# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
# Distributed under the terms of "New BSD License", see the LICENSE file.
import warnings
from typing import Any
import numpy as np
from ase.atoms import Atoms
from scipy.interpolate import interp1d
from structuretoolkit.common.helper import get_cell
__author__ = "Joerg Neugebauer, Sudarsan Surendralal"
__copyright__ = (
"Copyright 2021, Max-Planck-Institut für Eisenforschung GmbH - "
"Computational Materials Design (CM) Department"
)
__version__ = "1.0"
__maintainer__ = "Sudarsan Surendralal"
__email__ = "surendralal@mpie.de"
__status__ = "production"
__date__ = "Sep 1, 2017"
[docs]
def plot3d(
structure: Atoms,
mode: str = "NGLview",
show_cell: bool = True,
show_axes: bool = True,
camera: str = "orthographic",
spacefill: bool = True,
particle_size: float = 1.0,
select_atoms: np.ndarray | None = None,
background: str = "white",
color_scheme: str | None = None,
colors: np.ndarray | None = None,
scalar_field: np.ndarray | None = None,
scalar_start: float | None = None,
scalar_end: float | None = None,
scalar_cmap: Any | None = None,
vector_field: np.ndarray | None = None,
vector_color: np.ndarray | None = None,
magnetic_moments: bool = False,
view_plane: np.ndarray = np.array([0, 0, 1]),
distance_from_camera: float = 1.0,
opacity: float = 1.0,
height: float | None = None,
):
"""
Plot3d relies on NGLView or plotly to visualize atomic structures. Here, we construct a string in the "protein database"
The final widget is returned. If it is assigned to a variable, the visualization is suppressed until that
variable is evaluated, and in the meantime more NGL operations can be applied to it to modify the visualization.
Args:
mode (str): `NGLView`, `plotly` or `ase`
show_cell (bool): Whether or not to show the frame. (Default is True.)
show_axes (bool): Whether or not to show xyz axes. (Default is True.)
camera (str): 'perspective' or 'orthographic'. (Default is 'perspective'.)
spacefill (bool): Whether to use a space-filling or ball-and-stick representation. (Default is True, use
space-filling atoms.)
particle_size (float): Size of the particles. (Default is 1.)
select_atoms (numpy.ndarray): Indices of atoms to show, either as integers or a boolean array mask.
(Default is None, show all atoms.)
background (str): Background color. (Default is 'white'.)
color_scheme (str): NGLView color scheme to use. (Default is None, color by element.)
colors (numpy.ndarray): A per-atom array of HTML color names or hex color codes to use for atomic colors.
(Default is None, use coloring scheme.)
scalar_field (numpy.ndarray): Color each atom according to the array value (Default is None, use coloring
scheme.)
scalar_start (float): The scalar value to be mapped onto the low end of the color map (lower values are
clipped). (Default is None, use the minimum value in `scalar_field`.)
scalar_end (float): The scalar value to be mapped onto the high end of the color map (higher values are
clipped). (Default is None, use the maximum value in `scalar_field`.)
scalar_cmap (matplotlib.cm): The colormap to use. (Default is None, giving a blue-red divergent map.)
vector_field (numpy.ndarray): Add vectors (3 values) originating at each atom. (Default is None, no
vectors.)
vector_color (numpy.ndarray): Colors for the vectors (only available with vector_field). (Default is None,
vectors are colored by their direction.)
magnetic_moments (bool): Plot magnetic moments as 'scalar_field' or 'vector_field'.
view_plane (numpy.ndarray): A Nx3-array (N = 1,2,3); the first 3d-component of the array specifies
which plane of the system to view (for example, [1, 0, 0], [1, 1, 0] or the [1, 1, 1] planes), the
second 3d-component (if specified, otherwise [1, 0, 0]) gives the horizontal direction, and the third
component (if specified) is the vertical component, which is ignored and calculated internally. The
orthonormality of the orientation is internally ensured, and therefore is not required in the function
call. (Default is np.array([0, 0, 1]), which is view normal to the x-y plane.)
distance_from_camera (float): Distance of the camera from the structure. Higher = farther away.
