diff --git a/README.md b/README.md
index 2010d69..1008dee 100644
--- a/README.md
+++ b/README.md
@@ -35,10 +35,10 @@ So, why don't we take pandas to the structural biology world? Working with molec
 ![3eiy](./docs/sources/img/index/3eiy.png)
 
 ```python
-# Initialize a new PandasPDB object
+# Initialize a new PandasPdb object
 # and fetch the PDB file from rcsb.org
->>> from biopandas.pdb import PandasPDB
->>> ppdb = PandasPDB().fetch_pdb('3eiy')
+>>> from biopandas.pdb import PandasPdb
+>>> ppdb = PandasPdb().fetch_pdb('3eiy')
 >>> ppdb.df['ATOM'].head()
 ```
 
@@ -53,10 +53,10 @@ So, why don't we take pandas to the structural biology world? Working with molec
 ```python
 # Load structures from your drive and compute the
 # Root Mean Square Deviation
->>> from biopandas.pdb import PandasPDB
->>> pl1 = PandasPDB().read_pdb('./docking_pose_1.pdb')
->>> pl2 = PandasPDB().read_pdb('./docking_pose_2.pdb')
->>> r = PandasPDB.rmsd(pl1.df['HETATM'], pl2.df['HETATM'],
+>>> from biopandas.pdb import PandasPdb
+>>> pl1 = PandasPdb().read_pdb('./docking_pose_1.pdb')
+>>> pl2 = PandasPdb().read_pdb('./docking_pose_2.pdb')
+>>> r = PandasPdb.rmsd(pl1.df['HETATM'], pl2.df['HETATM'],
                        s='hydrogen', invert=True)
 >>> print('RMSD: %.4f Angstrom' % r)
 
diff --git a/biopandas/mol2/__init__.py b/biopandas/mol2/__init__.py
index ac7c71d..79358e2 100644
--- a/biopandas/mol2/__init__.py
+++ b/biopandas/mol2/__init__.py
@@ -9,7 +9,7 @@
 files in pandas DataFrames.
 """
 
-from .pandas_mol2 import PandasMOL2
+from .pandas_mol2 import PandasMol2
 from .mol2_io import split_multimol2
 
-__all__ = ["PandasMOL2", "split_multimol2"]
+__all__ = ["PandasMol2", "split_multimol2"]
diff --git a/biopandas/mol2/pandas_mol2.py b/biopandas/mol2/pandas_mol2.py
index 844dbaa..54a671d 100644
--- a/biopandas/mol2/pandas_mol2.py
+++ b/biopandas/mol2/pandas_mol2.py
@@ -24,7 +24,7 @@
 COLUMN_TYPES = (int, str, float, float, float, str, int, str, float)
 
 
-class PandasMOL2(object):
+class PandasMol2(object):
     """ Object for working with Tripos Mol2 structure files.
 
    Attributes
diff --git a/biopandas/mol2/tests/test_pandas_mol2.py b/biopandas/mol2/tests/test_pandas_mol2.py
index f6fa16c..34ebacc 100644
--- a/biopandas/mol2/tests/test_pandas_mol2.py
+++ b/biopandas/mol2/tests/test_pandas_mol2.py
@@ -5,7 +5,7 @@
 # Code Repository: https://github.com/rasbt/biopandas
 
 import os
-from biopandas.mol2 import PandasMOL2
+from biopandas.mol2 import PandasMol2
 from biopandas.mol2.mol2_io import split_multimol2
 
 this_dir = os.path.dirname(os.path.realpath(__file__))
@@ -17,7 +17,7 @@ def test_read_mol2():
     data_path_2 = os.path.join(this_dir, 'data', '40_mol2_files.mol2.gz')
 
     for data_path in (data_path_1, data_path_2):
-        pdmol = PandasMOL2().read_mol2(data_path)
+        pdmol = PandasMol2().read_mol2(data_path)
         assert pdmol.df.shape == (65, 9)
         assert pdmol.code == 'ZINC38611810'
 
@@ -32,7 +32,7 @@ def test_read_mol2_from_list():
     data_path = os.path.join(this_dir, 'data', '40_mol2_files.mol2')
     mol2 = next(split_multimol2(data_path))
 
-    pdmol = PandasMOL2().read_mol2_from_list(mol2_lines=mol2[1],
+    pdmol = PandasMol2().read_mol2_from_list(mol2_lines=mol2[1],
                                              mol2_code=mol2[0])
     assert pdmol.df.shape == (65, 9)
     assert pdmol.code == 'ZINC38611810'
@@ -42,8 +42,8 @@ def test_rmsd():
     data_path_1 = os.path.join(this_dir, 'data', '1b5e_1.mol2')
     data_path_2 = os.path.join(this_dir, 'data', '1b5e_2.mol2')
 
-    pdmol_1 = PandasMOL2().read_mol2(data_path_1)
-    pdmol_2 = PandasMOL2().read_mol2(data_path_2)
+    pdmol_1 = PandasMol2().read_mol2(data_path_1)
+    pdmol_2 = PandasMol2().read_mol2(data_path_2)
 
     assert pdmol_1.rmsd(pdmol_1.df, pdmol_2.df, heavy_only=False) == 1.5523
     assert pdmol_1.rmsd(pdmol_1.df, pdmol_2.df) == 1.1609
@@ -52,5 +52,5 @@ def test_rmsd():
 def test_distance():
     data_path = os.path.join(this_dir, 'data', '1b5e_1.mol2')
 
-    pdmol = PandasMOL2().read_mol2(data_path)
+    pdmol = PandasMol2().read_mol2(data_path)
     assert round(pdmol.distance().values[0], 3) == 31.185
diff --git a/biopandas/pdb/__init__.py b/biopandas/pdb/__init__.py
index 614fbea..f11af51 100644
--- a/biopandas/pdb/__init__.py
+++ b/biopandas/pdb/__init__.py
@@ -9,6 +9,6 @@
 files in pandas DataFrames.
 """
 
-from .pandas_pdb import PandasPDB
+from .pandas_pdb import PandasPdb
 
-__all__ = ["PandasPDB"]
+__all__ = ["PandasPdb"]
diff --git a/biopandas/pdb/pandas_pdb.py b/biopandas/pdb/pandas_pdb.py
index 679ee60..31dd547 100644
--- a/biopandas/pdb/pandas_pdb.py
+++ b/biopandas/pdb/pandas_pdb.py
@@ -19,7 +19,7 @@
 from .engines import amino3to1dict
 
 
-class PandasPDB(object):
+class PandasPdb(object):
     """ Object for working with Protein Databank structure files.
 
     Attributes
@@ -117,12 +117,12 @@ def get(self, s, df=None, invert=False):
             df = self._df['ATOM']
         return self._get_dict[s](df, invert=invert)
 
-    def impute_element(self, sections=['ATOM', 'HETATM'], inplace=False):
+    def impute_element(self, sections=('ATOM', 'HETATM'), inplace=False):
         """Impute element_symbol from atom_name section.
 
         Parameters
         ----------
-        sections : iterable (default: ['ATOM', 'HETATM'])
+        sections : iterable (default: ('ATOM', 'HETATM'))
             Coordinate sections for which the element symbols should be
             imputed.
 
@@ -181,7 +181,7 @@ def rmsd(df1, df2, s=None, invert=False):
         """
         if df1.shape[0] != df2.shape[0]:
             raise AttributeError('DataFrames have unequal lengths')
-        get_dict = PandasPDB._init_get_dict()
+        get_dict = PandasPdb._init_get_dict()
         if s:
             if s not in get_dict.keys():
                 raise AttributeError('s must be in '
@@ -198,11 +198,11 @@ def rmsd(df1, df2, s=None, invert=False):
     @staticmethod
     def _init_get_dict():
         """Initialize dictionary for filter operations."""
-        get_dict = {'main chain': PandasPDB._get_mainchain,
