Functions to plot networkx graphs of topology objects

codecov.yml

@@ -1,3 +1,4 @@
 ignore:
  - "gmso/examples"
  - "gmso/tests"
+ - "gmso/formats/networkx.py"

environment-dev.yml

@@ -18,4 +18,6 @@ dependencies:
  - pytest-cov
  - codecov
  - bump2version
+ - matplotlib
+ - ipywidgets
  - ele >= 0.2.0

gmso/core/topology.py

@@ -616,7 +616,6 @@ def _get_bonds_for(self, site):
 
  def _get_angles_for(self, site):
  """Return a list of angles in this Topology that the site is a part of"""
-
  angles = []
  for angle in self.angles:
  if site in angle.connection_members:

gmso/formats/__init__.py

@@ -3,3 +3,5 @@
 from .gsd import write_gsd
 from .xyz import read_xyz, write_xyz
 from .lammpsdata import write_lammpsdata
+from .networkx import (interactive_networkx_atomtypes, interactive_networkx_bonds, 
+interactive_networkx_angles, interactive_networkx_dihedrals)

gmso/formats/networkx.py

@@ -0,0 +1,319 @@
+from gmso.utils.io import import_, has_ipywidgets, run_from_ipython
+from gmso.utils import nx_utils
+widgets = import_('ipywidgets')
+plt = import_('matplotlib.pyplot')
+if has_ipywidgets:
+ from ipywidgets import interact, fixed
+
+from gmso.external.convert_networkx import to_networkx
+
+def interactive_networkx_atomtypes(topology, list_of_labels=None):
+ """Get an interactive networkx plot showing the atom types of a topology object.
+
+ Parameters
+ ----------
+ topology : gmso.Topology
+ This should be a gmso topology object that you want to visualize the atom types
+ that have been parameterized.
+ list_of_labels : List[str]
+ Default labels are ['atom_type.name','charge','mass','element','label','position'].
+ Any additonal labels can be appended from the list of:
+ `dir(list(topology.sites)[0])` or `dir(list(topology.sites)[0].atom_type)`
+
+ Notes
+ -------
+ This function will output interactive ipywidgets. An ipywidgets dropdown object will
+ select which atomtypes that should be shown on the networkx graph object below. This
+ graph object is a visual representation for the connections within a gmso.Topology
+ object.
+ Select from a list of labels labels to be included on the graph.
+ See:
+ gmso.formats.networkx.interactive_networkx_bonds, gmso.formats.networkx.interactive_networkx_angles,
+ gmso.formats.networkx.interactive_networkx_dihedrals
+ for other interactive visualization methods.
+
+ ipywidgets.Dropdown()
+ Two dropdown options, corresponding to:
+ Label = What labels are shown on the networkx graph.
+ Atom_Name = Which sites will show these labels.
+ """
+
+ if not run_from_ipython():
+ raise RuntimeError("Unsupported visualization outside of jupyter notebooks.")
+ networkx_graph = to_networkx(topology)
+ # get a unique list of site names
+ site_names = []
+ for node in networkx_graph.nodes:
+ site_names.append(node.name)
+ site_names = set(site_names)
+
+ # create a tuple of selectable names for each site
+ names_tuple = []
+ names_tuple.append(("All Sites", None))
+ for name in site_names:
+ names_tuple.append((name, name))
+
+ # Create list of labels to put on plot
+ if not list_of_labels:
+ list_of_labels = []
+ base_list = ["atom_type.name", "charge", "mass", "element", "label", "position"]
+ list_of_labels += base_list
+
+ @interact
+ def get_interactive_sites(Label=list_of_labels, Atom_Name=names_tuple):
+ # Plot atom types for the widget inputs
+ nx_utils.plot_networkx_atomtypes(topology, Atom_Name, [Label])
+
+ return
+
+ return
+
+
+def interactive_networkx_bonds(topology, additional_labels=None):
+ """Get an interactive networkx plot showing the bond types of a topology object.
+
+ Parameters
+ ----------
+ topology : A gmso.core.topology.Topology object
+ This should be a gmso topology object that you want to visualize the atom types
+ that have been parameterized.
+ additonal_labels : Labels at each site to be included on the plot.
+ Default labels are ['atom_type.name'].
+ Any additonal labels can be appended from the list of:
+ `dir(list(topology.sites)[0])` or `dir(list(topology.sites)[0].atom_type)`
+
+ Notes
+ -------
+ This function will output interactive ipywidgets. An ipywidgets dropdown object will
+ select which atom names that will make up the bonds shown on the networkx graph object below.