(Default is 14, which also seems to be the NGLView default value.)
height (int/float/None): height of the plot area in pixel (only
available in plotly) Default: 600
Possible NGLView color schemes:
" ", "picking", "random", "uniform", "atomindex", "residueindex",
"chainindex", "modelindex", "sstruc", "element", "resname", "bfactor",
"hydrophobicity", "value", "volume", "occupancy"
Returns:
(nglview.NGLWidget): The NGLView widget itself, which can be operated on further or viewed as-is.
Warnings:
* Many features only work with space-filling atoms (e.g. coloring by a scalar field).
* The colour interpretation of some hex codes is weird, e.g. 'green'.
"""
if mode == "NGLview":
if height is not None:
warnings.warn(
"`height` is not implemented in NGLview", SyntaxWarning, stacklevel=2
)
return _plot3d(
structure=structure,
show_cell=show_cell,
show_axes=show_axes,
camera=camera,
spacefill=spacefill,
particle_size=particle_size,
select_atoms=select_atoms,
background=background,
color_scheme=color_scheme,
colors=colors,
scalar_field=scalar_field,
scalar_start=scalar_start,
scalar_end=scalar_end,
scalar_cmap=scalar_cmap,
vector_field=vector_field,
vector_color=vector_color,
magnetic_moments=magnetic_moments,
view_plane=view_plane,
distance_from_camera=distance_from_camera,
)
elif mode == "plotly":
return _plot3d_plotly(
structure=structure,
show_cell=show_cell,
camera=camera,
particle_size=particle_size,
select_atoms=select_atoms,
scalar_field=scalar_field,
view_plane=view_plane,
distance_from_camera=distance_from_camera,
opacity=opacity,
height=height,
)
elif mode == "ase":
if height is not None:
warnings.warn(
"`height` is not implemented in ase", SyntaxWarning, stacklevel=2
)
return _plot3d_ase(
structure=structure,
show_cell=show_cell,
show_axes=show_axes,
camera=camera,
spacefill=spacefill,
particle_size=particle_size,
background=background,
color_scheme=color_scheme if color_scheme is not None else "element",
)
else:
raise ValueError("plot method not recognized")
def _get_box_skeleton(cell: np.ndarray) -> np.ndarray:
"""
Generate the skeleton of a box defined by the unit cell.
Args:
cell (np.ndarray): The unit cell of the structure.
Returns:
np.ndarray: The skeleton of the box defined by the unit cell.
"""
lines_dz = np.stack(np.meshgrid(*3 * [[0, 1]], indexing="ij"), axis=-1)
# eight corners of a unit cube, paired as four z-axis lines
all_lines = np.reshape(
[np.roll(lines_dz, i, axis=-1) for i in range(3)], (-1, 2, 3)
)
# All 12 two-point lines on the unit square
return all_lines @ cell
def _draw_box_plotly(fig: Any, structure: Atoms, px: Any, go: Any) -> Any:
"""
Draw the box skeleton of the atomic structure using Plotly.
Args:
fig (go.Figure): The Plotly figure object.
structure (Atoms): The atomic structure.
px (Any): The Plotly express module.
go (Any): The Plotly graph objects module.
Returns:
go.Figure: The updated Plotly figure object.
"""
cell = get_cell(structure)
data = fig.data
for lines in _get_box_skeleton(cell):
fig = px.line_3d(**dict(zip(["x", "y", "z"], lines.T, strict=True)))
fig.update_traces(line_color="#000000")
data = fig.data + data
return go.Figure(data=data)
def _plot3d_plotly(
structure: Atoms,
show_cell: bool = True,
scalar_field: np.ndarray | None = None,
select_atoms: np.ndarray | None = None,
particle_size: float = 1.0,
camera: str = "orthographic",
view_plane: np.ndarray = np.array([1, 1, 1]),
distance_from_camera: float = 1.0,
opacity: float = 1.0,
height: float | None = None,
):
"""
Make a 3D plot of the atomic structure.
Args:
camera (str): 'perspective' or 'orthographic'. (Default is 'perspective'.)
particle_size (float): Size of the particles. (Default is 1.)
scalar_field (numpy.ndarray): Color each atom according to the array value (Default is None, use coloring
scheme.)
view_plane (numpy.ndarray): A Nx3-array (N = 1,2,3); the first 3d-component of the array specifies
which plane of the system to view (for example, [1, 0, 0], [1, 1, 0] or the [1, 1, 1] planes), the
second 3d-component (if specified, otherwise [1, 0, 0]) gives the horizontal direction, and the third
component (if specified) is the vertical component, which is ignored and calculated internally. The
orthonormality of the orientation is internally ensured, and therefore is not required in the function
call. (Default is np.array([0, 0, 1]), which is view normal to the x-y plane.)
distance_from_camera (float): Distance of the camera from the structure. Higher = farther away.
