RNApolis 0.3.10__py3-none-any.whl → 0.3.12__py3-none-any.whl

{RNApolis-0.3.10.dist-info → RNApolis-0.3.12.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.3.10
+Version: 0.3.12
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{RNApolis-0.3.10.dist-info → RNApolis-0.3.12.dist-info}/RECORD

@@ -1,18 +1,17 @@
-rnapolis/annotator.py,sha256=8AwrCKy_5CKU3HsRgqj5U2aQrAXiysoAnqjsDdvCAEA,21481
-rnapolis/annotator_ml.py,sha256=eZYDIaUcAVWvUHKvA0lx6lWEaATU1THNYbfVKvVa9mQ,8226
+rnapolis/annotator.py,sha256=bcyqmUSSRyl0ejA3548K4czSElBMX3EpCKAfJ2tYjsw,21476
 rnapolis/clashfinder.py,sha256=jD3s_UovygWi01NUbQNeAeRRFkARTSRraLXUV43UbAA,8514
-rnapolis/common.py,sha256=DPmRpNkMaxuIai3vfLzSlP6IN0zpj6kmT3LoRjnJUWE,26440
+rnapolis/common.py,sha256=QdmAGF8DvG1EHpefumU27LceGm7l9obgWLhL4FELGT4,27381
 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/parser.py,sha256=Cmjt7p8UkiSNhSQDjc6I7BRqtuIIHs23Fp-Glb8Zikw,12216
 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-0.3.10.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
-RNApolis-0.3.10.dist-info/METADATA,sha256=qfgkAg8MMlyGyOkWsl8y5JOffR_9AbsQgYOXE3L5XrA,54301
-RNApolis-0.3.10.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-RNApolis-0.3.10.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
-RNApolis-0.3.10.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
-RNApolis-0.3.10.dist-info/RECORD,,
+RNApolis-0.3.12.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
+RNApolis-0.3.12.dist-info/METADATA,sha256=PGjy4PTp1C5K1afBs6ZjeWz4pLJ5iFaiZfUSdgwusDk,54301
+RNApolis-0.3.12.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
+RNApolis-0.3.12.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
+RNApolis-0.3.12.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
+RNApolis-0.3.12.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 +897,38 @@ 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)?([ACGTURYSWKMBDHVNacgturyswkmbdhvn.-]+)\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

@@ -300,7 +300,6 @@ def get_one_letter_name(
         key = (label.chain, label.number)
         if key in sequence:
             return sequence[key]
-
     # RNA
     if len(name) == 1:
         return name

