pidibble 1.4.0__tar.gz → 1.4.2__tar.gz

{pidibble-1.4.0 → pidibble-1.4.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pidibble
-Version: 1.4.0
+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 +91,10 @@ ATOM
 ```
 
 ## Release History
+* 1.4.2
+   * updated alphafold interface
+* 1.4.1
+   * Fixed parsing bug in `PDBRecordList`
 * 1.4.0
    * Introduced `PDBRecordList` and `PDBRecordDict` classes
 * 1.3.3

{pidibble-1.4.0 → pidibble-1.4.2}/README.md

@@ -73,6 +73,10 @@ ATOM
 ```
 
 ## Release History
+* 1.4.2
+   * updated alphafold interface
+* 1.4.1
+   * Fixed parsing bug in `PDBRecordList`
 * 1.4.0
    * Introduced `PDBRecordList` and `PDBRecordDict` classes
 * 1.3.3

{pidibble-1.4.0 → 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
@@ -407,13 +407,15 @@ def get_symm_ops(rec:PDBRecord):
     T : :class:`numpy.ndarray`
         The 3x1 translation vector.
     """
-    M=np.identity(3)
-    T=np.array([0.,0.,0.])
-    assert len(rec.row)==3,f'a transformation matrix record should not have more than 3 rows'
-    for c,r in zip(rec.coordinate,rec.row):
-        row=c-1
-        M[row][0]=r.m1
-        M[row][1]=r.m2
-        M[row][2]=r.m3
-        T[row]=r.t
-    return M,T
+    M = np.identity(3)
+    T = np.array([0., 0., 0.])
+    if not (hasattr(rec, 'row') and hasattr(rec, 'coordinate')):
+        raise ValueError('Invalid PDBRecord: missing row or coordinate attributes')
+    assert len(rec.row) == 3, f'a transformation matrix record should not have more than 3 rows'
+    for c, r in zip(rec.coordinate, rec.row):
+        row = c - 1
+        M[row][0] = r.m1
+        M[row][1] = r.m2
+        M[row][2] = r.m3
+        T[row] = r.t
+    return M, T

{pidibble-1.4.0 → pidibble-1.4.2}/pidibble/pdbrecord.py

@@ -7,10 +7,12 @@
 .. moduleauthor: Cameron F. Abrams, <cfa22@drexel.edu>
 
 """
+from __future__ import annotations
 from collections import UserList, UserDict
 from .baserecord import BaseRecord, BaseRecordParser
 from .baseparsers import StringParser
 import logging
+
 logger=logging.getLogger(__name__)
 
 class tokengroup:
@@ -130,6 +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.
@@ -482,7 +487,7 @@ class PDBRecordList(UserList):
 
     def __add__(self, other):
         self._validate_all(other)
-        return AList(super().__add__(other))
+        return PDBRecordList(super().__add__(other))
 
     def __iadd__(self, other):
         self._validate_all(other)

{pidibble-1.4.0 → 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-1.4.0 → pidibble-1.4.2}/pyproject.toml

@@ -3,7 +3,7 @@ requires = ["hatchling"]
 build-backend = "hatchling.build"
 [project]
 name = "pidibble"
-version = "1.4.0"
+version = "1.4.2"
 authors = [
   { name="Cameron F Abrams", email="cfa22@drexel.edu" },
 ]