f.write(orjson.dumps(structure2d))
 
 
-def write_csv(path: str, structure2d: Structure2D):
+def write_csv(path: str, structure2d: BaseInteractions):
     with open(path, "w") as f:
         writer = csv.writer(f)
         writer.writerow(["nt1", "nt2", "type", "classification-1", "classification-2"])

{RNApolis-0.1.5 → RNApolis-0.2.0}/src/rnapolis/common.py

@@ -897,12 +897,17 @@ class DotBracket:
 
 
 @dataclass(frozen=True, order=True)
-class Structure2D:
+class BaseInteractions:
     basePairs: List[BasePair]
     stackings: List[Stacking]
     baseRiboseInteractions: List[BaseRibose]
     basePhosphateInteractions: List[BasePhosphate]
     otherInteractions: List[OtherInteraction]
+
+
+@dataclass(frozen=True, order=True)
+class Structure2D:
+    baseInteractions: BaseInteractions
     bpseq: str
     dotBracket: str
     extendedDotBracket: str

{RNApolis-0.1.5 → RNApolis-0.2.0}/src/rnapolis/motif_extractor.py

@@ -1,14 +1,8 @@
 #! /usr/bin/env python
 import argparse
 import itertools
-from typing import IO, Dict, List
-
-import orjson
-from mmcif.io.IoAdapterPy import IoAdapterPy
-from mmcif.io.PdbxReader import DataContainer
 
 from rnapolis.common import BpSeq, DotBracket
-from rnapolis.util import handle_input_file
 
 
 def main():

{RNApolis-0.1.5 → RNApolis-0.2.0}/src/rnapolis/tertiary.py

@@ -1,7 +1,5 @@
-import itertools
 import logging
 import math
-import string
 from collections import defaultdict
 from dataclasses import dataclass, field
 from functools import cached_property, total_ordering
@@ -20,7 +18,6 @@ from rnapolis.common import (
     ResidueAuth,
     ResidueLabel,
     Stacking,
-    Structure2D,
 )
 
 BASE_ATOMS = {

{RNApolis-0.1.5 → RNApolis-0.2.0}/tests/test_annotator.py

@@ -1,7 +1,6 @@
 from collections import Counter
 
-from rnapolis.annotator import extract_secondary_structure
-from rnapolis.common import BR
+from rnapolis.annotator import extract_base_interactions
 from rnapolis.parser import read_3d_structure
 
 
@@ -11,14 +10,14 @@ def test_1ehz():
     """
     with open("tests/1ehz-assembly-1.cif") as f:
         structure3d = read_3d_structure(f, 1)
-    structure2d = extract_secondary_structure(structure3d, 1)
+    base_interactions = extract_base_interactions(structure3d, 1)
 
     interactions = [
-        structure2d.basePairs,
-        structure2d.stackings,
-        structure2d.baseRiboseInteractions,
-        structure2d.basePhosphateInteractions,
-        structure2d.otherInteractions,
+        base_interactions.basePairs,
+        base_interactions.stackings,
+        base_interactions.baseRiboseInteractions,
+        base_interactions.basePhosphateInteractions,
+        base_interactions.otherInteractions,
     ]
     labels = ["base pairs", "stackings", "base-ribose", "base-phosphate", "other"]
     for i in range(len(interactions)):

{RNApolis-0.1.5 → RNApolis-0.2.0}/tests/test_bugfixes.py

@@ -1,4 +1,4 @@
-from rnapolis.annotator import extract_secondary_structure
+from rnapolis.annotator import extract_base_interactions
 from rnapolis.common import ResidueAuth, ResidueLabel
 from rnapolis.parser import read_3d_structure
 from rnapolis.tertiary import Mapping2D3D
@@ -8,9 +8,9 @@ from rnapolis.tertiary import Mapping2D3D
 def test_1E7K():
     with open("tests/1E7K_1_C.cif") as f:
         structure3d = read_3d_structure(f, 1)
-    structure2d = extract_secondary_structure(structure3d)
+    base_interaction = extract_base_interactions(structure3d)
     mapping = Mapping2D3D(
-        structure3d, structure2d.basePairs, structure2d.stackings, True
+        structure3d, base_interaction.basePairs, base_interaction.stackings, True
     )
     assert len(mapping.strands_sequences) == 2
 
@@ -26,9 +26,9 @@ def test_1DFU():
     b2g = structure3d.find_residue(ResidueLabel("B", 2, "G"), None)
     assert b2g is not None
 
-    structure2d = extract_secondary_structure(structure3d)
+    base_interactions = extract_base_interactions(structure3d)
     mapping = Mapping2D3D(
-        structure3d, structure2d.basePairs, structure2d.stackings, True
+        structure3d, base_interactions.basePairs, base_interactions.stackings, True
     )
     assert b2g not in mapping.base_pair_graph[b1u]
     assert b1u not in mapping.base_pair_graph[b2g]
@@ -38,9 +38,9 @@ def test_1DFU():
 def test_4WTI():
     with open("tests/4WTI_1_T-P.cif") as f:
         structure3d = read_3d_structure(f, 1)
-    structure2d = extract_secondary_structure(structure3d)
+    base_interactions = extract_base_interactions(structure3d)
     mapping = Mapping2D3D(
-        structure3d, structure2d.basePairs, structure2d.stackings, True
+        structure3d, base_interactions.basePairs, base_interactions.stackings, True
     )
     assert mapping.dot_bracket == ">strand_T\nCGG\n.((\n>strand_P\nCC\n))"
 
