pidibble 1.4.1__tar.gz → 1.4.2__tar.gz

{pidibble-1.4.1 → pidibble-1.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pidibble
-Version: 1.4.1
+Version: 1.4.2
 Summary: A complete Protein Data Bank (PDB) file parser
 Project-URL: Source, https://github.com/cameronabrams/pidibble
 Project-URL: Documentation, https://pidibble.readthedocs.io/en/latest/
@@ -91,6 +91,8 @@ ATOM
 ```
 
 ## Release History
+* 1.4.2
+   * updated alphafold interface
 * 1.4.1
    * Fixed parsing bug in `PDBRecordList`
 * 1.4.0

{pidibble-1.4.1 → pidibble-1.4.2}/README.md

@@ -73,6 +73,8 @@ ATOM
 ```
 
 ## Release History
+* 1.4.2
+   * updated alphafold interface
 * 1.4.1
    * Fixed parsing bug in `PDBRecordList`
 * 1.4.0

{pidibble-1.4.1 → pidibble-1.4.2}/pidibble/pdbparse.py

@@ -14,7 +14,6 @@ import yaml
 import numpy as np
 from pathlib import Path
 from mmcif.io.IoAdapterCore import IoAdapterCore
-from typing import List, Dict
 from . import resources
 from .baseparsers import ListParsers, ListParser, str2int_sig, safe_float
 from .baserecord import BaseRecordParser
@@ -144,8 +143,9 @@ class PDBParser:
             self.filepath=f'{self.alphafold}.pdb'
             BASE_URL=self.pdb_format_dict['ALPHAFOLD_API_URL']
             target_url=os.path.join(BASE_URL,self.alphafold)
+            logger.debug(f'target url {target_url}')
             try:
-                urllib.request.urlretrieve(target_url,f'{self.alphafold}.json')
+                urllib.request.urlretrieve(target_url+r'?key='+self.pdb_format_dict['ALPHAFOLD_API_KEY'],f'{self.alphafold}.json')
             except:
                 logger.warning(f'Could not fetch metadata for entry with accession code {self.alphafold} from AlphaFold')
                 return False

{pidibble-1.4.1 → pidibble-1.4.2}/pidibble/pdbrecord.py

@@ -132,6 +132,9 @@ class PDBRecord(BaseRecord):
         inst.format=current_format
         return inst
 
+    def __repr__(self):
+        return f'<PDBRecord {self.__dict__}>'
+
     def get_token(self,key):
         """
         Retrieve a token value from the PDBRecord instance based on the provided key.

{pidibble-1.4.1 → pidibble-1.4.2}/pidibble/resources/pdb_format.yaml

@@ -11,7 +11,8 @@
 # 1. 28-FEB-2024: Alphafold stuff
 #
 BASE_URL: https://files.rcsb.org/download
-ALPHAFOLD_API_URL: https://alphafold.com/api/prediction
+ALPHAFOLD_API_URL: https://alphafold.ebi.ac.uk/api/prediction
+ALPHAFOLD_API_KEY: AIzaSyCeurAJz7ZGjPQUtEaerUkBZ3TaBkXrY94
 record_types:
   1: one-time-single-line
   2: one-time-multiple-line

{pidibble-1.4.1 → pidibble-1.4.2}/pyproject.toml

@@ -3,7 +3,7 @@ requires = ["hatchling"]
 build-backend = "hatchling.build"
 [project]
 name = "pidibble"
-version = "1.4.1"
+version = "1.4.2"
 authors = [
   { name="Cameron F Abrams", email="cfa22@drexel.edu" },
 ]