RNApolis 0.3.9__py3-none-any.whl → 0.3.11__py3-none-any.whl

{RNApolis-0.3.9.dist-info → RNApolis-0.3.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.3.9
+Version: 0.3.11
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

RNApolis-0.3.11.dist-info/RECORD

@@ -0,0 +1,17 @@
+rnapolis/annotator.py,sha256=bcyqmUSSRyl0ejA3548K4czSElBMX3EpCKAfJ2tYjsw,21476
+rnapolis/clashfinder.py,sha256=jD3s_UovygWi01NUbQNeAeRRFkARTSRraLXUV43UbAA,8514
+rnapolis/common.py,sha256=owupPG9oylz4Ed4DqVYJqWIKpovLJ3EIIApgca6tuhg,27344
+rnapolis/metareader.py,sha256=4qtMKRvww2sUStLeV8WVrLEt-ScydHUv4Gxx96tnf-M,1683
+rnapolis/molecule_filter.py,sha256=NhjuqdCRnXgPefWZPeTq77tifmnAzamQtA0ODqPPG9k,6918
+rnapolis/motif_extractor.py,sha256=duHvpi9Ulcny9K60E6VBpz5RpJZw-KdTB4_Ph0iP478,774
+rnapolis/parser.py,sha256=0uNKPnKiv5uaFVFGIzP8xbGLokimBkjs1XdlV0JmKIw,12217
+rnapolis/rfam_folder.py,sha256=3rgXEJR16uPFy_BOo8qkdClOAOQDVOkidnLE-yoRbeI,11112
+rnapolis/tertiary.py,sha256=iWMPD9c21rjMPpEdBd7mPCQgds65IbOr4_Fy06s0NoU,18957
+rnapolis/transformer.py,sha256=V9nOQvdq4-p7yUWo0vQg0CDQMpmyxz9t4TMSRVEKHnw,1817
+rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
+RNApolis-0.3.11.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
+RNApolis-0.3.11.dist-info/METADATA,sha256=J0a3wmvQoWPVFgSgvIxMkMFSBCz3KFHB8BHKFNtIdKw,54301
+RNApolis-0.3.11.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+RNApolis-0.3.11.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
+RNApolis-0.3.11.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
+RNApolis-0.3.11.dist-info/RECORD,,

rnapolis/annotator.py

@@ -486,7 +486,7 @@ def extract_secondary_structure(
     tertiary_structure: Structure3D,
     model: Optional[int] = None,
     find_gaps: bool = False,
-) -> BaseInteractions:
+) -> Structure2D:
     base_interactions = extract_base_interactions(tertiary_structure, model)
     mapping = Mapping2D3D(
         tertiary_structure,

rnapolis/common.py

@@ -1,6 +1,7 @@
 import itertools
 import logging
 import os
+import re
 import string
 from collections import defaultdict
 from collections.abc import Sequence
@@ -896,6 +897,37 @@ class DotBracket:
         return f"{self.sequence}\n{self.structure}"
 
 
+@dataclass
+class MultiStrandDotBracket(DotBracket):
+    strands: List[Strand]
+
+    @staticmethod
+    def from_string(input: str):
+        strands = []
+        first = 1
+
+        for match in re.finditer(
+            r"((>.*?\n)?([ACGUNacgun]+)\n([.()\[\]{}<>A-Za-z]+))", input
+        ):
+            sequence = match.group(3)
+            structure = match.group(4)
+            assert len(sequence) == len(structure)
+            last = first + len(sequence) - 1
+            strands.append(Strand(first, last, sequence, structure))
+            first = last + 1
+
+        return MultiStrandDotBracket(
+            "".join(strand.sequence for strand in strands),
+            "".join(strand.structure for strand in strands),
+            strands,
+        )
+
+    @staticmethod
+    def from_file(path: str):
+        with open(path) as f:
+            return MultiStrandDotBracket.from_string(f.read())
+
+
 @dataclass(frozen=True, order=True)
 class BaseInteractions:
     basePairs: List[BasePair]

rnapolis/parser.py

@@ -12,8 +12,15 @@ def read_3d_structure(
     atoms, modified, sequence = (
         parse_cif(cif_or_pdb) if is_cif(cif_or_pdb) else parse_pdb(cif_or_pdb)
     )
-    if model is not None:
-        atoms = list(filter(lambda atom: atom.model == model, atoms))
+    available_models = {atom.model: None for atom in atoms}
+    atoms_by_model = {
+        model: list(filter(lambda atom: atom.model == model, atoms))
+        for model in available_models
+    }
+    if model is not None and model in available_models:
+        atoms = atoms_by_model[model]
+    else:
+        atoms = atoms_by_model[list(available_models.keys())[0]]
     return group_atoms(atoms, modified, sequence, nucleic_acid_only)
 
 

RNApolis-0.3.9.dist-info/RECORD

@@ -1,17 +0,0 @@
-rnapolis/annotator.py,sha256=8AwrCKy_5CKU3HsRgqj5U2aQrAXiysoAnqjsDdvCAEA,21481
-rnapolis/clashfinder.py,sha256=jD3s_UovygWi01NUbQNeAeRRFkARTSRraLXUV43UbAA,8514
-rnapolis/common.py,sha256=DPmRpNkMaxuIai3vfLzSlP6IN0zpj6kmT3LoRjnJUWE,26440
-rnapolis/metareader.py,sha256=4qtMKRvww2sUStLeV8WVrLEt-ScydHUv4Gxx96tnf-M,1683
-rnapolis/molecule_filter.py,sha256=NhjuqdCRnXgPefWZPeTq77tifmnAzamQtA0ODqPPG9k,6918
-rnapolis/motif_extractor.py,sha256=duHvpi9Ulcny9K60E6VBpz5RpJZw-KdTB4_Ph0iP478,774
-rnapolis/parser.py,sha256=D2PwAFurTjZDP8WBV2AOxFHPLAFE8U1G_vC_5Y7BE4U,11948
-rnapolis/rfam_folder.py,sha256=3rgXEJR16uPFy_BOo8qkdClOAOQDVOkidnLE-yoRbeI,11112
-rnapolis/tertiary.py,sha256=iWMPD9c21rjMPpEdBd7mPCQgds65IbOr4_Fy06s0NoU,18957
-rnapolis/transformer.py,sha256=V9nOQvdq4-p7yUWo0vQg0CDQMpmyxz9t4TMSRVEKHnw,1817
-rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
-RNApolis-0.3.9.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
-RNApolis-0.3.9.dist-info/METADATA,sha256=E-6_MxMx9qQZK18G7EzHgwuxwYhchfkVXusFdBpG6nY,54300
-RNApolis-0.3.9.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-RNApolis-0.3.9.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
-RNApolis-0.3.9.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
-RNApolis-0.3.9.dist-info/RECORD,,