rnapolis/annotator_ml.py

@@ -1,278 +0,0 @@
-#! /usr/bin/env python
-import argparse
-import csv
-import logging
-import math
-import os
-from collections import defaultdict
-from typing import Dict, List, Optional, Tuple
-
-import numpy
-import numpy.typing
-import orjson
-from ordered_set import OrderedSet
-from scipy.spatial import KDTree
-
-from rnapolis.common import (
-    BaseInteractions,
-    BasePair,
-    BpSeq,
-    LeontisWesthof,
-    Residue,
-    Saenger,
-    Stacking,
-    Structure2D,
-)
-from rnapolis.parser import read_3d_structure
-from rnapolis.tertiary import (
-    AVERAGE_OXYGEN_PHOSPHORUS_DISTANCE_COVALENT,
-    Atom,
-    Mapping2D3D,
-    Residue3D,
-    Structure3D,
-    torsion_angle,
-)
-from rnapolis.util import handle_input_file
-
-C1P_MAX_DISTANCE = 10.0
-
-logging.basicConfig(level=os.getenv("LOGLEVEL", "INFO").upper())
-
-
-# TODO: implement this function
-def is_base_pair(residue_i: Residue3D, residue_j: Residue3D) -> bool:
-    return False
-
-
-# TODO: implement this function
-def classify_lw(residue_i: Residue3D, residue_j: Residue3D) -> Optional[LeontisWesthof]:
-    return None
-
-
-# TODO: implement this function
-def classify_saenger(residue_i: Residue3D, residue_j: Residue3D) -> Optional[Saenger]:
-    return None
-
-
-# TODO: implement this function
-def is_stacking(residue_i: Residue3D, residue_j: Residue3D) -> bool:
-    return False
-
-
-def find_candidates(
-    structure: Structure3D, model: Optional[int] = None
-) -> List[Tuple[Residue3D, Residue3D]]:
-    residue_map = {}
-    coordinates = []
-
-    for residue in structure.residues:
-        if model is not None and residue.model != model:
-            continue
-
-        atom = residue.find_atom("C1'")
-
-        if atom is not None:
-            atom_xyz = (atom.x, atom.y, atom.z)
-            residue_map[atom_xyz] = residue
-            coordinates.append(atom_xyz)
-
-    kdtree = KDTree(coordinates)
-    candidates = []
-
-    for i, j in kdtree.query_pairs(C1P_MAX_DISTANCE):
-        residue_i = residue_map[coordinates[i]]
-        residue_j = residue_map[coordinates[j]]
-        candidates.append((residue_i, residue_j))
-
-    return candidates
-
-
-def find_pairs(structure: Structure3D, model: Optional[int] = None) -> List[BasePair]:
-    base_pairs = []
-
-    for residue_i, residue_j in find_candidates(structure, model):
-        if is_base_pair(residue_i, residue_j):
-            lw = classify_lw(residue_i, residue_j)
-            saenger = classify_saenger(residue_i, residue_j)
-            base_pairs.append(
-                BasePair(
-                    Residue(residue_i.label, residue_i.auth),
-                    Residue(residue_j.label, residue_j.auth),
-                    lw,
-                    saenger,
-                )
-            )
-
-    return base_pairs
-
-
-def find_stackings(
-    structure: Structure3D, model: Optional[int] = None
-) -> List[Stacking]:
-    stackings = []
-
-    for residue_i, residue_j in find_candidates(structure, model):
-        if is_stacking(residue_i, residue_j):
-            stackings.append(
-                Stacking(
-                    Residue(residue_i.label, residue_i.auth),
-                    Residue(residue_j.label, residue_j.auth),
-                    None,
-                )
-            )
-
-    return stackings
-
-
-def extract_base_interactions(
-    tertiary_structure: Structure3D, model: Optional[int] = None
-) -> BaseInteractions:
-    base_pairs = find_pairs(tertiary_structure, model)
-    stackings = find_stackings(tertiary_structure, model)
-    return BaseInteractions(base_pairs, stackings, [], [], [])
-
-
-def extract_secondary_structure(
-    tertiary_structure: Structure3D,
-    model: Optional[int] = None,
-    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_interactions,
-        str(mapping.bpseq),
-        mapping.dot_bracket,
-        mapping.extended_dot_bracket,
-        stems,
-        single_strands,
-        hairpins,
-        loops,
-    )
-
-
-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):
-    with open(path, "w") as f:
-        writer = csv.writer(f)
-        writer.writerow(["nt1", "nt2", "type", "classification-1", "classification-2"])
-        for base_pair in structure2d.baseInteractions.basePairs:
-            writer.writerow(
-                [
-                    base_pair.nt1.full_name,
-                    base_pair.nt2.full_name,
-                    "base pair",
-                    base_pair.lw.value,
-                    (
-                        base_pair.saenger.value or ""
-                        if base_pair.saenger is not None
-                        else ""
-                    ),
-                ]
-            )
-        for stacking in structure2d.baseInteractions.stackings:
-            writer.writerow(
-                [
-                    stacking.nt1.full_name,
-                    stacking.nt2.full_name,
-                    "stacking",
-                    stacking.topology.value if stacking.topology is not None else "",
-                    "",
-                ]
-            )
-        for base_phosphate in structure2d.baseInteractions.basePhosphateInteractions:
-            writer.writerow(
-                [
-                    base_phosphate.nt1.full_name,
-                    base_phosphate.nt2.full_name,
-                    "base-phosphate interaction",
-                    base_phosphate.bph.value if base_phosphate.bph is not None else "",
-                    "",
-                ]
-            )
-        for base_ribose in structure2d.baseInteractions.basePhosphateInteractions:
-            writer.writerow(
-                [
-                    base_ribose.nt1.full_name,
-                    base_ribose.nt2.full_name,
-                    "base-ribose interaction",
-                    base_ribose.bph.value if base_ribose.bph is not None else "",
-                    "",
-                ]
-            )
-        for other in structure2d.baseInteractions.otherInteractions:
-            writer.writerow(
-                [
-                    other.nt1.full_name,
-                    other.nt2.full_name,
-                    "other interaction",
-                    "",
-                    "",
-                ]
-            )
-
-
-def write_bpseq(path: str, bpseq: BpSeq):
-    with open(path, "w") as f:
-        f.write(str(bpseq))
-
-
-def main():
-    parser = argparse.ArgumentParser()
-    parser.add_argument("input", help="Path to PDB or mmCIF file")
-    parser.add_argument("--bpseq", help="(optional) path to output BPSEQ file")
-    parser.add_argument("--csv", help="(optional) path to output CSV file")
-    parser.add_argument(
-        "--json",
-        help="(optional) path to output JSON file",
-    )
-    parser.add_argument(
-        "--extended",
-        action="store_true",
-        help="(optional) if set, the program will print extended secondary structure to the standard output",
-    )
-    parser.add_argument(
-        "--find-gaps",
-        action="store_true",
-        help="(optional) if set, the program will detect gaps and break the PDB chain into two or more strands; "
-        f"the gap is defined as O3'-P distance greater then {1.5 * AVERAGE_OXYGEN_PHOSPHORUS_DISTANCE_COVALENT}",
-    )
-    parser.add_argument("--dot", help="(optional) path to output DOT file")
-    args = parser.parse_args()
-
-    breakpoint()
-
-    file = handle_input_file(args.input)
-    structure3d = read_3d_structure(file, None)
-    structure2d = extract_secondary_structure(structure3d, None, args.find_gaps)
-
-    if args.csv:
-        write_csv(args.csv, structure2d)
-
-    if args.json:
-        write_json(args.json, structure2d)
-
-    if args.bpseq:
-        write_bpseq(args.bpseq, structure2d.bpseq)
-
-    if args.extended:
-        print(structure2d.extendedDotBracket)
-    else:
-        print(structure2d.dotBracket)
-
-    if args.dot:
-        print(BpSeq.from_string(structure2d.bpseq).graphviz)
-
-
-if __name__ == "__main__":
-    main()