def test_msonable(self):
legend = Legend(self.struct)
legend_dict = legend.as_dict()
legend_from_dict = Legend.from_dict(legend_dict)
assert legend.get_legend() == legend_from_dict.get_legend()
def get_scene_and_legend(self) -> Tuple[Scene, Dict[str, str]]:
legend = Legend(self.graph.structure,
color_scheme="VESTA",
cmap_range=None)
legend.uniform_radius = 0.3
scene = get_structure_graph_scene(
self.graph,
draw_image_atoms=True,
bonded_sites_outside_unit_cell=False,
hide_incomplete_edges=True,
explicitly_calculate_polyhedra_hull=False,
group_by_symmetry=True,
draw_polyhedra=False,
legend=legend)
scene.name = "DefectStructureComponentScene"
lattice: Lattice = self.graph.structure.lattice
origin = -self.graph.structure.lattice.get_cartesian_coords(
[0.5, 0.5, 0.5])
scene_json = scene.to_json()
for idx, i in enumerate(self.interstitials, 1):
site = Site(species=DummySpecie(),
coords=lattice.get_cartesian_coords(i.frac_coords))
interstitial_scene = site.get_scene(origin=origin)
interstitial_scene.name = f"i{idx}"
interstitial_scene.contents[0].contents[0].tooltip = f"i{idx}"
scene_json["contents"].append(interstitial_scene.to_json())
return scene_json, legend.get_legend()
def get_scene_and_legend(
graph: Optional[Union[StructureGraph, MoleculeGraph]],
name,
color_scheme=DEFAULTS["color_scheme"],
color_scale=None,
radius_strategy=DEFAULTS["radius_strategy"],
draw_image_atoms=DEFAULTS["draw_image_atoms"],
bonded_sites_outside_unit_cell=DEFAULTS[
"bonded_sites_outside_unit_cell"],
hide_incomplete_bonds=DEFAULTS["hide_incomplete_bonds"],
explicitly_calculate_polyhedra_hull=False,
scene_additions=None,
show_compass=DEFAULTS["show_compass"],
) -> Tuple[Scene, Dict[str, str]]:
# default scene name will be name of component, "_ct_..."
# strip leading _ since this will cause problems in JavaScript land
scene = Scene(name=name[1:])
if graph is None:
return scene, {}
struct_or_mol = StructureMoleculeComponent._get_struct_or_mol(graph)
# TODO: add radius_scale
legend = Legend(
struct_or_mol,
color_scheme=color_scheme,
radius_scheme=radius_strategy,
cmap_range=color_scale,
)
if isinstance(graph, StructureGraph):
scene = graph.get_scene(
draw_image_atoms=draw_image_atoms,
bonded_sites_outside_unit_cell=bonded_sites_outside_unit_cell,
hide_incomplete_edges=hide_incomplete_bonds,
explicitly_calculate_polyhedra_hull=
explicitly_calculate_polyhedra_hull,
legend=legend,
)
elif isinstance(graph, MoleculeGraph):
scene = graph.get_scene(legend=legend)
scene.name = name
if hasattr(struct_or_mol, "lattice"):
axes = struct_or_mol.lattice._axes_from_lattice()
# TODO: fix pop-in ?
axes.visible = show_compass
scene.contents.append(axes)
if scene_additions:
# TODO: need a Scene.from_json() to make this work
raise NotImplementedError
scene["contents"].append(scene_additions)
return scene.to_json(), legend.get_legend()
def get_scene_and_legend(
graph: Optional[Union[StructureGraph, MoleculeGraph]],
color_scheme=DEFAULTS["color_scheme"],
color_scale=None,
radius_strategy=DEFAULTS["radius_strategy"],
draw_image_atoms=DEFAULTS["draw_image_atoms"],
bonded_sites_outside_unit_cell=DEFAULTS[
"bonded_sites_outside_unit_cell"],
hide_incomplete_bonds=DEFAULTS["hide_incomplete_bonds"],
explicitly_calculate_polyhedra_hull=False,
scene_additions=None,
show_compass=DEFAULTS["show_compass"],
group_by_site_property=None,
) -> Tuple[Scene, Dict[str, str]]:
scene = Scene(name="StructureMoleculeComponentScene")
if graph is None:
return scene, {}
struct_or_mol = StructureMoleculeComponent._get_struct_or_mol(graph)
# TODO: add radius_scale
legend = Legend(
struct_or_mol,
color_scheme=color_scheme,
radius_scheme=radius_strategy,
cmap_range=color_scale,
)
if isinstance(graph, StructureGraph):
scene = graph.get_scene(
draw_image_atoms=draw_image_atoms,
bonded_sites_outside_unit_cell=bonded_sites_outside_unit_cell,
hide_incomplete_edges=hide_incomplete_bonds,
explicitly_calculate_polyhedra_hull=
explicitly_calculate_polyhedra_hull,
group_by_site_property=group_by_site_property,
legend=legend,
)
elif isinstance(graph, MoleculeGraph):
scene = graph.get_scene(legend=legend)
scene.name = "StructureMoleculeComponentScene"
if hasattr(struct_or_mol, "lattice"):
axes = struct_or_mol.lattice._axes_from_lattice()
axes.visible = show_compass
scene.contents.append(axes)
scene_json = scene.to_json()
if scene_additions:
# TODO: this might be cleaner if we had a Scene.from_json() method
scene_json["contents"].append(scene_additions)
return scene_json, legend.get_legend()
def get_scene_and_legend(
graph: Optional[Union[StructureGraph, MoleculeGraph]],
color_scale=None,
