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docs/api_modules/biopandas.mol2/PandasMol2.md

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+## PandasMol2
+
+*PandasMol2()*
+
+Object for working with Tripos Mol2 structure files.
+
+**Attributes**
+
+- `df` : pandas.DataFrame
+
+    DataFrame of a Mol2's ATOM section
+
+
+- `mol2_text` : str
+
+    Mol2 file contents in string format
+
+
+- `code` : str
+
+    ID, code, or name of the molecule stored
+
+
+- `pdb_path` : str
+
+    Location of the MOL2 file that was read in via `read_mol2`
+
+### Methods
+
+<hr>
+
+*distance(xyz=(0.0, 0.0, 0.0))*
+
+Computes Euclidean distance between atoms in
+    self.df and a 3D point.
+
+**Parameters**
+
+- `xyz` : tuple (0.00, 0.00, 0.00)
+
+    X, Y, and Z coordinate of the reference center for the distance
+    computation
+
+**Returns**
+
+- `pandas.Series` : Pandas Series object containing the Euclidean
+
+    distance between the atoms in the atom section and `xyz`.
+
+<hr>
+
+*distance_df(df, xyz=(0.0, 0.0, 0.0))*
+
+Computes Euclidean distance between atoms and a 3D point.
+
+**Parameters**
+
+- `df` : DataFrame
+
+    DataFrame containing entries similar to the PandasMol2.df
+    format for the
+    the distance computation to the `xyz` reference coordinates.
+
+- `xyz` : tuple (0.00, 0.00, 0.00)
+
+    X, Y, and Z coordinate of the reference center for the distance
+    computation
+
+**Returns**
+
+- `pandas.Series` : Pandas Series object containing the Euclidean
+
+    distance between the atoms in the atom section and `xyz`.
+
+<hr>
+
+*read_mol2(path, columns=None)*
+
+Reads Mol2 files (unzipped or gzipped) from local drive
+
+    Note that if your mol2 file contains more than one molecule,
+    only the first molecule is loaded into the DataFrame
+
+**Attributes**
+
+- `path` : str
+
+    Path to the Mol2 file in .mol2 format or gzipped format (.mol2.gz)
+
+
+- `columns` : dict or None (default: None)
+
+    If None, this methods expects a 9-column ATOM section that contains
+    the following columns:
+
+    {0:('atom_id', int), 1:('atom_name', str),
+    2:('x', float), 3:('y', float), 4:('z', float),
+    5:('atom_type', str), 6:('subst_id', int),
+    7:('subst_name', str), 8:('charge', float)}
+
+    If your Mol2 files are formatted differently, you can provide your
+    own column_mapping dictionary in a format similar to the one above.
+    However, note that not all assert_raise_message methods
+    may be supported then.
+
+**Returns**
+
+self
+
+<hr>
+
+*read_mol2_from_list(mol2_lines, mol2_code, columns=None)*
+
+Reads Mol2 file from a list into DataFrames
+
+**Attributes**
+
+- `mol2_lines` : list
+
+    A list of lines containing the mol2 file contents. For example,
+    ['@<TRIPOS>MOLECULE\n',
+    'ZINC38611810\n',
+    '   65    68     0     0     0\n',
+    'SMALL\n',
+    'NO_CHARGES\n',
+    '\n',
+    '@<TRIPOS>ATOM\n',
+    '      1 C1  -1.1786  2.7011  -4.0323 C.3  1 <0>   -0.1537\n',
+    '      2 C2  -1.2950  1.2442  -3.5798 C.3  1 <0>   -0.1156\n',
+    ...]
+
+
+- `mol2_code` : str or None
+
+    Name or ID of the molecule.
+
+
+- `columns` : dict or None (default: None)
+
+    If None, this methods expects a 9-column ATOM section that contains
+    the following columns:
+    {0:('atom_id', int), 1:('atom_name', str),
+    2:('x', float), 3:('y', float), 4:('z', float),
+    5:('atom_type', str), 6:('subst_id', int),
+    7:('subst_name', str), 8:('charge', float)}
+    If your Mol2 files are formatted differently, you can provide your
+    own column_mapping dictionary in a format similar to the one above.
+    However, note that not all assert_raise_message methods may be
+    supported then.
+
+**Returns**
+
+self
+
+<hr>
+
+*rmsd(df1, df2, heavy_only=True)*
+
+Compute the Root Mean Square Deviation between molecules
+
+**Parameters**
+
+- `df1` : pandas.DataFrame
+
+    DataFrame with HETATM, ATOM, and/or ANISOU entries
+
+- `df2` : pandas.DataFrame
+
+    Second DataFrame for RMSD computation against df1. Must have the
+    same number of entries as df1
+
+- `heavy_only` : bool (default: True)
+
+    Which atoms to compare to compute the RMSD. If `True` (default),
+    computes the RMSD between non-hydrogen atoms only.
+
+**Returns**
+
+- `rmsd` : float
+
+    Root Mean Square Deviation between df1 and df2
+
+### Properties
+
+<hr>
+
+*df*
+
+Acccesses the pandas DataFrame
+

docs/api_modules/biopandas.mol2/split_multimol2.md

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+## split_multimol2
+
+*split_multimol2(mol2_path)*
+
+Splits a multi-mol2 file into individual Mol2 file contents.
+
+**Parameters**
+
+- `mol2_path` : str
+
+    Path to the multi-mol2 file. Parses gzip files if the filepath
+    ends on .gz.
+
+**Returns**
+
+A generator object for lists for every extracted mol2-file. Lists contain
+    the molecule ID and the mol2 file contents.
+    e.g., ['ID1234', ['@<TRIPOS>MOLECULE\n', '...']]. Note that bytestrings
+    are returned (for reasons of efficieny) if the Mol2 content is read
+    from a gzip (.gz) file.
+