-                    'hydrogen': PandasPDB._get_hydrogen,
-                    'c-alpha': PandasPDB._get_calpha,
-                    'carbon': PandasPDB._get_carbon,
-                    'heavy': PandasPDB._get_heavy}
+        get_dict = {'main chain': PandasPdb._get_mainchain,
+                    'hydrogen': PandasPdb._get_hydrogen,
+                    'c-alpha': PandasPdb._get_calpha,
+                    'carbon': PandasPdb._get_carbon,
+                    'heavy': PandasPdb._get_heavy}
         return get_dict
 
     @staticmethod
diff --git a/biopandas/pdb/tests/test_amino3to1.py b/biopandas/pdb/tests/test_amino3to1.py
index 867b52a..16e9dce 100644
--- a/biopandas/pdb/tests/test_amino3to1.py
+++ b/biopandas/pdb/tests/test_amino3to1.py
@@ -4,14 +4,14 @@
 # Project Website: http://rasbt.github.io/biopandas/
 # Code Repository: https://github.com/rasbt/biopandas
 
-from biopandas.pdb import PandasPDB
+from biopandas.pdb import PandasPdb
 import os
 
 
 def test_defaults():
     TESTDATA_1t48 = os.path.join(os.path.dirname(__file__), 'data',
                                                             '1t48_995.pdb')
-    p1t48 = PandasPDB()
+    p1t48 = PandasPdb()
     p1t48.read_pdb(TESTDATA_1t48)
     expect = ['M', 'E', 'M', 'E', 'K', 'E', 'F', 'E', 'Q',
               'I', 'D', 'K', 'S', 'G', 'S', 'W', 'A', 'A',
diff --git a/biopandas/pdb/tests/test_distance.py b/biopandas/pdb/tests/test_distance.py
index 377d5ac..2070e8e 100644
--- a/biopandas/pdb/tests/test_distance.py
+++ b/biopandas/pdb/tests/test_distance.py
@@ -5,7 +5,7 @@
 # Code Repository: https://github.com/rasbt/biopandas
 
 import pandas as pd
-from biopandas.pdb import PandasPDB
+from biopandas.pdb import PandasPdb
 import os
 from nose.tools import raises
 
@@ -14,7 +14,7 @@ def test_equal():
     TESTDATA_1t48 = os.path.join(os.path.dirname(__file__), 'data',
                                                             '1t48_995.pdb')
 
-    p1t48 = PandasPDB()
+    p1t48 = PandasPdb()
     p1t48.read_pdb(TESTDATA_1t48)
     dist = p1t48.distance(xyz=(70.785, 15.477, 23.359), record='ATOM')
 
diff --git a/biopandas/pdb/tests/test_impute.py b/biopandas/pdb/tests/test_impute.py
index 8c688d9..e035306 100644
--- a/biopandas/pdb/tests/test_impute.py
+++ b/biopandas/pdb/tests/test_impute.py
@@ -5,7 +5,7 @@
 # Code Repository: https://github.com/rasbt/biopandas
 
 
-from biopandas.pdb import PandasPDB
+from biopandas.pdb import PandasPdb
 import os
 import numpy as np
 import pandas as pd
@@ -14,7 +14,7 @@
 TESTDATA_FILENAME = os.path.join(os.path.dirname(__file__), 'data',
                                  '3eiy_stripped_no_ele.pdb')
 
-ppdb = PandasPDB()
+ppdb = PandasPdb()
 ppdb.read_pdb(TESTDATA_FILENAME)
 
 
diff --git a/biopandas/pdb/tests/test_read_pdb.py b/biopandas/pdb/tests/test_read_pdb.py
index e0bdbe2..9d0a420 100644
--- a/biopandas/pdb/tests/test_read_pdb.py
+++ b/biopandas/pdb/tests/test_read_pdb.py
@@ -5,7 +5,7 @@
 # Code Repository: https://github.com/rasbt/biopandas
 
 
-from biopandas.pdb import PandasPDB
+from biopandas.pdb import PandasPdb
 import os
 import numpy as np
 import pandas as pd
@@ -50,7 +50,7 @@
 
 def test__read_pdb():
     """Test private _read_pdb"""
-    ppdb = PandasPDB()
+    ppdb = PandasPdb()
     txt = ppdb._read_pdb(TESTDATA_FILENAME)
     print(txt)
     assert txt == three_eiy
@@ -60,7 +60,7 @@ def test_fetch_pdb():
     """Test fetch_pdb"""
 
     try:
-        ppdb = PandasPDB()
+        ppdb = PandasPdb()
         txt = ppdb._fetch_pdb('3eiy')
     except HTTPError:
         pass
@@ -73,14 +73,14 @@ def test_fetch_pdb():
 
 def test__read_pdb_gz():
     """Test public _read_pdb with gzip files"""
-    ppdb = PandasPDB()
+    ppdb = PandasPdb()
     txt = ppdb._read_pdb(TESTDATA_FILENAME_GZ)
     assert txt == three_eiy
 
 
 def test__construct_df():
     """Test pandas dataframe construction"""
-    ppdb = PandasPDB()
+    ppdb = PandasPdb()
     dfs = ppdb._construct_df(three_eiy.splitlines())
     assert set(dfs.keys()) == {'OTHERS', 'ATOM', 'ANISOU', 'HETATM'}
     assert set(dfs['ATOM'].columns) == set(ATOM_DF_COLUMNS)
@@ -102,7 +102,7 @@ def test__construct_df():
 
 def test_read_pdb():
     """Test public read_pdb"""
-    ppdb = PandasPDB()
+    ppdb = PandasPdb()
     ppdb.read_pdb(TESTDATA_FILENAME)
     assert ppdb.pdb_text == three_eiy
     assert ppdb.code == '3eiy', ppdb.code
@@ -110,7 +110,7 @@ def test_read_pdb():
 
 def test_anisou_input_handling():
     """Test public read_pdb"""
-    ppdb = PandasPDB()
+    ppdb = PandasPdb()
     ppdb.read_pdb(TESTDATA_FILENAME2)
     assert ppdb.pdb_text == four_eiy
     assert ppdb.code == '4eiy', ppdb.code
@@ -118,20 +118,20 @@ def test_anisou_input_handling():
 
 @raises(AttributeError)
 def test_get_exceptions():
-    ppdb = PandasPDB()
+    ppdb = PandasPdb()
     ppdb.read_pdb(TESTDATA_FILENAME)
     ppdb.get('main-chai')
 
 
 def test_get_all():
-    ppdb = PandasPDB()
+    ppdb = PandasPdb()
     ppdb.read_pdb(TESTDATA_FILENAME)
     for i in ['c-alpha', 'hydrogen', 'main chain']:
         ppdb.get(i)
 
 
 def test_get_df():
-    ppdb = PandasPDB()
+    ppdb = PandasPdb()
     ppdb.read_pdb(TESTDATA_FILENAME)
 
     shape = ppdb.get('c-alpha').shape
diff --git a/biopandas/pdb/tests/test_rmsd.py b/biopandas/pdb/tests/test_rmsd.py
index edb680a..44529ae 100644
--- a/biopandas/pdb/tests/test_rmsd.py
+++ b/biopandas/pdb/tests/test_rmsd.py
@@ -4,7 +4,7 @@
 # Project Website: http://rasbt.github.io/biopandas/
 # Code Repository: https://github.com/rasbt/biopandas
 
-from biopandas.pdb import PandasPDB
+from biopandas.pdb import PandasPdb
 import os
 from nose.tools import raises
 
@@ -18,50 +18,50 @@
 TESTDATA_lig2 = os.path.join(os.path.dirname(__file__), 'data',
                                                         'lig_conf_2.pdb')
 
-p1t48 = PandasPDB()
+p1t48 = PandasPdb()
 p1t48.read_pdb(TESTDATA_1t48)
-p1t49 = PandasPDB()
+p1t49 = PandasPdb()
 p1t49.read_pdb(TESTDATA_1t49)
 
-pl1 = PandasPDB()
+pl1 = PandasPdb()
 pl1.read_pdb(TESTDATA_lig1)
-pl2 = PandasPDB()
+pl2 = PandasPdb()
 pl2.read_pdb(TESTDATA_lig2)
 
 
 def test_equal():
-    r = PandasPDB.rmsd(p1t48.df['ATOM'], p1t48.df['ATOM'], s=None)
