Add PandasPdb.read_pdb_from_list method + unit test

biopandas/pdb/pandas_pdb.py

@@ -92,6 +92,24 @@ def read_pdb(self, path):
         self.header, self.code = self._parse_header_code()
         return self
 
+    def read_pdb_from_list(self, pdb_lines):
+        """Reads PDB file from a list into DataFrames
+
+        Attributes
+        ----------
+        pdb_lines : list
+            A list of lines containing the pdb file contents.
+
+        Returns
+        ---------
+        self
+
+        """
+        self.pdb_text = ''.join(pdb_lines)
+        self._df = self._construct_df(pdb_lines)
+        self.header, self.code = self._parse_header_code()
+        return self
+
     def fetch_pdb(self, pdb_code):
         """Fetches PDB file contents from the Protein Databank at rcsb.org.
 

biopandas/pdb/tests/test_read_pdb.py

@@ -112,6 +112,17 @@ def test_read_pdb():
     assert ppdb.pdb_path == TESTDATA_FILENAME
 
 
+def test_read_pdb_from_list():
+    """Test public read_pdb_from_list"""
+
+    for pdb_text, code in zip([three_eiy, four_eiy], ['3eiy', '4eiy']):
+        ppdb = PandasPdb()
+        ppdb.read_pdb_from_list(pdb_text.splitlines(True))
+        assert ppdb.pdb_text == pdb_text
+        assert ppdb.code == code
+        assert ppdb.pdb_path == ''
+
+
 def test_anisou_input_handling():
     """Test public read_pdb"""
     ppdb = PandasPdb()

docs/sources/api_subpackages/biopandas.mol2.md

@@ -1,4 +1,4 @@
-biopandas version: 0.2.6
+biopandas version: 0.2.7
 ## PandasMol2
 
 *PandasMol2()*

docs/sources/api_subpackages/biopandas.pdb.md

@@ -1,4 +1,4 @@
-biopandas version: 0.2.6
+biopandas version: 0.2.7
 ## PandasPdb
 
 *PandasPdb()*
@@ -229,6 +229,22 @@ self
 
 <hr>
 
+*read_pdb_from_list(pdb_lines)*
+
+Reads PDB file from a list into DataFrames
+
+**Attributes**
+
+- `pdb_lines` : list
+
+    A list of lines containing the pdb file contents.
+
+**Returns**
+
+self
+
+<hr>
+
 *rmsd(df1, df2, s=None, invert=False)*
 
 Compute the Root Mean Square Deviation between molecules.

docs/sources/api_subpackages/biopandas.testutils.md

@@ -1,4 +1,4 @@
-biopandas version: 0.2.6
+biopandas version: 0.2.7
 ## assert_raises
 
 *assert_raises(exception_type, message, func, *args, **kwargs)*