+ This graph object is a visual representation for the connections within a gmso.Topology
+ object, and the bonds that makeup that bondtype are highlighted in red.
+ Select from a list of available sites, the sites that make up bonds to be highlighted on the graph.
+ See:
+ gmso.formats.networkx.interactive_networkx_atomtypes, gmso.formats.networkx.interactive_networkx_angles,
+ gmso.formats.networkx.interactive_networkx_dihedrals
+ for other interactive visualization methods.
+
+ ipywidgets.Dropdown()
+ Two dropdown options, corresponding to:
+ Atom1 (req) = Filters through all bonds to find bonds that contain this site. If not specified,
+ only bonds with missing bondtypes will be highlighted (in red).
+ Atom2 (opt) = A second site to specify which bonds can be selected on the graph.
+ A third dropdown option:
+ list_of_bonds = a list of the bonds labeled by the types that makeup the two sites.
+
+ matplotlib.pyplot.figure()
+ A figure showing the networkx.graph object of the molecule with highlighted edges corresponding to the
+ selected bonds
+
+ ipywidgets.checkbox()
+ A checkbox that will allow you to print the parameters associated with the selected bond in the list_of_bonds
+ dropdown option.
+ """
+ if not run_from_ipython():
+ raise RuntimeError("Unsupported visualization outside of jupyter notebooks.")
+ networkx_graph = to_networkx(topology)
+
+ # Create a list of labels to go on the nodes
+ if not additional_labels:
+ additional_labels = []
+ base_list = ["atom_type.name"]
+ list_of_labels = base_list + additional_labels
+
+ # Create list of nodes to plot
+ site_names = []
+ for node in networkx_graph.nodes:
+ site_names.append(node.name)
+ site_names = set(site_names)
+
+ # Create a tuple of keys for each selected site
+ names_tuple = []
+ names_tuple.append(("All Sites", None))
+ for name in site_names:
+ names_tuple.append((name, name))
+ atom_selection = []
+ descriptions = ["Atom1 (req)", "Atom2 (opt)"]
+ for i in [0, 1]:
+ atom_selection.append(
+ widgets.Dropdown(
+ options=names_tuple,
+ layout=widgets.Layout(width="30%"),
+ style=dict(description_width="initial"),
+ description=descriptions[i],
+ )
+ )
+ interact(
+ nx_utils.call_interactive_sites,
+ Atom1=atom_selection[0],
+ Atom2=atom_selection[1],
+ list_of_labels=fixed(list_of_labels),
+ networkx_graph=fixed(networkx_graph),
+ topology=fixed(topology),
+ )
+
+ return
+
+
+def interactive_networkx_angles(topology):
+ """Get an interactive networkx plot showing the angle types of a topology object.
+
+ Parameters
+ ----------
+ topology : A gmso.core.topology.Topology object
+ This should be a gmso topology object that you want to visualize the angle types
+ that have been parameterized.
+
+ Notes
+ -------
+ This function will output interactive ipywidgets. An ipywidgets dropdown object will
+ select which atom names that will make up the angles shown on the networkx graph object below.
+ This graph object is a visual representation for the connections within a gmso.Topology
+ object.
+ Select from a list of available sites, the sites that make up angles to be highlighted (in red) on the graph.
+ See:
+ gmso.formats.networkx.interactive_networkx_atomtypes, gmso.formats.networkx.interactive_networkx_bonds,
+ gmso.formats.networkx.interactive_networkx_dihedrals
+ for other interactive visualization methods.
+
+ ipywidgets.Dropdown()
+ Three dropdown options, corresponding to:
+ Central Atom1 (req) = Filters through all angles to find angles that contain this site as the center of the angle.
+ If not specified only angles with missing angletypes will be highlighted.
+ Atom2 (opt) = A second site to filter which angles can be selected on the graph.
+ Atom3 (opt) = A third site to filter which angles can be selected on the graph.
+ A fourth dropdown option:
+ Selected Edge = a list of the angles labeled by the types that makeup the three sites.
+
+ matplotlib.pyplot.figure()
+ A figure showing the networkx.graph object of the molecule with highlighted (in red) edges corresponding to the
+ selected angles.
+
+ ipywidgets.checkbox()
+ A checkbox that will allow you to print the parameters associated with the selected angle in the Selected Edge
+ dropdown option.
+ """
+ if not run_from_ipython():