+    r = PandasPdb.rmsd(p1t48.df['ATOM'], p1t48.df['ATOM'], s=None)
     assert r == 0.000, r
 
 
 @raises(AttributeError)
 def test_wrong_arg():
-    PandasPDB.rmsd(p1t48.df['ATOM'].loc[1:, :], p1t48.df['ATOM'], s='bla')
+    PandasPdb.rmsd(p1t48.df['ATOM'].loc[1:, :], p1t48.df['ATOM'], s='bla')
 
 
 @raises(AttributeError)
 def test_incompatible():
-    PandasPDB.rmsd(p1t48.df['ATOM'].loc[1:, :], p1t48.df['ATOM'], s=None)
+    PandasPdb.rmsd(p1t48.df['ATOM'].loc[1:, :], p1t48.df['ATOM'], s=None)
 
 
 @raises(AttributeError)
 def test_invalid_query():
-    PandasPDB.rmsd(p1t48.df['ATOM'].loc[1:, :], p1t48.df['ATOM'], s='bla')
+    PandasPdb.rmsd(p1t48.df['ATOM'].loc[1:, :], p1t48.df['ATOM'], s='bla')
 
 
 def test_protein():
-    r = PandasPDB.rmsd(p1t48.df['ATOM'], p1t49.df['ATOM'],
+    r = PandasPdb.rmsd(p1t48.df['ATOM'], p1t49.df['ATOM'],
                        s='c-alpha', invert=False)
     assert r == 0.4785, r
 
 
 def test_ligand():
-    r = PandasPDB.rmsd(pl1.df['HETATM'], pl2.df['HETATM'],
+    r = PandasPdb.rmsd(pl1.df['HETATM'], pl2.df['HETATM'],
                        s='hydrogen', invert=True)
     assert r == 1.9959, r
 
 
 def test_ligand_default():
-    r = PandasPDB.rmsd(pl1.df['HETATM'], pl2.df['HETATM'],
+    r = PandasPdb.rmsd(pl1.df['HETATM'], pl2.df['HETATM'],
                        s=None)
     assert r == 2.6444, r
diff --git a/biopandas/pdb/tests/test_write_pdb.py b/biopandas/pdb/tests/test_write_pdb.py
index 161a415..d8bf949 100644
--- a/biopandas/pdb/tests/test_write_pdb.py
+++ b/biopandas/pdb/tests/test_write_pdb.py
@@ -4,7 +4,7 @@
 # Project Website: http://rasbt.github.io/biopandas/
 # Code Repository: https://github.com/rasbt/biopandas
 
-from biopandas.pdb import PandasPDB
+from biopandas.pdb import PandasPdb
 import warnings
 import pandas as pd
 import os
@@ -27,7 +27,7 @@
 
 
 def test_defaults():
-    ppdb = PandasPDB()
+    ppdb = PandasPdb()
     ppdb.read_pdb(TESTDATA_FILENAME)
     ppdb.to_pdb(path=OUTFILE, records=None)
     with open(TESTDATA_FILENAME, 'r') as f:
@@ -39,7 +39,7 @@ def test_defaults():
 
 
 def test_nonexpected_column():
-    ppdb = PandasPDB()
+    ppdb = PandasPdb()
     ppdb.read_pdb(TESTDATA_FILENAME)
     ppdb.df['HETATM']['test'] = pd.Series('test',
                                           index=ppdb.df['HETATM'].index)
@@ -53,7 +53,7 @@ def test_nonexpected_column():
 
 def test_records():
     """Test private _read_pdb."""
-    ppdb = PandasPDB()
+    ppdb = PandasPdb()
     ppdb.read_pdb(TESTDATA_FILENAME)
     ppdb.to_pdb(path=OUTFILE, records=['HETATM'])
     with open(OUTFILE, 'r') as f:
@@ -64,7 +64,7 @@ def test_records():
 
 def test_anisou():
     """Test writing ANISOU entries."""
-    ppdb = PandasPDB()
+    ppdb = PandasPdb()
     ppdb.read_pdb(TESTDATA_FILENAME2)
     ppdb.to_pdb(path=OUTFILE, records=None)
     with open(OUTFILE, 'r') as f:
diff --git a/docs/sources/CHANGELOG.md b/docs/sources/CHANGELOG.md
index 7d199f5..662d8a4 100755
--- a/docs/sources/CHANGELOG.md
+++ b/docs/sources/CHANGELOG.md
@@ -8,14 +8,14 @@
 
 ##### New Features
 
-- Added an `amino3to1` method to `PandasPDB` data frames to convert 3-amino acid letter codes to 1-letter codes.
-- Added a `distance` method to `PandasPDB` data frames to compute the Euclidean distance between atoms and a reference point.
-- Added the `PandasMOL2` class for working with Tripos MOL2 files in pandas DataFrames
+- Added an `amino3to1` method to `PandasPdb` data frames to convert 3-amino acid letter codes to 1-letter codes.
+- Added a `distance` method to `PandasPdb` data frames to compute the Euclidean distance between atoms and a reference point.
+- Added the `PandasMol2` class for working with Tripos MOL2 files in pandas DataFrames
 
 
 ##### Changes
 
-- Raises a warning if `PandasPDB` is written to PDB and ATOM and HETAM section contains unexpected columns; these columns will now be skipped.
+- Raises a warning if `PandasPdb` is written to PDB and ATOM and HETAM section contains unexpected columns; these columns will now be skipped.
 
 ##### Bug Fixes
 
@@ -31,13 +31,13 @@
 
 ##### New Features
 
-- Added an `impute_element` method to `PandasPDB` objects to infer the Element Symbol from the Atom Name column.
-- Added two new selection types for `PandasPDB` ATOM and HETATM coordinate sections: `'heavy'` and `'carbon'`.
+- Added an `impute_element` method to `PandasPdb` objects to infer the Element Symbol from the Atom Name column.
+- Added two new selection types for `PandasPdb` ATOM and HETATM coordinate sections: `'heavy'` and `'carbon'`.
 
 ##### Changes
 
 - Include test data in the PyPI package; add install_requires for pandas.
-- The `'hydrogen'` atom selection in `PandasPDB` methods is now based on the element type instead of the atom name.
+- The `'hydrogen'` atom selection in `PandasPdb` methods is now based on the element type instead of the atom name.
 - By default, the RMSD is now computed on all atoms unless a specific selection is defined.
 
 ##### Bug Fixes
diff --git a/docs/sources/api_subpackages/biopandas.mol2.md b/docs/sources/api_subpackages/biopandas.mol2.md
index 530cca9..e69772d 100644
--- a/docs/sources/api_subpackages/biopandas.mol2.md
+++ b/docs/sources/api_subpackages/biopandas.mol2.md
@@ -1,7 +1,7 @@
 biopandas version: 0.2.0.dev0
-## PandasMOL2
+## PandasMol2
 
-*PandasMOL2()*
+*PandasMol2()*
 
 Object for working with Tripos Mol2 structure files.
 
diff --git a/docs/sources/api_subpackages/biopandas.pdb.md b/docs/sources/api_subpackages/biopandas.pdb.md
index 8b3421c..ea85fe4 100644
--- a/docs/sources/api_subpackages/biopandas.pdb.md
+++ b/docs/sources/api_subpackages/biopandas.pdb.md
@@ -1,7 +1,7 @@
 biopandas version: 0.2.0.dev0
-## PandasPDB
+## PandasPdb
 
-*PandasPDB()*
+*PandasPdb()*
 
 Object for working with Protein Databank structure files.
 
diff --git a/docs/sources/index.md b/docs/sources/index.md
index ade843a..67aed03 100755
--- a/docs/sources/index.md
+++ b/docs/sources/index.md
@@ -40,10 +40,10 @@ So, why don't we take pandas to the structural biology world? Working with molec
 ![3eiy](./img/index/3eiy.png)
 
