RNApolis 0.3.16__py3-none-any.whl → 0.3.18__py3-none-any.whl

{RNApolis-0.3.16.dist-info → RNApolis-0.3.18.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.3.16
+Version: 0.3.18
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok
@@ -21,6 +21,7 @@ Requires-Dist: mmcif
 Requires-Dist: numpy
 Requires-Dist: ordered-set
 Requires-Dist: orjson
+Requires-Dist: pandas
 Requires-Dist: pulp
 Requires-Dist: requests
 Requires-Dist: scipy

RNApolis-0.3.18.dist-info/RECORD

@@ -0,0 +1,17 @@
+rnapolis/annotator.py,sha256=7U3f0gchKdIGc6FwJx0UAc_95HJI5SgECj-b7-1yBhc,22086
+rnapolis/clashfinder.py,sha256=i95kp0o6OWNqmJDBr-PbsZd7RY2iJtBDr7QqolJSuAQ,8513
+rnapolis/common.py,sha256=PUYF01P2vevhyImhZjGYE0jJlsxWHX6GQmsxI4W7S-E,30255
+rnapolis/metareader.py,sha256=I1-cXc2YNBPwa3zihAnMTjEsAo79tEKzSmWu5yvN1Pk,2071
+rnapolis/molecule_filter.py,sha256=hB6-nXgjmw7FAsQ3bj0cZ2FvuW2I1PXunEfcdwEUB1o,7389
+rnapolis/motif_extractor.py,sha256=duHvpi9Ulcny9K60E6VBpz5RpJZw-KdTB4_Ph0iP478,774
+rnapolis/parser.py,sha256=rQuzaRqsNTdHCS8_dKW5uT_nSi0xLnixF5xfy8puo_s,12665
+rnapolis/rfam_folder.py,sha256=SjiiyML_T1__saruFwSMJEoQ7Y55GIU8ktS8ZUn5-fw,11111
+rnapolis/tertiary.py,sha256=wy8n7gfLHj_lIAydGgIwn_RMvBYiJzkSxXU_eff3ym0,19657
+rnapolis/transformer.py,sha256=V9nOQvdq4-p7yUWo0vQg0CDQMpmyxz9t4TMSRVEKHnw,1817
+rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
+RNApolis-0.3.18.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
+RNApolis-0.3.18.dist-info/METADATA,sha256=OkVdmxEbvCPPkUD1R49oZv5j89ng8-tds1yQeZYzORk,54323
+RNApolis-0.3.18.dist-info/WHEEL,sha256=HiCZjzuy6Dw0hdX5R3LCFPDmFS4BWl8H-8W39XfmgX4,91
+RNApolis-0.3.18.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
+RNApolis-0.3.18.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
+RNApolis-0.3.18.dist-info/RECORD,,

{RNApolis-0.3.16.dist-info → RNApolis-0.3.18.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.43.0)
+Generator: setuptools (72.2.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

rnapolis/annotator.py

@@ -10,8 +10,6 @@ from typing import Dict, List, Optional, Set, Tuple
 import numpy
 import numpy.typing
 from ordered_set import OrderedSet
-from scipy.spatial import KDTree
-
 from rnapolis.common import (
     BR,
     BaseInteractions,
@@ -43,6 +41,7 @@ from rnapolis.tertiary import (
     torsion_angle,
 )
 from rnapolis.util import handle_input_file
+from scipy.spatial import KDTree
 
 HYDROGEN_BOND_MAX_DISTANCE = 4.0
 HYDROGEN_BOND_ANGLE_RANGE = (50.0, 130.0)  # 90 degrees is ideal, so allow +- 40 degrees
@@ -149,7 +148,7 @@ def detect_bph_br_classification(
 
 
 def merge_and_clean_bph_br(
-    pairs: List[Tuple[Residue3D, Residue3D, int]]
+    pairs: List[Tuple[Residue3D, Residue3D, int]],
 ) -> Dict[Tuple[Residue3D, Residue3D], OrderedSet[int]]:
     bph_br_map: Dict[Tuple[Residue3D, Residue3D], OrderedSet[int]] = defaultdict(
         OrderedSet
@@ -588,7 +587,7 @@ def main():
         "-a",
         "--all-dot-brackets",
         action="store_true",
-        help=")optional) print all dot-brackets, not only optimal one (exclusive with -e/--extended)",
+        help="(optional) print all dot-brackets, not only optimal one (exclusive with -e/--extended)",
     )
     parser.add_argument("-b", "--bpseq", help="(optional) path to output BPSEQ file")
     parser.add_argument("-c", "--csv", help="(optional) path to output CSV file")

rnapolis/clashfinder.py

@@ -8,11 +8,10 @@ from functools import cached_property
 from typing import List, Optional
 
 import numpy as np
-from scipy.spatial import KDTree
-
 from rnapolis.metareader import read_metadata
 from rnapolis.parser import read_3d_structure
 from rnapolis.tertiary import Atom, Residue3D
+from scipy.spatial import KDTree
 
 CARBON_RADIUS = 0.6
 NITROGEN_RADIUS = 0.54

rnapolis/common.py

@@ -8,7 +8,6 @@ from collections.abc import Sequence
 from dataclasses import dataclass
 from enum import Enum
 from functools import cache, cached_property, total_ordering
-from itertools import permutations
 from typing import Dict, List, Optional, Tuple
 
 import graphviz

rnapolis/metareader.py

@@ -3,9 +3,9 @@ import argparse
 from typing import IO, Dict, List
 
 import orjson
+import pandas as pd
 from mmcif.io.IoAdapterPy import IoAdapterPy
 from mmcif.io.PdbxReader import DataContainer
-
 from rnapolis.util import handle_input_file
 