+ raise RuntimeError("Unsupported visualization outside of jupyter notebooks.")
+
+ networkx_graph = to_networkx(topology)
+
+ # Create list of nodes to plot
+ site_names = []
+ for node in networkx_graph.nodes:
+ site_names.append(node.name)
+ site_names = set(site_names)
+
+ # Create a tuple of keys for each selected site
+ names_tuple = []
+ names_tuple.append(("All Sites", None))
+ for name in site_names:
+ names_tuple.append((name, name))
+
+ # Call recursive interacts. The top level determines what bonds can be selected
+ atom_selection = []
+ descriptions = ["Central Atom1 (req)", "Atom2 (opt)", "Atom3 (opt)"]
+ for i in [0, 1, 2]:
+ atom_selection.append(
+ widgets.Dropdown(
+ options=names_tuple,
+ layout=widgets.Layout(width="30%"),
+ style=dict(description_width="initial"),
+ description=descriptions[i],
+ )
+ )
+ interact(
+ nx_utils.select_angles_from_sites,
+ networkx_graph=fixed(networkx_graph),
+ top=fixed(topology),
+ Atom1=atom_selection[0],
+ Atom2=atom_selection[1],
+ Atom3=atom_selection[2],
+ )
+
+ return
+
+
+def interactive_networkx_dihedrals(topology):
+ """Get an interactive networkx plot showing the dihedral types of a topology object.
+
+ Parameters
+ ----------
+ topology : A gmso.core.topology.Topology object
+ This should be a gmso topology object that you want to visualize the dihedral types
+ that have been parameterized.
+
+ Notes
+ -------
+ This function will output interactive ipywidgets. An ipywidgets dropdown object will
+ select which atom names that will make up the dihedrals shown on the networkx graph object below.
+ This graph object is a visual representation for the connections within a gmso.Topology
+ object.
+ Select from a list of available sites, the sites that make up dihedrals to be highlighted (in red) on the graph.
+ See:
+ gmso.formats.networkx.interactive_networkx_atomtypes, gmso.formats.networkx.interactive_networkx_bonds,
+ gmso.formats.networkx.interactive_networkx_angles
+ for other interactive visualization methods.
+
+ ipywidgets.Dropdown()
+ Four dropdown options, corresponding to:
+ Central Atom1 (req) = Filters through all bonds to find dihedrals that contain this site in one of its central
+ two positions. If not specified, only dihedrals with missing dihedraltypes will be highlighted.
+ Central Atom2 (req) = Filters through all bonds to find dihedrals that contain this site in one of its central
+ two positions. If not specified, only dihedrals with missing dihedraltypes will be highlighted.
+ Atom3 (opt) = A third site to filter which dihedrals can be selected on the graph.
+ Atom4 (opt) = A fourth site to filter which dihedrals can be selected on the graph.
+ A fourth dropdown option:
+ Selected Edge = a list of the angles labeled by the types that makeup the three sites.
+
+ matplotlib.pyplot.figure()
+ A figure showing the networkx.graph object of the molecule with highlighted (in red) edges corresponding to the
+ selected dihedrals.
+
+ ipywidgets.checkbox()
+ A checkbox that will allow you to print the parameters associated with the selected dihedral in the Selected Edge
+ dropdown option.
+ """
+ if not run_from_ipython():
+ raise RuntimeError("Unsupported visualization outside of jupyter notebooks.")
+
+ networkx_graph = to_networkx(topology)
+ # Create list of nodes to plot
+ site_names = []
+ for node in networkx_graph.nodes:
+ site_names.append(node.name)
+ site_names = set(site_names)
+
+ # Create a tuple of keys for each selected site
+ names_tuple = []
+ names_tuple.append(("All Sites", None))
+ for name in site_names:
+ names_tuple.append((name, name))
+
+ # Call recursive interacts. The top level determines what bonds can be selected
+ atom_selection = []
+ descriptions = [
+ "Central Atom1 (req)",
+ "Central Atom2 (req)",
+ "Atom3 (opt)",
+ "Atom4 (opt)",
+ ]
+ for i in [0, 1, 2, 3]:
+ atom_selection.append(
+ widgets.Dropdown(
+ options=(names_tuple),
+ layout=widgets.Layout(width="30%"),
+ style=dict(description_width="initial"),
+ description=descriptions[i],
+ )
+ )
+ interact(
+ nx_utils.select_dihedrals_from_sites,
+ networkx_graph=fixed(networkx_graph),
+ top=fixed(topology),
+ Atom1=atom_selection[0],
+ Atom2=atom_selection[1],
+ Atom3=atom_selection[2],
+ Atom4=atom_selection[3],
+ )
+
+ return