 ```python
-# Initialize a new PandasPDB object
+# Initialize a new PandasPdb object
 # and fetch the PDB file from rcsb.org
->>> from biopandas.pdb import PandasPDB
->>> ppdb = PandasPDB().fetch_pdb('3eiy')
+>>> from biopandas.pdb import PandasPdb
+>>> ppdb = PandasPdb().fetch_pdb('3eiy')
 >>> ppdb.df['ATOM'].head()
 ```
 
@@ -57,10 +57,10 @@ So, why don't we take pandas to the structural biology world? Working with molec
 ```python
 # Load structures from your drive and compute the
 # Root Mean Square Deviation
->>> from biopandas.pdb import PandasPDB
->>> pl1 = PandasPDB().read_pdb('./docking_pose_1.pdb')
->>> pl2 = PandasPDB().read_pdb('./docking_pose_2.pdb')
->>> r = PandasPDB.rmsd(pl1.df['HETATM'], pl2.df['HETATM'])
+>>> from biopandas.pdb import PandasPdb
+>>> pl1 = PandasPdb().read_pdb('./docking_pose_1.pdb')
+>>> pl2 = PandasPdb().read_pdb('./docking_pose_2.pdb')
+>>> r = PandasPdb.rmsd(pl1.df['HETATM'], pl2.df['HETATM'])
 >>> print('RMSD: %.4f Angstrom' % r)
 RMSD: 2.6444 Angstrom
 ```
diff --git a/docs/sources/tutorials/Working_with_MOL2_Structures_in_DataFrames.ipynb b/docs/sources/tutorials/Working_with_MOL2_Structures_in_DataFrames.ipynb
index a954fbc..43a8448 100644
--- a/docs/sources/tutorials/Working_with_MOL2_Structures_in_DataFrames.ipynb
+++ b/docs/sources/tutorials/Working_with_MOL2_Structures_in_DataFrames.ipynb
@@ -43,7 +43,7 @@
    },
    "outputs": [],
    "source": [
-    "from biopandas.mol2 import PandasMOL2\n",
+    "from biopandas.mol2 import PandasMol2\n",
     "import pandas as pd\n",
     "pd.set_option('display.width', 600)\n",
     "pd.set_option('display.max_columns', 8)"
@@ -85,9 +85,9 @@
    },
    "outputs": [],
    "source": [
-    "from biopandas.mol2 import PandasMOL2\n",
+    "from biopandas.mol2 import PandasMol2\n",
     "\n",
-    "pmol = PandasMOL2().read_mol2('./data/1b5e_1.mol2')"
+    "pmol = PandasMol2().read_mol2('./data/1b5e_1.mol2')"
    ]
   },
   {
@@ -107,14 +107,14 @@
    },
    "outputs": [],
    "source": [
-    "pmol = PandasMOL2().read_mol2('./data/40_mol2_files.mol2.gz')"
+    "pmol = PandasMol2().read_mol2('./data/40_mol2_files.mol2.gz')"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "After the file was succesfully loaded, we have access to the following basic `PandasMOL2` attributes:"
+    "After the file was succesfully loaded, we have access to the following basic `PandasMol2` attributes:"
    ]
   },
   {
@@ -158,7 +158,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The most interesting and useful attribute, however, is the [`PandasMOL2.df`](../api/biopandas.mol2#pandasmol2df) DataFrame, which contains the ATOM section of the MOL2 structure. Let's print the first 3 lines from the `ATOM` coordinate section to see how it looks like:"
+    "The most interesting and useful attribute, however, is the [`PandasMol2.df`](../api/biopandas.mol2#pandasmol2df) DataFrame, which contains the ATOM section of the MOL2 structure. Let's print the first 3 lines from the `ATOM` coordinate section to see how it looks like:"
    ]
   },
   {
@@ -258,7 +258,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "`PandasMOL2` expects the MOL2 file to be in the standard Tripos MOL2 format, and most importantly, that the \"@<TRIPOS>ATOM\" section is consistent with the following format convention:\n",
+    "`PandasMol2` expects the MOL2 file to be in the standard Tripos MOL2 format, and most importantly, that the \"@<TRIPOS>ATOM\" section is consistent with the following format convention:\n",
     "\n",
     "\n",
     "> Format:\n",
@@ -500,9 +500,9 @@
     }
    ],
    "source": [
-    "from biopandas.pdb import PandasPDB\n",
+    "from biopandas.pdb import PandasPdb\n",
     "\n",
-    "pmol = PandasMOL2()\n",
+    "pmol = PandasMol2()\n",
     "pmol.read_mol2('./data/1b5e_1.mol2')\n",
     "pmol.df.tail(10)"
    ]
@@ -868,7 +868,7 @@
     {
      "data": {
       "text/plain": [
-       "<biopandas.mol2.pandas_mol2.PandasMOL2 at 0x1067e2b70>"
+       "<biopandas.mol2.pandas_mol2.PandasMol2 at 0x1067e2b70>"
       ]
      },
      "execution_count": 10,
@@ -877,9 +877,9 @@
     }
    ],
    "source": [
-    "from biopandas.pdb import PandasPDB\n",
+    "from biopandas.pdb import PandasPdb\n",
     "\n",
-    "pmol = PandasMOL2()\n",
+    "pmol = PandasMol2()\n",
     "pmol.read_mol2('./data/1b5e_1.mol2')"
    ]
   },
@@ -1044,13 +1044,13 @@
     }
    ],
    "source": [
-    "from biopandas.mol2 import PandasMOL2\n",
+    "from biopandas.mol2 import PandasMol2\n",
     "\n",
-    "l_1 = PandasMOL2().read_mol2('./data/1b5e_1.mol2')\n",
-    "l_2 = PandasMOL2().read_mol2('./data/1b5e_2.mol2')\n",
+    "l_1 = PandasMol2().read_mol2('./data/1b5e_1.mol2')\n",
+    "l_2 = PandasMol2().read_mol2('./data/1b5e_2.mol2')\n",
     "\n",
-    "r_heavy = PandasMOL2.rmsd(l_1.df, l_2.df)\n",
-    "r_all  = PandasMOL2.rmsd(l_1.df, l_2.df, heavy_only=False)\n",
+    "r_heavy = PandasMol2.rmsd(l_1.df, l_2.df)\n",
+    "r_all  = PandasMol2.rmsd(l_1.df, l_2.df, heavy_only=False)\n",
     "\n",
     "print('Heavy-atom RMSD: %.4f Angstrom' % r_heavy)\n",
     "print('All-atom RMSD: %.4f Angstrom' % r_all)"
@@ -1126,9 +1126,9 @@
     }
    ],
    "source": [
-    "from biopandas.pdb import PandasPDB\n",
+    "from biopandas.pdb import PandasPdb\n",
     "\n",
-    "pmol = PandasMOL2().read_mol2('./data/1b5e_1.mol2')\n",
+    "pmol = PandasMol2().read_mol2('./data/1b5e_1.mol2')\n",
