Pandas simplification v2

gmso/core/topology.py

@@ -1250,83 +1250,6 @@ def write_forcefield(self, filename, overwrite=False):
         ff = self.get_forcefield()
         ff.to_xml(filename=filename, overwrite=overwrite)
 
-    def to_dataframe(self, parameter="sites", site_attrs=None, unyts_bool=True):
-        """Return a pandas dataframe object for the sites in a topology
-
-        Parameters
-        ----------
-        parameter : str, default='sites'
-            A string determining what aspects of the gmso topology will be reported.
-            Options are: 'sites', 'bonds', 'angles', 'dihedrals', and 'impropers'. Defaults to 'sites'.
-        site_attrs : list of str, default=None
-             List of strings that are attributes of the topology site and can be included as entries in the pandas dataframe.
-            Examples of these can be found by printing `topology.sites[0].__dict__`.
-            See https://gmso.mosdef.org/en/stable/data_structures.html#gmso.Atom for additional information on labeling.
-        unyts_bool: bool, default=True
-            Determine if numerical values are saved as unyt quantities or floats. See
-            https://unyt.readthedocs.io/en/stable/usage.html
-            for more information about manipulating unyt quantities.
-            Default is True.
-
-        Returns
-        -------
-        Pandas Dataframe
-            A pandas.Dataframe object, see https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.html
-            for further information.
-
-        Examples
-        ________
-        >>> topology.to_dataframe(parameter = 'sites', site_attrs = ['charge'])
-            This will return a dataframe with a listing of the sites and include the charges that correspond to each site.
-        >>> topology.to_dataframe(parameter = 'dihedrals', site_attrs = ['positions'])
-            This will return a dataframe with a listing of the sites that make up each dihedral, the positions of each of
-            those sites, and the parameters that are associated with the dihedrals.
-
-        Notes
-        ____
-        A dataframe is easily manipulated. In order to change the rounding to two decimals places for a column named `label`:
-            >>> df['label'] = df['label'].round(2)
-        The column labels can also be easily modified. This line can take a dataframe `df` and rename a column labeled
-        `Atom0` to `newname` using a dictionary.
-            >>> df.rename(columns = {'Atom0':'newname'})
-        See https://pandas.pydata.org/pandas-docs/stable/getting_started/intro_tutorials/index.html for further information.
-        """
-        from gmso.utils.io import import_
-
-        pd = import_("pandas")
-        if not site_attrs:
-            site_attrs = []
-        df = pd.DataFrame()
-        if not self.is_typed():
-            raise GMSOError(
-                "This topology is not typed, please type this object before converting to a pandas dataframe"
-            )
-        if parameter == "sites":
-            df["atom_types"] = list(site.atom_type.name for site in self.sites)
-            df["names"] = list(site.name for site in self.sites)
-            for attr in site_attrs:
-                df = self._parse_dataframe_attrs(df, attr, parameter, unyts_bool)
-        elif parameter in ["bonds", "angles", "dihedrals", "impropers"]:
-            if len(getattr(self, parameter)) == 0:
-                raise GMSOError(
-                    f"There arent any {parameter} in the topology. The dataframe would be empty."
-                )
-            df = self._pandas_from_parameters(
-                df,
-                parameter=parameter,
-                site_attrs=site_attrs,
-                unyts_bool=unyts_bool,
-            )
-            df = self._parse_parameter_expression(df, parameter, unyts_bool)
-        else:
-            raise AttributeError(
-                "{} is not yet supported for outputting parameters to a dataframe. \
-            Please use  one of 'sites', 'bonds', 'angles', 'dihedrals', or \
-            'impropers'".format(str(parameter))
-            )
-
-        return df
-
     def get_forcefield(self):
         """Get an instance of gmso.ForceField out of this topology
 

gmso/external/__init__.py

@@ -1,6 +1,7 @@
 # ruff: noqa: F401
 """Support for various in-memory representations of chemical systems."""
 
+from .convert_dataframe import to_dataframeDict
 from .convert_hoomd import (
     to_gsd_snapshot,
     to_hoomd_forcefield,