deprecate MMTF parsing from PDB hosting

Author: Arian Jamasb

biopandas/mmtf/pandas_mmtf.py

@@ -58,12 +58,7 @@ def read_mmtf(self, filename: Union[str, os.PathLike]):
         return self
 
     def fetch_mmtf(self, pdb_code: str):
-        self.code = pdb_code
-        self.mmtf = fetch(pdb_code)
-        df = self._mmtf_to_df(self.mmtf)
-        self._df["ATOM"] = df.loc[df.record_name == "ATOM"]
-        self._df["HETATM"] = df.loc[df.record_name == "HETATM"]
-        return self
+        raise DeprecationWarning("PDB No longer serves MMTF files.")
 
     @staticmethod
     def _mmtf_to_df(mmtf_obj: MMTFDecoder) -> pd.DataFrame:

biopandas/mmtf/tests/test_read_mmtf.py

@@ -4,7 +4,7 @@
 # Project Website: http://rasbt.github.io/biopandas/
 # Code Repository: https://github.com/rasbt/biopandas
 
-
+import pytest
 import os
 from urllib.error import HTTPError, URLError
 from urllib.request import urlopen
@@ -42,6 +42,7 @@
     #"charge",
 ]
 
+@pytest.mark.skip(reason="PDB No longer serves MMTF files.")
 def test_fetch_pdb():
     """Test fetch_pdb"""
     ppdb = PandasMmtf()

biopandas/mmtf/tests/test_write_mmtf.py

@@ -1,11 +1,12 @@
 import os
+import pytest
 
 import pandas as pd
 from pandas.testing import assert_frame_equal
 
 from biopandas.mmtf.pandas_mmtf import PandasMmtf, write_mmtf
 
-
+@pytest.mark.skip(reason="PDB No longer serves MMTF files.")
 def test_write_mmtf_bp():
     PDB_CODES = ["4hhb", "3eiy", "1t48", "1ehz", "4ggb", "1bxa", "1cbn", "1rcf"]
     for pdb in PDB_CODES:
@@ -20,6 +21,8 @@ def test_write_mmtf_bp():
 
     os.remove("test.mmtf")
 
+
+@pytest.mark.skip(reason="PDB No longer serves MMTF files.")
 def test_write_mmtf():
     PDB_CODES = ["4hhb", "3eiy", "1t48", "1ehz", "4ggb", "1bxa", "1cbn", "1rcf"]
     for pdb in PDB_CODES: