pidibble 1.3.0__tar.gz → 1.3.2__tar.gz

{pidibble-1.3.0 → pidibble-1.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pidibble
-Version: 1.3.0
+Version: 1.3.2
 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 +91,9 @@ ATOM
 ```
 
 ## Release History
+* 1.3.2
+   * implemented `filepath` parameter in `PDBParser()` to make
+     reading local files more transparent
 * 1.3.0
    * streamline class attribute usage; full API documentation
 * 1.2.3:

{pidibble-1.3.0 → pidibble-1.3.2}/README.md

@@ -73,6 +73,9 @@ ATOM
 ```
 
 ## Release History
+* 1.3.2
+   * implemented `filepath` parameter in `PDBParser()` to make
+     reading local files more transparent
 * 1.3.0
    * streamline class attribute usage; full API documentation
 * 1.2.3:

pidibble-1.3.2/docs/requirements.txt

@@ -0,0 +1,15 @@
+pillow 
+mock==1.0.1
+alabaster>=0.7,<0.8,!=0.7.5 
+commonmark==0.9.1
+recommonmark==0.5.0
+sphinx 
+sphinx-rtd-theme 
+readthedocs-sphinx-ext<2.3
+furo
+sphinx-copybutton
+pidibble
+readthedocs-sphinx-ext<2.3
+sphinx-copybutton
+sphinxcontrib-mermaid
+pyyaml

{pidibble-1.3.0 → pidibble-1.3.2}/pidibble/pdbparse.py

@@ -12,6 +12,7 @@ import os
 import logging
 import yaml
 import numpy as np
+from pathlib import Path
 from mmcif.io.IoAdapterCore import IoAdapterCore
 from . import resources
 from .baseparsers import ListParsers, ListParser, str2int_sig, safe_float
@@ -24,7 +25,6 @@ import importlib.metadata
 import json
 from .hex import str2atomSerial, hex_reset
 
-
 __version__ = importlib.metadata.version("pidibble")
 
 class PDBParser:
@@ -52,6 +52,7 @@ class PDBParser:
                  input_format='PDB',
                  overwrite=False,
                  alphafold='',
+                 filepath: Path = None,
                  mappers={'HxInteger':str2atomSerial,'Integer':str2int_sig,'String':str,'Float':safe_float},
                  pdbcode_synonyms=['PDBcode','pdb_code','pdbCode','pdbcode','pdbID','pdb_id','pdbid','PDBID','PDBId','PDBid'],
                  comment_chars=['#'],
@@ -62,6 +63,7 @@ class PDBParser:
         self.input_format=input_format
         self.overwrite=overwrite
         self.alphafold=alphafold
+        self.filepath=filepath
         self.mappers=mappers
         self.mappers.update(ListParsers)
         self.pdb_code=''
@@ -118,7 +120,7 @@ class PDBParser:
         bool
             True if the file was successfully fetched, False otherwise.
         """
-        assert self.pdb_code!='' or self.alphafold!=''
+        assert self.pdb_code!='' or self.alphafold!='' or self.filepath is not None, "PDB code or AlphaFold ID must be provided, or a path to a PDB file must be specified."
         if self.pdb_code!='':
             if self.input_format=='PDB':
                 self.filepath=f'{self.pdb_code}.pdb'
@@ -153,6 +155,11 @@ class PDBParser:
                 logger.warning(f'Could not retrieve {result[0]["pdbUrl"]}')
                 return False
             return True
+        elif self.filepath is not None:
+            if not os.path.exists(self.filepath):
+                logger.warning(f'File {self.filepath} does not exist.')
+                return False
+            return True
         else:
             pass # assert statement at top of method body should suppress this branch
 

{pidibble-1.3.0 → pidibble-1.3.2}/pyproject.toml

@@ -3,7 +3,7 @@ requires = ["hatchling"]
 build-backend = "hatchling.build"
 [project]
 name = "pidibble"
-version = "1.3.0"
+version = "1.3.2"
 authors = [
   { name="Cameron F Abrams", email="cfa22@drexel.edu" },
 ]

pidibble-1.3.0/docs/requirements.txt

@@ -1,8 +0,0 @@
-pillow 
-mock==1.0.1
-alabaster>=0.7,<0.8,!=0.7.5 
-commonmark==0.9.1
-recommonmark==0.5.0
-sphinx 
-sphinx-rtd-theme 
-readthedocs-sphinx-ext<2.3