     "\n",
     "keto_coord = pmol.df[pmol.df['atom_type'] == 'O.2'][['x', 'y', 'z']]\n",
     "keto_coord"
@@ -1499,7 +1499,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "As mentioned earlier, `PandasMOL2.read_mol2()` only reads in the first molecule if it is given a multi-MOL2 file. However, if we want to create DataFrames from multiple structures in a MOL2 file, we can use the handy `split_multimol2` generator.\n",
+    "As mentioned earlier, `PandasMol2.read_mol2()` only reads in the first molecule if it is given a multi-MOL2 file. However, if we want to create DataFrames from multiple structures in a MOL2 file, we can use the handy `split_multimol2` generator.\n",
     "\n",
     "The `split_multimol2` generator yields tuples containing the molecule IDs and the MOL2 content as strings in a list -- each line in the MOL2 file is stored as a string in the list."
    ]
@@ -1535,7 +1535,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We can now use this generator to loop over all files in a multi-MOL2 file and create PandasMOL2 DataFrames. A typical use case would be the filtering of mol2 files by certain properties:"
+    "We can now use this generator to loop over all files in a multi-MOL2 file and create PandasMol2 DataFrames. A typical use case would be the filtering of mol2 files by certain properties:"
    ]
   },
   {
@@ -1546,7 +1546,7 @@
    },
    "outputs": [],
    "source": [
-    "pdmol = PandasMOL2()\n",
+    "pdmol = PandasMol2()\n",
     "\n",
     "with open('./data/filtered.mol2', 'w') as f:\n",
     "    for mol2 in split_multimol2('./data/40_mol2_files.mol2'):\n",
diff --git a/docs/sources/tutorials/Working_with_PDB_Structures_in_DataFrames.ipynb b/docs/sources/tutorials/Working_with_PDB_Structures_in_DataFrames.ipynb
index 6431144..713e979 100644
--- a/docs/sources/tutorials/Working_with_PDB_Structures_in_DataFrames.ipynb
+++ b/docs/sources/tutorials/Working_with_PDB_Structures_in_DataFrames.ipynb
@@ -43,7 +43,7 @@
    },
    "outputs": [],
    "source": [
-    "from biopandas.pdb import PandasPDB\n",
+    "from biopandas.pdb import PandasPdb\n",
     "import pandas as pd\n",
     "pd.set_option('display.width', 600)\n",
     "pd.set_option('display.max_columns', 8)"
@@ -67,7 +67,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "There are 2 1/2 ways to load a PDB structure into a `PandasPDB` object.\n"
+    "There are 2 1/2 ways to load a PDB structure into a `PandasPdb` object.\n"
    ]
   },
   {
@@ -75,7 +75,7 @@
    "metadata": {},
    "source": [
     "#### 1\n",
-    "PDB files can be directly fetched from The Protein Data Bank at [http://www.rcsb.org](http://www.rcsb.org) via its unique 4-letter after initializing a new [`PandasPDB`](../api/biopandas.pdb#pandaspdb) object and calling the [`fetch_pdb`](../api/biopandas.pdb#pandaspdbfetch_pdb) method:"
+    "PDB files can be directly fetched from The Protein Data Bank at [http://www.rcsb.org](http://www.rcsb.org) via its unique 4-letter after initializing a new [`PandasPdb`](../api/biopandas.pdb#pandaspdb) object and calling the [`fetch_pdb`](../api/biopandas.pdb#pandaspdbfetch_pdb) method:"
    ]
   },
   {
@@ -86,11 +86,11 @@
    },
    "outputs": [],
    "source": [
-    "from biopandas.pdb import PandasPDB\n",
+    "from biopandas.pdb import PandasPdb\n",
     "\n",
-    "# Initialize a new PandasPDB object\n",
+    "# Initialize a new PandasPdb object\n",
     "# and fetch the PDB file from rcsb.org\n",
-    "ppdb = PandasPDB().fetch_pdb('3eiy')"
+    "ppdb = PandasPdb().fetch_pdb('3eiy')"
    ]
   },
   {
@@ -112,7 +112,7 @@
     {
      "data": {
       "text/plain": [
-       "<biopandas.pdb.pandas_pdb.PandasPDB at 0x106795898>"
+       "<biopandas.pdb.pandas_pdb.PandasPdb at 0x106795898>"
       ]
      },
      "execution_count": 4,
@@ -143,7 +143,7 @@
     {
      "data": {
       "text/plain": [
-       "<biopandas.pdb.pandas_pdb.PandasPDB at 0x106795898>"
+       "<biopandas.pdb.pandas_pdb.PandasPdb at 0x106795898>"
       ]
      },
      "execution_count": 5,
@@ -205,7 +205,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "The most interesting / useful attribute is the [`PandasPDB.df`](../api/biopandas.pdb#pandaspdbdf) DataFrame dictionary though, which gives us access to the PDB files as pandas DataFrames. Let's print the first 3 lines from the `ATOM` coordinate section to see how it looks like:"
+    "The most interesting / useful attribute is the [`PandasPdb.df`](../api/biopandas.pdb#pandaspdbdf) DataFrame dictionary though, which gives us access to the PDB files as pandas DataFrames. Let's print the first 3 lines from the `ATOM` coordinate section to see how it looks like:"
    ]
   },
   {
@@ -373,7 +373,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "After loading a PDB file from rcsb.org or our local drive, the [`PandasPDB.df`](../api/biopandas.pdb/#pandaspdbdf) attribute should contain the following 4 DataFrame objects:"
+    "After loading a PDB file from rcsb.org or our local drive, the [`PandasPdb.df`](../api/biopandas.pdb/#pandaspdbdf) attribute should contain the following 4 DataFrame objects:"
    ]
   },
   {
@@ -395,8 +395,8 @@
     }
    ],
    "source": [
-    "from biopandas.pdb import PandasPDB\n",
-    "ppdb = PandasPDB()\n",
+    "from biopandas.pdb import PandasPdb\n",
+    "ppdb = PandasPdb()\n",
     "ppdb.read_pdb('./data/3eiy.pdb')\n",
     "ppdb.df.keys()"