@@ -49,9 +49,9 @@ def test_4WTI():
 def test_1HMH():
     with open("tests/1HMH_1_E.cif") as f:
         structure3d = read_3d_structure(f, 1)
-    structure2d = extract_secondary_structure(structure3d)
+    base_interactions = extract_base_interactions(structure3d)
     mapping = Mapping2D3D(
-        structure3d, structure2d.basePairs, structure2d.stackings, True
+        structure3d, base_interactions.basePairs, base_interactions.stackings, True
     )
     assert mapping.dot_bracket == ">strand_E\nUG\n.."
 

{RNApolis-0.1.5 → RNApolis-0.2.0}/tests/test_common.py

@@ -1,25 +1,21 @@
 from collections import Counter
 
-from hypothesis import HealthCheck, given, settings
+from hypothesis import given, settings
 from hypothesis import strategies as st
 
 from rnapolis.common import (
+    BaseInteractions,
     BasePair,
     BasePhosphate,
     BaseRibose,
     BpSeq,
     DotBracket,
-    Hairpin,
     Interaction,
-    Loop,
     OtherInteraction,
     Residue,
     ResidueAuth,
     ResidueLabel,
-    SingleStrand,
     Stacking,
-    Stem,
-    Structure2D,
 )
 
 
@@ -82,7 +78,7 @@ def test_rnapdbee_adapters_api_compliance_other(obj):
     assert obj.__dict__.keys() == {"nt1", "nt2"}
 
 
-@given(st.from_type(Structure2D))
+@given(st.from_type(BaseInteractions))
 @settings(max_examples=10)
 def test_rnapdbee_adapters_api_compliance_structure2d(obj):
     assert obj.__dict__.keys() >= {

{RNApolis-0.1.5 → RNApolis-0.2.0}/tests/test_quadruplexes.py

@@ -1,4 +1,4 @@
-from rnapolis.annotator import extract_secondary_structure
+from rnapolis.annotator import extract_base_interactions
 from rnapolis.common import ResidueAuth, ResidueLabel
 from rnapolis.parser import read_3d_structure
 from rnapolis.tertiary import Mapping2D3D
@@ -8,9 +8,9 @@ from rnapolis.tertiary import Mapping2D3D
 def test_2HY9():
     with open("tests/2HY9.cif") as f:
         structure3d = read_3d_structure(f, 1)
-    structure2d = extract_secondary_structure(structure3d)
+    base_interactions = extract_base_interactions(structure3d)
     mapping = Mapping2D3D(
-        structure3d, structure2d.basePairs, structure2d.stackings, True
+        structure3d, base_interactions.basePairs, base_interactions.stackings, True
     )
 
     # tract 1
@@ -61,9 +61,9 @@ def test_2HY9():
 def test_6RS3():
     with open("tests/6RS3.cif") as f:
         structure3d = read_3d_structure(f, 1)
-    structure2d = extract_secondary_structure(structure3d)
+    base_interactions = extract_base_interactions(structure3d)
     mapping = Mapping2D3D(
-        structure3d, structure2d.basePairs, structure2d.stackings, True
+        structure3d, base_interactions.basePairs, base_interactions.stackings, True
     )
 
     g1 = structure3d.find_residue(ResidueLabel("A", 1, "DG"), None)
@@ -106,9 +106,9 @@ def test_6RS3():
 def test_1JJP():
     with open("tests/1JJP.cif") as f:
         structure3d = read_3d_structure(f, 1)
-    structure2d = extract_secondary_structure(structure3d)
+    base_interactions = extract_base_interactions(structure3d)
     mapping = Mapping2D3D(
-        structure3d, structure2d.basePairs, structure2d.stackings, True
+        structure3d, base_interactions.basePairs, base_interactions.stackings, True
     )
 
     ag1 = structure3d.find_residue(ResidueLabel("A", 1, "DG"), None)
@@ -180,9 +180,9 @@ def test_1JJP():
 def test_6FC9():
     with open("tests/6FC9.cif") as f:
         structure3d = read_3d_structure(f, 1)
-    structure2d = extract_secondary_structure(structure3d)
+    base_interactions = extract_base_interactions(structure3d)
     mapping = Mapping2D3D(
-        structure3d, structure2d.basePairs, structure2d.stackings, True
+        structure3d, base_interactions.basePairs, base_interactions.stackings, True
     )
 
     g1 = structure3d.find_residue(ResidueLabel("A", 1, "DG"), None)
@@ -256,9 +256,9 @@ def test_6FC9():
 def test_UGG_md():
     with open("tests/q-ugg-5k-salt_400-500ns_frame1065.pdb") as f:
         structure3d = read_3d_structure(f, 1)
-    structure2d = extract_secondary_structure(structure3d)
+    base_interactions = extract_base_interactions(structure3d)
     mapping = Mapping2D3D(
-        structure3d, structure2d.basePairs, structure2d.stackings, True
+        structure3d, base_interactions.basePairs, base_interactions.stackings, True
     )
 
     u1 = structure3d.find_residue(None, ResidueAuth(" ", 1, None, "U5"))