(Default is 14, which also seems to be the NGLView default value.)
opacity (float): opacity
height (int/float/None): height of the plot area in pixel. Default: 600
Returns:
(plotly.express): The NGLView widget itself, which can be operated on further or viewed as-is.
"""
try:
import plotly.express as px
import plotly.graph_objects as go
except ModuleNotFoundError:
raise ModuleNotFoundError("plotly not installed - use plot3d instead")
if select_atoms is None:
select_atoms = np.arange(len(structure))
elements = structure.get_chemical_symbols()
atomic_numbers = structure.get_atomic_numbers()
if scalar_field is None:
scalar_field = elements
fig = px.scatter_3d(
x=structure.positions[select_atoms, 0],
y=structure.positions[select_atoms, 1],
z=structure.positions[select_atoms, 2],
color=scalar_field,
opacity=opacity,
size=_atomic_number_to_radius(
atomic_numbers,
scale=particle_size / (0.1 * structure.get_volume() ** (1 / 3)),
),
)
if show_cell:
fig = _draw_box_plotly(fig, structure, px, go)
fig.layout.scene.camera.projection.type = camera
rot = _get_orientation(view_plane).T
rot[0, :] *= distance_from_camera * 1.25
angle = {
"up": {"x": rot[2, 0], "y": rot[2, 1], "z": rot[2, 2]},
"eye": {"x": rot[0, 0], "y": rot[0, 1], "z": rot[0, 2]},
}
fig.update_layout(scene_camera=angle)
fig.update_traces(marker={"line": {"width": 0.1, "color": "DarkSlateGrey"}})
fig.update_scenes(aspectmode="data")
if height is None:
height = 600
fig.update_layout(autosize=True, height=height)
fig.update_layout(legend={"itemsizing": "constant"})
return fig
def _plot3d(
structure: Atoms,
show_cell: bool = True,
show_axes: bool = True,
camera: str = "orthographic",
spacefill: bool = True,
particle_size: float = 1.0,
select_atoms: np.ndarray | None = None,
background: str = "white",
color_scheme: str | None = None,
colors: np.ndarray | None = None,
scalar_field: np.ndarray | None = None,
scalar_start: float | None = None,
scalar_end: float | None = None,
scalar_cmap: Any | None = None,
vector_field: np.ndarray | None = None,
vector_color: np.ndarray | None = None,
magnetic_moments: bool = False,
view_plane: np.ndarray = np.array([0, 0, 1]),
distance_from_camera: float = 1.0,
):
"""
Plot3d relies on NGLView to visualize atomic structures. Here, we construct a string in the "protein database"
("pdb") format, then turn it into an NGLView "structure". PDB is a white-space sensitive format, so the
string snippets are carefully formatted.
The final widget is returned. If it is assigned to a variable, the visualization is suppressed until that
variable is evaluated, and in the meantime more NGL operations can be applied to it to modify the visualization.
Args:
show_cell (bool): Whether or not to show the frame. (Default is True.)
show_axes (bool): Whether or not to show xyz axes. (Default is True.)
camera (str): 'perspective' or 'orthographic'. (Default is 'perspective'.)
spacefill (bool): Whether to use a space-filling or ball-and-stick representation. (Default is True, use
space-filling atoms.)
particle_size (float): Size of the particles. (Default is 1.)
select_atoms (numpy.ndarray): Indices of atoms to show, either as integers or a boolean array mask.
(Default is None, show all atoms.)
background (str): Background color. (Default is 'white'.)
color_scheme (str): NGLView color scheme to use. (Default is None, color by element.)
colors (numpy.ndarray): A per-atom array of HTML color names or hex color codes to use for atomic colors.