    ]
@@ -954,8 +954,8 @@
     }
    ],
    "source": [
-    "from biopandas.pdb import PandasPDB\n",
-    "ppdb = PandasPDB()\n",
+    "from biopandas.pdb import PandasPdb\n",
+    "ppdb = PandasPdb()\n",
     "ppdb.read_pdb('./data/3eiy.pdb.gz')\n",
     "ppdb.df['ATOM'].head()"
    ]
@@ -1381,8 +1381,8 @@
    },
    "outputs": [],
    "source": [
-    "from biopandas.pdb import PandasPDB\n",
-    "ppdb = PandasPDB().read_pdb('./data/3eiy.pdb.gz')"
+    "from biopandas.pdb import PandasPdb\n",
+    "ppdb = PandasPdb().read_pdb('./data/3eiy.pdb.gz')"
    ]
   },
   {
@@ -1530,11 +1530,11 @@
     }
    ],
    "source": [
-    "from biopandas.pdb import PandasPDB\n",
+    "from biopandas.pdb import PandasPdb\n",
     "\n",
-    "l_1 = PandasPDB().read_pdb('./data/lig_conf_1.pdb')\n",
-    "l_2 = PandasPDB().read_pdb('./data/lig_conf_2.pdb')\n",
-    "r = PandasPDB.rmsd(l_1.df['HETATM'], l_2.df['HETATM'],\n",
+    "l_1 = PandasPdb().read_pdb('./data/lig_conf_1.pdb')\n",
+    "l_2 = PandasPdb().read_pdb('./data/lig_conf_2.pdb')\n",
+    "r = PandasPdb.rmsd(l_1.df['HETATM'], l_2.df['HETATM'],\n",
     "                   s=None) # all atoms, including hydrogens\n",
     "print('RMSD: %.4f Angstrom' % r)"
    ]
@@ -1555,7 +1555,7 @@
     }
    ],
    "source": [
-    "r = PandasPDB.rmsd(l_1.df['HETATM'], l_2.df['HETATM'], \n",
+    "r = PandasPdb.rmsd(l_1.df['HETATM'], l_2.df['HETATM'], \n",
     "                   s='carbon') # carbon atoms only\n",
     "print('RMSD: %.4f Angstrom' % r)"
    ]
@@ -1576,7 +1576,7 @@
     }
    ],
    "source": [
-    "r = PandasPDB.rmsd(l_1.df['HETATM'], l_2.df['HETATM'], \n",
+    "r = PandasPdb.rmsd(l_1.df['HETATM'], l_2.df['HETATM'], \n",
     "                   s='heavy') # heavy atoms only\n",
     "print('RMSD: %.4f Angstrom' % r)"
    ]
@@ -1613,9 +1613,9 @@
     }
    ],
    "source": [
-    "p_1 = PandasPDB().read_pdb('./data/1t48_995.pdb')\n",
-    "p_2 = PandasPDB().read_pdb('./data/1t49_995.pdb')\n",
-    "r = PandasPDB.rmsd(p_1.df['ATOM'], p_2.df['ATOM'], s='heavy')\n",
+    "p_1 = PandasPdb().read_pdb('./data/1t48_995.pdb')\n",
+    "p_2 = PandasPdb().read_pdb('./data/1t49_995.pdb')\n",
+    "r = PandasPdb.rmsd(p_1.df['ATOM'], p_2.df['ATOM'], s='heavy')\n",
     "print('RMSD: %.4f Angstrom' % r)"
    ]
   },
@@ -1642,9 +1642,9 @@
     }
    ],
    "source": [
-    "p_1 = PandasPDB().read_pdb('./data/1t48_995.pdb')\n",
-    "p_2 = PandasPDB().read_pdb('./data/1t49_995.pdb')\n",
-    "r = PandasPDB.rmsd(p_1.df['ATOM'], p_2.df['ATOM'], s='main chain')\n",
+    "p_1 = PandasPdb().read_pdb('./data/1t48_995.pdb')\n",
+    "p_2 = PandasPdb().read_pdb('./data/1t49_995.pdb')\n",
+    "r = PandasPdb.rmsd(p_1.df['ATOM'], p_2.df['ATOM'], s='main chain')\n",
     "print('RMSD: %.4f Angstrom' % r)"
    ]
   },
@@ -1677,7 +1677,7 @@
    },
    "outputs": [],
    "source": [
-    "p_1 = PandasPDB().read_pdb('./data/3eiy.pdb')\n",
+    "p_1 = PandasPdb().read_pdb('./data/3eiy.pdb')\n",
     "\n",
     "reference_point = (9.362, 41.410, 10.542)\n",
     "distances = p_1.distance(xyz=reference_point, record='ATOM')"
@@ -1940,8 +1940,8 @@
     }
    ],
    "source": [
-    "from biopandas.pdb import PandasPDB\n",
-    "ppdb = PandasPDB().read_pdb('./data/3eiy.pdb.gz')\n",
+    "from biopandas.pdb import PandasPdb\n",
+    "ppdb = PandasPdb().read_pdb('./data/3eiy.pdb.gz')\n",
     "ppdb.amino3to1()\n",
     "# By default, `amino3to1` returns a pandas Series object,\n",
     "# and to convert it into a Python list, you can wrap it in list\n",
@@ -1978,8 +1978,8 @@
    },
    "outputs": [],
    "source": [
-    "from biopandas.pdb import PandasPDB\n",
-    "ppdb = PandasPDB().read_pdb('./data/3eiy.pdb.gz')\n",
+    "from biopandas.pdb import PandasPdb\n",
+    "ppdb = PandasPdb().read_pdb('./data/3eiy.pdb.gz')\n",
     "ppdb.df['ATOM'] = ppdb.df['ATOM'][ppdb.df['ATOM']['element_symbol'] != 'H']"
    ]
   },
@@ -1987,7 +1987,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "We can save the file using the [`PandasPDB.to_pdb`](../api/biopandas.pdb#pandaspdbto_pdb) method:"
+    "We can save the file using the [`PandasPdb.to_pdb`](../api/biopandas.pdb#pandaspdbto_pdb) method:"
    ]
   },
   {
diff --git a/docs/sources/tutorials/Working_with_PDB_Structures_in_DataFrames.md b/docs/sources/tutorials/Working_with_PDB_Structures_in_DataFrames.md
index 661a3d0..43068b0 100644
--- a/docs/sources/tutorials/Working_with_PDB_Structures_in_DataFrames.md
+++ b/docs/sources/tutorials/Working_with_PDB_Structures_in_DataFrames.md
@@ -3,19 +3,19 @@
 
 ## Loading PDB Files
 
-There are 2 1/2 ways to load a PDB structure into a `PandasPDB` object.
+There are 2 1/2 ways to load a PDB structure into a `PandasPdb` object.
 
 
 #### 1
-PDB files can be directly fetched from The Protein Data Bank at [http://www.rcsb.org](http://www.rcsb.org) via its unique 4-letter after initializing a new [`PandasPDB`](../api/biopandas.pdb#pandaspdb) object and calling the [`fetch_pdb`](../api/biopandas.pdb#pandaspdbfetch_pdb) method:
+PDB files can be directly fetched from The Protein Data Bank at [http://www.rcsb.org](http://www.rcsb.org) via its unique 4-letter after initializing a new [`PandasPdb`](../api/biopandas.pdb#pandaspdb) object and calling the [`fetch_pdb`](../api/biopandas.pdb#pandaspdbfetch_pdb) method:
 
 
 ```python
-from biopandas.pdb import PandasPDB
+from biopandas.pdb import PandasPdb
 
