RNApolis 0.3.15__py3-none-any.whl → 0.3.16__py3-none-any.whl

{RNApolis-0.3.15.dist-info → RNApolis-0.3.16.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: RNApolis
-Version: 0.3.15
+Version: 0.3.16
 Summary: A Python library containing RNA-related bioinformatics functions and classes
 Home-page: https://github.com/tzok/rnapolis-py
 Author: Tomasz Zok

{RNApolis-0.3.15.dist-info → RNApolis-0.3.16.dist-info}/RECORD

@@ -4,14 +4,14 @@ 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=Cmjt7p8UkiSNhSQDjc6I7BRqtuIIHs23Fp-Glb8Zikw,12216
+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-0.3.15.dist-info/LICENSE,sha256=ZGRu12MzCgbYA-Lt8MyBlmjvPZh7xfiD5u5wBx0enq4,1066
-RNApolis-0.3.15.dist-info/METADATA,sha256=JINDTFBZOiXrJUB3-jnBW8YIHcRUc3mQ2EKoaFDS5zE,54301
-RNApolis-0.3.15.dist-info/WHEEL,sha256=GJ7t_kWBFywbagK5eo9IoUwLW6oyOeTKmQ-9iHFVNxQ,92
-RNApolis-0.3.15.dist-info/entry_points.txt,sha256=foN2Pn5e-OzEz0fFmNoX6PnFSZFQntOlY8LbognP5F0,308
-RNApolis-0.3.15.dist-info/top_level.txt,sha256=LcO18koxZcWoJ21KDRRRo_tyIbmXL5z61dPitZpy8yc,9
-RNApolis-0.3.15.dist-info/RECORD,,
+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,,

rnapolis/parser.py

@@ -1,3 +1,4 @@
+import logging
 from typing import IO, Dict, List, Optional, Tuple, Union
 
 from mmcif.io.IoAdapterPy import IoAdapterPy
@@ -5,6 +6,9 @@ from mmcif.io.IoAdapterPy import IoAdapterPy
 from rnapolis.common import ResidueAuth, ResidueLabel
 from rnapolis.tertiary import BASE_ATOMS, Atom, Residue3D, Structure3D
 
+logging.basicConfig(level=logging.INFO)
+logger = logging.getLogger(__name__)
+
 
 def read_3d_structure(
     cif_or_pdb: IO[str], model: Optional[int] = None, nucleic_acid_only: bool = False
@@ -104,6 +108,14 @@ def parse_cif(
                         auth_residue_name,
                     )
 
+                if label is None and auth is None:
+                    # this should not happen in a valid mmCIF file
+                    # skipping the line
+                    logger.debug(
+                        f"Cannot parse an atom line without chain name, residue number, and residue name: {row}"
+                    )
+                    continue
+
                 model = int(row_dict.get("pdbx_PDB_model_num", "1"))
                 atom_name = row_dict["label_atom_id"]
                 x = float(row_dict["Cartn_x"])