(Default is None, use coloring scheme.)
scalar_field (numpy.ndarray): Color each atom according to the array value (Default is None, use coloring
scheme.)
scalar_start (float): The scalar value to be mapped onto the low end of the color map (lower values are
clipped). (Default is None, use the minimum value in `scalar_field`.)
scalar_end (float): The scalar value to be mapped onto the high end of the color map (higher values are
clipped). (Default is None, use the maximum value in `scalar_field`.)
scalar_cmap (matplotlib.cm): The colormap to use. (Default is None, giving a blue-red divergent map.)
vector_field (numpy.ndarray): Add vectors (3 values) originating at each atom. (Default is None, no
vectors.)
vector_color (numpy.ndarray): Colors for the vectors (only available with vector_field). (Default is None,
vectors are colored by their direction.)
magnetic_moments (bool): Plot magnetic moments as 'scalar_field' or 'vector_field'.
view_plane (numpy.ndarray): A Nx3-array (N = 1,2,3); the first 3d-component of the array specifies
which plane of the system to view (for example, [1, 0, 0], [1, 1, 0] or the [1, 1, 1] planes), the
second 3d-component (if specified, otherwise [1, 0, 0]) gives the horizontal direction, and the third
component (if specified) is the vertical component, which is ignored and calculated internally. The
orthonormality of the orientation is internally ensured, and therefore is not required in the function
call. (Default is np.array([0, 0, 1]), which is view normal to the x-y plane.)
distance_from_camera (float): Distance of the camera from the structure. Higher = farther away.
(Default is 14, which also seems to be the NGLView default value.)
Possible NGLView color schemes:
" ", "picking", "random", "uniform", "atomindex", "residueindex",
"chainindex", "modelindex", "sstruc", "element", "resname", "bfactor",
"hydrophobicity", "value", "volume", "occupancy"
Returns:
(nglview.NGLWidget): The NGLView widget itself, which can be operated on further or viewed as-is.
Warnings:
* Many features only work with space-filling atoms (e.g. coloring by a scalar field).
* The colour interpretation of some hex codes is weird, e.g. 'green'.
"""
try: # If the graphical packages are not available, the GUI will not work.
import nglview
except ImportError:
raise ImportError(
"The package nglview needs to be installed for the plot3d() function!"
)
if (
magnetic_moments is True
and np.sum(np.abs(structure.get_initial_magnetic_moments())) > 0
):
if len(structure.get_initial_magnetic_moments().shape) == 1:
scalar_field = structure.get_initial_magnetic_moments()
else:
vector_field = structure.get_initial_magnetic_moments()
elements = structure.get_chemical_symbols()
atomic_numbers = structure.get_atomic_numbers()
positions = structure.positions
# If `select_atoms` was given, visualize only a subset of the `parent_basis`
if select_atoms is not None:
select_atoms = np.array(select_atoms, dtype=int)
elements = np.array(elements)[select_atoms]
atomic_numbers = atomic_numbers[select_atoms]
positions = positions[select_atoms]
if colors is not None:
colors = np.array(colors)
colors = colors[select_atoms]
if scalar_field is not None:
scalar_field = np.array(scalar_field)
scalar_field = scalar_field[select_atoms]
if vector_field is not None:
vector_field = np.array(vector_field)
vector_field = vector_field[select_atoms]
if vector_color is not None:
vector_color = np.array(vector_color)
vector_color = vector_color[select_atoms]
# Write the nglview protein-database-formatted string
struct = nglview.TextStructure(
_ngl_write_structure(elements, positions, structure.cell)
)
# Parse the string into the displayable widget
view = nglview.NGLWidget(struct)
if spacefill:
# Color by scheme
if color_scheme is not None:
if colors is not None:
warnings.warn("`color_scheme` is overriding `colors`", stacklevel=2)
if scalar_field is not None:
warnings.warn(
"`color_scheme` is overriding `scalar_field`", stacklevel=2
)
view = _add_colorscheme_spacefill(
view, elements, atomic_numbers, particle_size, color_scheme
)
# Color by per-atom colors
elif colors is not None:
if scalar_field is not None:
warnings.warn("`colors` is overriding `scalar_field`", stacklevel=2)
view = _add_custom_color_spacefill(
view, atomic_numbers, particle_size, colors
)
# Color by per-atom scalars
elif scalar_field is not None: # Color by per-atom scalars
colors = _scalars_to_hex_colors(
scalar_field, scalar_start, scalar_end, scalar_cmap
)
view = _add_custom_color_spacefill(
view, atomic_numbers, particle_size, colors
)
# Color by element
else:
view = _add_colorscheme_spacefill(
view, elements, atomic_numbers, particle_size
)
view.remove_ball_and_stick()
else:
view.add_ball_and_stick()
if (
show_cell
and structure.cell is not None
and all(np.max(structure.cell, axis=0) > 1e-2)
):
view.add_unitcell()
if vector_color is None and vector_field is not None:
vector_color = (
0.5
* np.array(vector_field)
/ np.linalg.norm(vector_field, axis=-1)[:, np.newaxis]
+ 0.5
)
elif (
vector_field is not None and vector_field is not None
): # WARNING: There must be a bug here...