radius_strategy=DEFAULTS["radius_strategy"],
draw_image_atoms=DEFAULTS["draw_image_atoms"],
bonded_sites_outside_unit_cell=DEFAULTS[
"bonded_sites_outside_unit_cell"],
hide_incomplete_bonds=DEFAULTS["hide_incomplete_bonds"],
explicitly_calculate_polyhedra_hull=False,
scene_additions=None,
show_compass=DEFAULTS["show_compass"],
) -> Tuple[Scene, Dict[str, str]]:
scene = Scene(name="AceStructureMoleculeComponentScene")
if graph is None:
return scene, {}
structure = StructureComponent._get_structure(graph)
# TODO: add radius_scale
legend = Legend(
structure,
color_scheme="VESTA",
radius_scheme=radius_strategy,
cmap_range=color_scale,
)
scene = graph.get_scene(
draw_image_atoms=draw_image_atoms,
bonded_sites_outside_unit_cell=bonded_sites_outside_unit_cell,
hide_incomplete_edges=hide_incomplete_bonds,
explicitly_calculate_polyhedra_hull=
explicitly_calculate_polyhedra_hull,
legend=legend,
)
scene.name = "StructureComponentScene"
if hasattr(structure, "lattice"):
axes = structure.lattice._axes_from_lattice()
axes.visible = show_compass
scene.contents.append(axes)
scene = scene.to_json()
if scene_additions:
# TODO: need a Scene.from_json() to make this work
# raise NotImplementedError
scene["contents"].append(scene_additions)
return scene, legend.get_legend()
def get_scene_and_legend(self,
scene_additions=None
) -> Tuple[Scene, Dict[str, str]]:
legend = Legend(self.graph.structure,
color_scheme="VESTA",
radius_scheme="uniform",
cmap_range=None)
legend.uniform_radius = 0.2
scene = get_structure_graph_scene(
self.graph,
draw_image_atoms=True,
bonded_sites_outside_unit_cell=False,
hide_incomplete_edges=True,
explicitly_calculate_polyhedra_hull=False,
group_by_symmetry=False,
legend=legend)
scene.name = "DefectStructureComponentScene"
# axes = graph.structure.lattice._axes_from_lattice()
# axes.visible = True
# scene.contents.append(axes)
scene = scene.to_json()
if scene_additions:
scene["contents"].append(scene_additions)
lattice = self.graph.structure.lattice
origin = -self.graph.structure.lattice.get_cartesian_coords(
[0.5, 0.5, 0.5])
for name, frac_coords in self.vacancy_sites:
site = Site(species=DummySpecie(name),
coords=lattice.get_cartesian_coords(frac_coords))
vac_scene = site.get_scene(origin=origin)
vac_scene.name = f"{name}_{frac_coords}"
vac_scene.contents[0].contents[0].tooltip = name
scene["contents"].append(vac_scene.to_json())
return scene, legend.get_legend()
def test_get_color(self):
# test default
legend = Legend(self.struct, color_scheme="VESTA")
color = legend.get_color(self.sp0)
assert color == "#ffcccc"
# element-based color schemes shouldn't change if you supply a site
color = legend.get_color(self.sp0, site=self.site0)
assert color == "#ffcccc"
color = legend.get_color(self.sp2)
assert color == "#a67573"
assert legend.get_legend()["colors"] == {
"#a67573": "In",
"#fe0300": "O",
"#ffcccc": "H",
}
# test alternate
legend = Legend(self.struct, color_scheme="Jmol")
color = legend.get_color(self.sp0)
assert color == "#ffffff"
assert legend.get_legend()["colors"] == {
"#a67573": "In",
"#ff0d0d": "O",
"#ffffff": "H",
}
# test coloring by site properties
legend = Legend(self.struct, color_scheme="example_site_prop")
color = legend.get_color(self.sp0, site=self.site0)
assert color == "#b30326"
color = legend.get_color(self.sp1, site=self.site1)
assert color == "#dddcdb"
color = legend.get_color(self.sp2, site=self.site2)
assert color == "#7b9ef8"
assert legend.get_legend()["colors"] == {
"#7b9ef8": "-3.00",
"#b30326": "5.00",
"#dddcdb": "0.00",
}
# test accessible
legend = Legend(self.struct, color_scheme="accessible")
color = legend.get_color(self.sp0, site=self.site0)
assert color == "#ffffff"
color = legend.get_color(self.sp1, site=self.site1)
assert color == "#d55e00"
color = legend.get_color(self.sp2, site=self.site2)
assert color == "#cc79a7"
assert legend.get_legend()["colors"] == {
"#cc79a7": "In",
"#d55e00": "O",
"#ffffff": "H",
}
# test disordered
legend = Legend(self.struct_disordered)
color = legend.get_color(self.site_d_sp0, site=self.site_d)
assert color == "#a67573"
color = legend.get_color(self.site_d_sp1, site=self.site_d)
assert color == "#bfa6a6"
assert legend.get_legend()["colors"] == {
"#a67573": "In",
"#bfa6a6": "Al",
"#ff0d0d": "O",
"#ffffff": "H",
}
# test categorical
legend = Legend(self.struct,
color_scheme="example_categorical_site_prop")
assert legend.get_legend()["colors"] == {
"#377eb8": "8b",
"#e41a1c": "4a"
}
# test pre-defined
legend = Legend(self.struct_manual)
assert legend.get_legend()["colors"] == {
"#0000ff": "O2-",
"#00ff00": "In",
"#ff0000": "H",
}