 
@@ -46,6 +46,10 @@ def main():
         help="read the mmCIF file and list categories available inside",
         action="store_true",
     )
+    parser.add_argument(
+        "--csv-directory",
+        help="directory where to output CSV per each category",
+    )
     args = parser.parse_args()
 
     file = handle_input_file(args.path)
@@ -57,6 +61,12 @@ def main():
         result = read_metadata(file, args.category)
         print(orjson.dumps(result).decode("utf-8"))
 
+        if args.csv_directory:
+            for category in result:
+                with open(f"{args.csv_directory}/{category}.csv", "w") as f:
+                    df = pd.DataFrame(result[category])
+                    df.to_csv(f, index=False)
+
 
 if __name__ == "__main__":
     main()

rnapolis/molecule_filter.py

@@ -5,7 +5,6 @@ from typing import List, Set, Tuple
 
 from mmcif.io.IoAdapterPy import IoAdapterPy
 from mmcif.io.PdbxReader import DataCategory, DataContainer
-
 from rnapolis.util import handle_input_file
 
 # Source: https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_entity_poly.type.html
@@ -158,11 +157,17 @@ def main():
     parser = argparse.ArgumentParser()
     parser.add_argument(
         "--type",
-        help="a type of molecule to select (default: polyribonucleotide)",
+        help="a type of molecule to select, you can provide this argument multiple times (default: polyribonucleotide)",
         action="append",
         default=["polyribonucleotide"],
         choices=ENTITY_POLY_TYPES,
     )
+    parser.add_argument(
+        "--chain",
+        help="a chain ID (label_asym_id) to select, you can provide this argument multiple times (if provided, it overrides the --type argument)",
+        action="append",
+        default=[],
+    )
     parser.add_argument("path", help="path to a PDBx/mmCIF file")
     args = parser.parse_args()
 
@@ -171,8 +176,15 @@ def main():
     data = adapter.readFile(file.name)
     output = DataContainer("rnapolis")
 
-    entity_ids = select_ids(data, "entity_poly", "type", "entity_id", set(args.type))
-    asym_ids = select_ids(data, "struct_asym", "entity_id", "id", entity_ids)
+    if args.chain:
+        entity_ids = select_ids(data, "struct_asym", "id", "entity_id", set(args.chain))
+        asym_ids = set(args.chain)
+    else:
+        entity_ids = select_ids(
+            data, "entity_poly", "type", "entity_id", set(args.type)
+        )
+        asym_ids = select_ids(data, "struct_asym", "entity_id", "id", entity_ids)
+
     auth_asym_ids = select_ids(
         data, "atom_site", "label_asym_id", "auth_asym_id", asym_ids
     )

rnapolis/parser.py

@@ -2,7 +2,6 @@ import logging
 from typing import IO, Dict, List, Optional, Tuple, Union
 
 from mmcif.io.IoAdapterPy import IoAdapterPy
-
 from rnapolis.common import ResidueAuth, ResidueLabel
 from rnapolis.tertiary import BASE_ATOMS, Atom, Residue3D, Structure3D
 
@@ -212,7 +211,7 @@ def parse_pdb(
             if alternate_location != " ":
                 continue
             atom_name = line[12:16].strip()
-            residue_name = line[18:20].strip()
+            residue_name = line[17:20].strip()
             chain_identifier = line[21]
             residue_number = int(line[22:26].strip())
             insertion_code = line[26] if line[26] != " " else None

rnapolis/rfam_folder.py

@@ -14,7 +14,6 @@ from typing import List
 import appdirs
 import requests
 import RNA
-
 from rnapolis.common import BpSeq, DotBracket
 
 COMBINED_CM = "https://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.cm.gz"

rnapolis/tertiary.py

@@ -7,7 +7,6 @@ from typing import Dict, List, Optional, Set, Tuple, Union
 
 import numpy
 import numpy.typing
-
 from rnapolis.common import (
     BasePair,
     BpSeq,

RNApolis-0.3.16.dist-info/RECORD

@@ -1,17 +0,0 @@
-rnapolis/annotator.py,sha256=XnjFBeu3P_2UMdkD4Ao7m7K6JfeqYa-13xRzghrLvt8,22086
-rnapolis/clashfinder.py,sha256=jD3s_UovygWi01NUbQNeAeRRFkARTSRraLXUV43UbAA,8514
-rnapolis/common.py,sha256=tbmKV64nLClmzNN0HyKnvWA0-5aSyf4x8CGpBjpIJ4M,30290
-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=6xEeQghil0eXIzi0bNUkebknfqIxx9EfOfT9q33eN4A,12666
-rnapolis/rfam_folder.py,sha256=3rgXEJR16uPFy_BOo8qkdClOAOQDVOkidnLE-yoRbeI,11112
-rnapolis/tertiary.py,sha256=VuATTN2SD7lBL9iUgT-doDwuEYsLodgV2u-SwQsyQcU,19658
-rnapolis/transformer.py,sha256=V9nOQvdq4-p7yUWo0vQg0CDQMpmyxz9t4TMSRVEKHnw,1817
-rnapolis/util.py,sha256=IdquFO3PV1_KDqodjupzm0Rqvgy0CeSzxGHaGEHYXVU,543
-RNApolis-0.3.16.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
-RNApolis-0.3.16.dist-info/METADATA,sha256=k4D9WCUq94R1lGhWmYJqTjfh9ww8RPRjxg_IOHiPEcg,54301
-RNApolis-0.3.16.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-RNApolis-0.3.16.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
-RNApolis-0.3.16.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
-RNApolis-0.3.16.dist-info/RECORD,,