-# Initialize a new PandasPDB object
+# Initialize a new PandasPdb object
 # and fetch the PDB file from rcsb.org
-ppdb = PandasPDB().fetch_pdb('3eiy')
+ppdb = PandasPdb().fetch_pdb('3eiy')
 ```
 
 #### 2 a)
@@ -30,7 +30,7 @@ ppdb.read_pdb('./data/3eiy.pdb')
 
 
 
-    <biopandas.pdb.pandas_pdb.PandasPDB at 0x104937cf8>
+    <biopandas.pdb.pandas_pdb.PandasPdb at 0x104937cf8>
 
 
 
@@ -46,7 +46,7 @@ ppdb.read_pdb('./data/3eiy.pdb.gz')
 
 
 
-    <biopandas.pdb.pandas_pdb.PandasPDB at 0x104937cf8>
+    <biopandas.pdb.pandas_pdb.PandasPdb at 0x104937cf8>
 
 
 
@@ -80,7 +80,7 @@ print('\nRaw PDB file contents:\n\n%s\n...' % ppdb.pdb_text[:1000])
     ...
 
 
-The most interesting / useful attribute is the [`PandasPDB.df`](../api/biopandas.pdb#pandaspdbdf) DataFrame dictionary though, which gives us access to the PDB files as pandas DataFrames. Let's print the first 3 lines from the `ATOM` coordinate section to see how it looks like:
+The most interesting / useful attribute is the [`PandasPdb.df`](../api/biopandas.pdb#pandaspdbdf) DataFrame dictionary though, which gives us access to the PDB files as pandas DataFrames. Let's print the first 3 lines from the `ATOM` coordinate section to see how it looks like:
 
 
 ```python
@@ -195,12 +195,12 @@ Below is an example of how this would look like in an actual PDB file:
     ATOM    153  CG2AVAL A  25      30.835  18.826  57.661  0.28 13.58      A1   C
     ATOM    154  CG2BVAL A  25      29.909  16.996  55.922  0.72 13.25      A1   C
 
