Merge branch 'main' into patch-0.4.1

Author: rasbt

.gitignore

@@ -1,5 +1,9 @@
 site
-
+docs/tutorials/*.md
+docs/tutorials/Working_with_mmCIF_Structures_in_DataFrames_files/*
+docs/tutorials/Working_with_MOL2_Structures_in_DataFrames_files/*
+docs/tutorials/Working_with_PDB_Structures_in_DataFrames_files/*
+docs/tutorials/data/3eiy_stripped.pdb.gz
 docs/api_subpackages/
 docs/api_modules
 docs/py-docstring-parser/

biopandas/mmcif/pandas_mmcif.py

@@ -8,20 +8,15 @@
 
 import gzip
 import sys
-from typing import Dict
+import warnings
+from distutils.version import LooseVersion
+from typing import Dict, Optional
+from urllib.error import HTTPError, URLError
+from urllib.request import urlopen
 
 import numpy as np
 import pandas as pd
 
-try:
-    from urllib.error import HTTPError, URLError
-    from urllib.request import urlopen
-except ImportError:
-    raise ValueError("Python 2.7 is no longer supported")
-
-import warnings
-from distutils.version import LooseVersion
-
 from ..pdb.engines import amino3to1dict
 from .engines import ANISOU_DF_COLUMNS, mmcif_col_types
 from .mmcif_parser import load_cif_data
@@ -72,20 +67,51 @@ def read_mmcif(self, path):
         self.code = self.data["entry"]["id"][0].lower()
         return self
 
-    def fetch_mmcif(self, pdb_code: str):
-        """Fetches mmCIF file contents from the Protein Databank at rcsb.org.
+    def fetch_mmcif(self, pdb_code: Optional[str] = None, uniprot_id: Optional[str] = None, source: str = "pdb"):
+        """Fetches mmCIF file contents from the Protein Databank at rcsb.org or AlphaFold database at https://alphafold.ebi.ac.uk/.
+.
 
         Parameters
         ----------
-        pdb_code : str
-            A 4-letter PDB code, e.g., "3eiy".
+        pdb_code : str, optional
+            A 4-letter PDB code, e.g., `"3eiy"` to retrieve structures from the PDB. Defaults to `None`.
+
+        uniprot_id : str, optional
+            A UniProt Identifier, e.g., `"Q5VSL9"` to retrieve structures from the AF2 database. Defaults to `None`.
+
+        source : str
+            The source to retrieve the structure from (`"pdb"`, `"alphafold2-v1"` or `"alphafold2-v2"`). Defaults to `"pdb"`.
 
         Returns
         ---------
         self
 
         """
-        self.mmcif_path, self.mmcif_text = self._fetch_mmcif(pdb_code)
+        # Sanitize input
+        invalid_input_identifier_1 = pdb_code is None and uniprot_id is None
+        invalid_input_identifier_2 = pdb_code is not None and uniprot_id is not None
+        invalid_input_combination_1 = uniprot_id is not None and source == "pdb"
+        invalid_input_combination_2 = pdb_code is not None and source in {"alphafold2-v1", "alphafold2-v2"}
+
+        if invalid_input_identifier_1 or invalid_input_identifier_2:
+            raise ValueError("Please provide either a PDB code or a UniProt ID.")
+
+        if invalid_input_combination_1 :
+            raise ValueError("Please use a 'pdb_code' instead of 'uniprot_id' for source='pdb'.")
+        elif invalid_input_combination_2 :
+            raise ValueError(f"Please use a 'uniprot_id' instead of 'pdb_code' for source={source}.")
+
+        if source == "pdb":
+            self.mmcif_path, self.mmcif_text = self._fetch_mmcif(pdb_code)
+        elif source == "alphafold2-v1":
+            af2_version = 1
+            self.mmcif_path, self.mmcif_text = self._fetch_af2(uniprot_id, af2_version)
+        elif source == "alphafold2-v2":
+            af2_version = 2
+            self.mmcif_path, self.mmcif_text = self._fetch_af2(uniprot_id, af2_version)
+        else:
+            raise ValueError(f"Invalid source: {source}. Please use one of 'pdb', 'alphafold2-v1' or 'alphafold-v2'.")
+
         self._df = self._construct_df(text=self.mmcif_text)
         return self
 
@@ -121,6 +147,25 @@ def _fetch_mmcif(pdb_code):
             print(f"URL Error {e.args}")
         return url, txt
 
+    @staticmethod
+    def _fetch_af2(uniprot_id: str, af2_version: int = 2):
+        """Load MMCIF file from https://alphafold.ebi.ac.uk/."""
+        txt = None
+        url = f"https://alphafold.ebi.ac.uk/files/AF-{uniprot_id.upper()}-F1-model_v{af2_version}.cif"
+
+        try:
+            response = urlopen(url)
+            txt = response.read()
+            if sys.version_info[0] >= 3:
+                txt = txt.decode('utf-8')
+            else:
+                txt = txt.encode('ascii')
+        except HTTPError as e:
+            print('HTTP Error %s' % e.code)
+        except URLError as e:
+            print('URL Error %s' % e.args)
+        return url, txt
+
     @staticmethod
     def _read_mmcif(path):
         """Read MMCIF file from local drive."""