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Methods for converting to Pandas Dataframes (#524)
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* add base functions for converting to dataframes

* update atomtypes_to_dataframes so it can handle labels that need to be split at a '.'

* add functions for plotting connection parameters

* add docstrings for unit conversions, create a function that includes specified labels in the dataframes objest

* apply black

* add associated unyt tests

* remove unused variable

* fix charge output from bonds

* Add unit tests for labels with a  and parameter sites

* fix bug with testing charges read into pandas df

* update position values used in test__pandas_df

* delete changes brought in for networkx visualization PR

* fixes for testing bugs

* delete requirements-test.txt

* add generalization for parameters in different bonds, angles, dihedrals. Also, add a unyts_bool flag to allow someone to output numeric quantities as unyt quantities or floats

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* change function name from to_datatables to data_frame

* address reviews and add a few modular functions to break up into smaller bits. Add improper support

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* Update gmso/core/topology.py

Co-authored-by: Umesh Timalsina <umesh.timalsina@vanderbilt.edu>

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* use unyt_to_dict to handle printing units in tables

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* fix units on charge conversions

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* allow for optional pandas dependency

* replace labels argument for to_dataframes function with site_attrs to make it more clear what is being output to the dataframe

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* Fix bug in gmso/tests/test_topology.py test_to_dataframe

* remove has_pandas import in test_topology.py

* Push import_ for soft import of pandas directly into to_dataframe function within topology.py

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* Update gmso/tests/test_topology.py

Co-authored-by: Umesh Timalsina <umesh.timalsina@vanderbilt.edu>

* Add pandas dependency to environment-dev.yml for testing

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* replace missing code in index connections function.

* Update gmso/core/topology.py

Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>

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* Use f string formatting

Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>

* f string formatting

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* f string formatting

Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>

* f string formatting

Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>

* f string formatting

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* Fixes for more f-string formatting, added default unit registry for conversion of elementary_charge units

* Add tests for unit registry module adding new unit values

* fixes to default registry calls

---------

Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Justin Gilmer <justin.b.gilmer@vanderbilt.edu>
Co-authored-by: Umesh Timalsina <umesh.timalsina@vanderbilt.edu>
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@ dependencies:
- ipywidgets
- ele>=0.2.0
- pre-commit
- pandas
- symengine
- python-symengine
- hoomd>=3
274 changes: 274 additions & 0 deletions gmso/core/topology.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@

import gmso
from gmso.abc.abstract_site import Site
from gmso.abc.serialization_utils import unyt_to_dict
from gmso.core.angle import Angle
from gmso.core.angle_type import AngleType
from gmso.core.atom import Atom
Expand All @@ -25,6 +26,7 @@
from gmso.utils.connectivity import (
identify_connections as _identify_connections,
)
from gmso.utils.units import GMSO_UnitRegsitry as UnitReg

scaling_interaction_idxes = {"12": 0, "13": 1, "14": 2}

Expand Down Expand Up @@ -1157,6 +1159,87 @@ def get_index(self, member):

return index

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
Expand Down Expand Up @@ -1417,6 +1500,190 @@ def __str__(self):
"""Return custom format to represent topology as a string."""
return f"<Topology {self.name}, {self.n_sites} sites, id: {id(self)}>"

def _pandas_from_parameters(
self, df, parameter, site_attrs=None, unyts_bool=True
):
"""Add to a pandas dataframe the site indices for each connection member in a
multimember topology attribute such as a bond. Also include information about
those sites in the site_attrs list"""
if site_attrs is None:
site_attrs = []
sites_per_connection = len(
getattr(self, parameter)[0].connection_members
)
for site_index in np.arange(sites_per_connection):
df["Atom" + str(site_index)] = list(
str(connection.connection_members[site_index].name)
+ f"({self.get_index(connection.connection_members[site_index])})"
for connection in getattr(self, parameter)
)
for attr in site_attrs:
df = self._parse_dataframe_attrs(
df, attr, parameter, sites_per_connection, unyts_bool
)
return df