-After loading a PDB file from rcsb.org or our local drive, the [`PandasPDB.df`](../api/biopandas.pdb/#pandaspdbdf) attribute should contain the following 4 DataFrame objects:
+After loading a PDB file from rcsb.org or our local drive, the [`PandasPdb.df`](../api/biopandas.pdb/#pandaspdbdf) attribute should contain the following 4 DataFrame objects:
 
 
 ```python
-from biopandas.pdb import PandasPDB
-ppdb = PandasPDB()
+from biopandas.pdb import PandasPdb
+ppdb = PandasPdb()
 ppdb.read_pdb('./data/3eiy.pdb')
 ppdb.df.keys()
 ```
@@ -474,8 +474,8 @@ In the previous sections, we've seen how to load PDB structures into DataFrames,
 
 
 ```python
-from biopandas.pdb import PandasPDB
-ppdb = PandasPDB()
+from biopandas.pdb import PandasPdb
+ppdb = PandasPdb()
 ppdb.read_pdb('./data/3eiy.pdb.gz')
 ppdb.df['ATOM'].head()
 ```
@@ -874,8 +874,8 @@ Since we are using pandas under the hood, which in turns uses matplotlib under t
 
 
 ```python
-from biopandas.pdb import PandasPDB
-ppdb = PandasPDB().read_pdb('./data/3eiy.pdb.gz')
+from biopandas.pdb import PandasPdb
+ppdb = PandasPdb().read_pdb('./data/3eiy.pdb.gz')
 ```
 
 
@@ -942,11 +942,11 @@ we can compute the RMSD as follows:
 
 
 ```python
-from biopandas.pdb import PandasPDB
+from biopandas.pdb import PandasPdb
 
-l_1 = PandasPDB().read_pdb('./data/lig_conf_1.pdb')
-l_2 = PandasPDB().read_pdb('./data/lig_conf_2.pdb')
-r = PandasPDB.rmsd(l_1.df['HETATM'], l_2.df['HETATM'],
+l_1 = PandasPdb().read_pdb('./data/lig_conf_1.pdb')
+l_2 = PandasPdb().read_pdb('./data/lig_conf_2.pdb')
+r = PandasPdb.rmsd(l_1.df['HETATM'], l_2.df['HETATM'],
                    s=None) # all atoms, including hydrogens
 print('RMSD: %.4f Angstrom' % r)
 ```
@@ -956,7 +956,7 @@ print('RMSD: %.4f Angstrom' % r)
 
 
 ```python
-r = PandasPDB.rmsd(l_1.df['HETATM'], l_2.df['HETATM'],
+r = PandasPdb.rmsd(l_1.df['HETATM'], l_2.df['HETATM'],
                    s='carbon') # carbon atoms only
 print('RMSD: %.4f Angstrom' % r)
 ```
@@ -966,7 +966,7 @@ print('RMSD: %.4f Angstrom' % r)
 
 
 ```python
-r = PandasPDB.rmsd(l_1.df['HETATM'], l_2.df['HETATM'],
+r = PandasPdb.rmsd(l_1.df['HETATM'], l_2.df['HETATM'],
                    s='heavy') # heavy atoms only
 print('RMSD: %.4f Angstrom' % r)
 ```
@@ -982,9 +982,9 @@ The hydrogen-free RMSD:
 
 
 ```python
-p_1 = PandasPDB().read_pdb('./data/1t48_995.pdb')
-p_2 = PandasPDB().read_pdb('./data/1t49_995.pdb')
-r = PandasPDB.rmsd(p_1.df['ATOM'], p_2.df['ATOM'], s='heavy')
+p_1 = PandasPdb().read_pdb('./data/1t48_995.pdb')
+p_2 = PandasPdb().read_pdb('./data/1t49_995.pdb')
+r = PandasPdb.rmsd(p_1.df['ATOM'], p_2.df['ATOM'], s='heavy')
 print('RMSD: %.4f Angstrom' % r)
 ```
 
@@ -995,9 +995,9 @@ Or the RMSD between the main chains only:
 
 
 ```python
-p_1 = PandasPDB().read_pdb('./data/1t48_995.pdb')
-p_2 = PandasPDB().read_pdb('./data/1t49_995.pdb')
-r = PandasPDB.rmsd(p_1.df['ATOM'], p_2.df['ATOM'], s='main chain')
+p_1 = PandasPdb().read_pdb('./data/1t48_995.pdb')
+p_2 = PandasPdb().read_pdb('./data/1t49_995.pdb')
+r = PandasPdb.rmsd(p_1.df['ATOM'], p_2.df['ATOM'], s='main chain')
 print('RMSD: %.4f Angstrom' % r)
 ```
 
@@ -1016,12 +1016,12 @@ Let's say we loaded a PDB structure, removed it from it's hydrogens:
 
 
 ```python
-from biopandas.pdb import PandasPDB
-ppdb = PandasPDB().read_pdb('./data/3eiy.pdb.gz')
+from biopandas.pdb import PandasPdb
+ppdb = PandasPdb().read_pdb('./data/3eiy.pdb.gz')
 ppdb.df['ATOM'] = ppdb.df['ATOM'][ppdb.df['ATOM']['element_symbol'] != 'H']
 ```
 
-We can save the file using the [`PandasPDB.to_pdb`](../api/biopandas.pdb#pandaspdbto_pdb) method:
+We can save the file using the [`PandasPdb.to_pdb`](../api/biopandas.pdb#pandaspdbto_pdb) method:
 
 
 ```python