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update docstrings for interactive methods
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@CalCraven
CalCraven committed Apr 7, 2021
1 parent 3dde79b commit d203888
Showing 1 changed file with 95 additions and 57 deletions.
152 changes: 95 additions & 57 deletions gmso/formats/networkx.py
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Original file line number Diff line number Diff line change
Expand Up @@ -51,20 +51,22 @@ def interactive_networkx_atomtypes(topology, list_of_labels=None):
Any additonal labels can be appended from the list of:
`dir(list(topology.sites)[0])` or `dir(list(topology.sites)[0].atom_type)`
Returns
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
matplotlib.pyplot.figure
The drawn networkx plot of the topology on a matplotlib editable figures
matplotlib.pyplot.axis
The axis information that corresponds to that figure. This output can be
shown using
matplotlib.pyplot.show()
Label = What labels are shown on the networkx graph.
Atom_Name = Which sites will show these labels.
"""

networkx_graph = to_networkx(topology)
Expand Down Expand Up @@ -109,7 +111,34 @@ def interactive_networkx_bonds(topology, additional_labels=None):
Any additonal labels can be appended from the list of:
`dir(list(topology.sites)[0])` or `dir(list(topology.sites)[0].atom_type)`
Returns
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.
"""
-------
ipywidgets.Dropdown()
Three dropdown options, corresponding to:
Expand Down Expand Up @@ -224,30 +253,36 @@ def interactive_networkx_angles(topology):
This should be a gmso topology object that you want to visualize the angle types
that have been parameterized.

Returns
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 = The central site for which the angle can be visualized.
If it is not specified, missing angles will be shown.
Atom2 = An optional atom that will specify one end of the angle.
Atom3 = An optional atom that will specify the second end of the angle. Atom2
must be selected first.
Selected Angle = The dropdown will show all angles that match the above site
criteria. Angles are listed by three characterstic atomtypes. Multiple angles
may satisfy the selected angle, and so more than three edges may be selected
on the plot. Use the atomtype definitions to verify the correct angles.
matplotlib.pyplot.figure
The drawn networkx plot of the topology on a matplotlib editable figures. Thick dark red lines
indicate which angles have been selected.
ipywidgets.Checkbox()
Show parameters = True or False
Will determine if the necessary angle parameters for the selected angle type are shown
below the figure.
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.
"""
networkx_graph = to_networkx(topology)
# Create list of nodes to plot
Expand Down Expand Up @@ -316,32 +351,36 @@ def interactive_networkx_dihedrals(topology):
This should be a gmso topology object that you want to visualize the dihedral types
that have been parameterized.

Returns
Notes
-------
ipywidgets.Dropdown()
Three dropdown options, corresponding to:
Central Atom1 = One of the two central sites for which dihedrals can be visualized.
If it is not specified, missing dihedrals will be shown.
Central Atom2 = The second central site to select dihedrals. All dihedrals that
contain these two atom sites in their center will be listed. If it is not
specified, missing dihedrals will be shown.
Atom3 = An optional atom that will specify one end of the dihedral.
Atom4 = An optional atom that will specify the second end of the dihedral. Atom3
must be selected.
Selected Dihedral = The dropdown will show all dihedrals that match the above site
criteria. Dihedrals are listed by four characterstic atomtypes. Multiple dihedrals
may satisfy the selected dihedral, and so more than four edges may be selected
on the plot. Use the atomtype definitions to verify the correct dihedrals.
matplotlib.pyplot.figure
The drawn networkx plot of the topology on a matplotlib editable figures. Thick dark red lines
indicate which dihedrals have been selected.
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.Checkbox()
Show parameters = True or False
Will determine if the necessary dihedral parameters for the selected dihedral type are shown
below the figure.
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.
"""
networkx_graph = to_networkx(topology)
Expand Down Expand Up @@ -782,7 +821,6 @@ def get_edges(networkx_graph, atom_name1, atom_name2):
# Create a list of the edges that have been selected corresponding to the selected atom_name1
# and atom_name2. If both are None, then select edges that are missing bond types.
labeled_bonds = []
selectable_dict = {}
mia_bond_flag = 0
if atom_name1 and atom_name2:
Expand Down

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