try:
if (
vector_color is not None
and vector_color.shape != np.ones((len(structure), 3)).shape
):
vector_color = np.outer(
np.ones(len(structure)),
vector_color / np.linalg.norm(vector_color),
)
except AttributeError:
if vector_color is not None:
vector_color = np.ones((len(structure), 3)) * vector_color
if vector_field is not None:
assert vector_color is not None
for arr, pos, col in zip(vector_field, positions, vector_color, strict=True):
view.shape.add_arrow(list(pos), list(pos + arr), list(col), 0.2)
if show_axes: # Add axes
axes_origin = -np.ones(3)
arrow_radius = 0.1
text_size = 1
text_color = [0, 0, 0]
arrow_names = ["x", "y", "z"]
for n in [0, 1, 2]:
start = list(axes_origin)
shift = np.zeros(3)
shift[n] = 1
end = list(start + shift)
color = list(shift)
# We cast as list to avoid JSON warnings
view.shape.add_arrow(start, end, color, arrow_radius)
view.shape.add_text(end, text_color, text_size, arrow_names[n])
if camera not in ("perspective", "orthographic"):
warnings.warn(
"Only perspective or orthographic is (likely to be) permitted for camera",
stacklevel=2,
)
view.camera = camera
view.background = background
orientation = _get_flattened_orientation(
view_plane=view_plane, distance_from_camera=distance_from_camera * 14
)
view.control.orient(orientation)
return view
def _plot3d_ase(
structure: Atoms,
spacefill: bool = True,
show_cell: bool = True,
camera: str = "perspective",
particle_size: float = 0.5,
background: str = "white",
color_scheme: str = "element",
show_axes: bool = True,
):
"""
Possible color schemes:
" ", "picking", "random", "uniform", "atomindex", "residueindex",
"chainindex", "modelindex", "sstruc", "element", "resname", "bfactor",
"hydrophobicity", "value", "volume", "occupancy"
Returns:
"""
try: # If the graphical packages are not available, the GUI will not work.
import nglview
except ImportError:
raise ImportError(
"The package nglview needs to be installed for the plot3d() function!"
)
# Always visualize the parent basis
view = nglview.show_ase(structure)
if spacefill:
view.add_spacefill(
radius_type="vdw", color_scheme=color_scheme, radius=particle_size
)
view.remove_ball_and_stick()
else:
view.add_ball_and_stick()
if (
show_cell
and structure.cell is not None
and all(np.max(structure.cell, axis=0) > 1e-2)
):
view.add_unitcell()
if show_axes:
view.shape.add_arrow([-2, -2, -2], [2, -2, -2], [1, 0, 0], 0.5)
view.shape.add_arrow([-2, -2, -2], [-2, 2, -2], [0, 1, 0], 0.5)
view.shape.add_arrow([-2, -2, -2], [-2, -2, 2], [0, 0, 1], 0.5)
if camera not in ("perspective", "orthographic"):
print("Only perspective or orthographic is permitted")
return None
view.camera = camera
view.background = background
return view
def _ngl_write_cell(
a1: float,
a2: float,
a3: float,
f1: float = 90.0,
f2: float = 90.0,
f3: float = 90.0,
):
"""
Writes a PDB-formatted line to represent the simulation cell.
Args:
a1, a2, a3 (float): Lengths of the cell vectors.
f1, f2, f3 (float): Angles between the cell vectors (which angles exactly?) (in degrees).
Returns:
(str): The line defining the cell in PDB format.
"""
return f"CRYST1 {a1:8.3f} {a2:8.3f} {a3:8.3f} {f1:6.2f} {f2:6.2f} {f3:6.2f} P 1\n"
def _ngl_write_atom(
num: int,
species: str,
x: float,
y: float,
z: float,
group: str | None = None,
num2: int | None = None,
occupancy: float = 1.0,
temperature_factor: float = 0.0,
) -> str:
"""
Writes a PDB-formatted line to represent an atom.
