Merge pull request #492 from CalCraven/vis_atype

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