def _parse_dataframe_attrs(
self, df, attr, parameter, sites_per_connection=1, unyts_bool=True
):
"""Parses an attribute string to correctly format and return the topology attribute
into a pandas dataframe"""
if parameter == "sites":
if "." in attr:
try:
attr1, attr2 = attr.split(".")
df[attr] = list(
_return_float_for_unyt(
getattr(getattr(site, attr1), attr2),
unyts_bool,
)
for site in self.sites
)
except AttributeError:
raise AttributeError(
f"The attribute {attr} is not in this gmso object."
)
elif attr == "positions" or attr == "position":
for i, dimension in enumerate(["x", "y", "z"]):
df[dimension] = list(
_return_float_for_unyt(
getattr(site, "position")[i], unyts_bool
)
for site in self.sites
)
elif attr == "charge" or attr == "charges":
df["charge (e)"] = list(
site.charge.in_units(
u.Unit(
"elementary_charge", registry=UnitReg.default_reg()
)
).to_value()
for site in self.sites
)
else:
try:
df[attr] = list(
_return_float_for_unyt(getattr(site, attr), unyts_bool)
for site in self.sites
)
except AttributeError:
raise AttributeError(
f"The attribute {attr} is not in this gmso object."
)

elif parameter in ["bonds", "angles", "dihedrals", "impropers"]:
for site_index in np.arange(sites_per_connection):
if "." in attr:
try:
attr1, attr2 = attr.split(".")
df[attr + " Atom" + str(site_index)] = list(
_return_float_for_unyt(
getattr(
getattr(
connection.connection_members[
site_index
],
attr1,
),
attr2,
),
unyts_bool,
)
for connection in getattr(self, parameter)
)
except AttributeError:
raise AttributeError(
f"The attribute {attr} is not in this gmso object."
)
elif attr == "positions" or attr == "position":
df["x Atom" + str(site_index) + " (nm)"] = list(
_return_float_for_unyt(
getattr(
connection.connection_members[site_index],
"position",
)[0],
unyts_bool,
)
for connection in getattr(self, parameter)
)
df["y Atom" + str(site_index) + " (nm)"] = list(
_return_float_for_unyt(
getattr(
connection.connection_members[site_index],
"position",
)[1],
unyts_bool,
)
for connection in getattr(self, parameter)
)
df["z Atom" + str(site_index) + " (nm)"] = list(
_return_float_for_unyt(
getattr(
connection.connection_members[site_index],
"position",
)[2],
unyts_bool,
)
for connection in getattr(self, parameter)
)
elif attr == "charge" or attr == "charges":
df["charge Atom" + str(site_index) + " (e)"] = list(
getattr(
connection.connection_members[site_index],
"charge",
)
.in_units(
u.Unit(
"elementary_charge",
registry=UnitReg.default_reg(),
)
)
.value
for connection in getattr(self, parameter)
)
else:
try:
df[f"{attr} Atom {site_index}"] = list(
_return_float_for_unyt(
getattr(
connection.connection_members[site_index],
attr,
),
unyts_bool,
)
for connection in getattr(self, parameter)
)
except AttributeError:
raise AttributeError(
f"The attribute {attr} is not in this gmso object."
)
else:
raise AttributeError(
f"{parameter} is not yet supported for adding labels to a dataframe. \
Please use one of 'sites', 'bonds', 'angles', 'dihedrals', or 'impropers'"
)
return df

def _parse_parameter_expression(self, df, parameter, unyts_bool):
"""Take a given topology attribute and return the parameters associated with it"""
for i, param in enumerate(
getattr(
getattr(self, parameter)[0], parameter[:-1] + "_type"
).parameters
):
df[
f"Parameter {i} ({param}) {getattr(getattr(self, parameter)[0], parameter[:-1]+'_type').parameters[param].units}"
] = list(
_return_float_for_unyt(
getattr(connection, parameter[:-1] + "_type").parameters[
param
],
unyts_bool,
)
for connection in getattr(self, parameter)
)
return df

@classmethod
def load(cls, filename, **kwargs):
"""Load a file to a topology"""
Expand All @@ -1425,3 +1692,10 @@ def load(cls, filename, **kwargs):

loader = LoadersRegistry.get_callable(filename.suffix)
return loader(filename, **kwargs)


def _return_float_for_unyt(unyt_quant, unyts_bool):
try:
return unyt_quant if unyts_bool else unyt_to_dict(unyt_quant)["array"]
except TypeError:
return unyt_quant
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