Args:
num (int): Atomic index.
species (str): Elemental species.
x, y, z (float): Cartesian coordinates of the atom.
group (str): A...group name? (Default is None, repeat elemental species.)
num2 (int): An "alternate" index. (Don't ask me...) (Default is None, repeat first number.)
occupancy (float): PDB occupancy parameter. (Default is 1.)
temperature_factor (float): PDB temperature factor parameter. (Default is 0.
Returns:
(str): The line defining an atom in PDB format
Warnings:
* The [PDB docs](https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html) indicate that
the xyz coordinates might need to be in some sort of orthogonal basis. If you have weird behaviour,
this might be a good place to investigate.
"""
if group is None:
group = species
if num2 is None:
num2 = num
return f"ATOM {num:>6} {species:>4} {group:>4} {num2:>5} {x:10.3f} {y:7.3f} {z:7.3f} {occupancy:5.2f} {temperature_factor:5.2f} {species:>11} \n"
def _ngl_write_structure(
elements: np.ndarray, positions: np.ndarray, cell: np.ndarray
) -> str:
"""
Turns structure information into a NGLView-readable protein-database-formatted string.
Args:
elements (numpy.ndarray/list): Element symbol for each atom.
positions (numpy.ndarray/list): Vector of Cartesian atom positions.
cell (numpy.ndarray/list): Simulation cell Bravais matrix.
Returns:
(str): The PDB-formatted representation of the structure.
"""
from ase.geometry import cell_to_cellpar, cellpar_to_cell
if cell is None or any(np.max(cell, axis=0) < 1e-2):
# Define a dummy cell if it doesn't exist (eg. for clusters)
max_pos = np.max(positions, axis=0) - np.min(positions, axis=0)
max_pos[np.abs(max_pos) < 1e-2] = 10
cell = np.eye(3) * max_pos
cellpar = cell_to_cellpar(cell)
exportedcell = cellpar_to_cell(cellpar)
rotation = np.linalg.solve(cell, exportedcell)
pdb_str = _ngl_write_cell(*cellpar)
pdb_str += "MODEL 1\n"
if rotation is not None:
positions = np.array(positions).dot(rotation)
for i, p in enumerate(positions):
pdb_str += _ngl_write_atom(i, elements[i], *p)
pdb_str += "ENDMDL \n"
return pdb_str
def _atomic_number_to_radius(
atomic_number: int, shift: float = 0.2, slope: float = 0.1, scale: float = 1.0
) -> float:
"""
Give the atomic radius for plotting, which scales like the root of the atomic number.
Args:
atomic_number (int/float): The atomic number.
shift (float): A constant addition to the radius. (Default is 0.2.)
slope (float): A multiplier for the root of the atomic number. (Default is 0.1)
scale (float): How much to rescale the whole thing by.
Returns:
(float): The radius. (Not physical, just for visualization!)
"""
return (shift + slope * np.sqrt(atomic_number)) * scale
def _add_colorscheme_spacefill(
view,
elements: np.ndarray,
atomic_numbers: np.ndarray,
particle_size: float,
scheme: str = "element",
):
"""
Set NGLView spacefill parameters according to a color-scheme.
Args:
view (NGLWidget): The widget to work on.
elements (numpy.ndarray/list): Elemental symbols.
atomic_numbers (numpy.ndarray/list): Integer atomic numbers for determining atomic size.
particle_size (float): A scale factor for the atomic size.
scheme (str): The scheme to use. (Default is "element".)
Possible NGLView color schemes:
" ", "picking", "random", "uniform", "atomindex", "residueindex",
"chainindex", "modelindex", "sstruc", "element", "resname", "bfactor",
"hydrophobicity", "value", "volume", "occupancy"
Returns:
(nglview.NGLWidget): The modified widget.
"""
for elem, num in set(zip(elements, atomic_numbers, strict=True)):
view.add_spacefill(
selection="#" + elem,
radius_type="vdw",
radius=_atomic_number_to_radius(num, scale=particle_size),
color_scheme=scheme,
)
return view
def _add_custom_color_spacefill(
view, atomic_numbers: np.ndarray, particle_size: float, colors: np.ndarray
):
"""
Set NGLView spacefill parameters according to per-atom colors.
Args:
view (NGLWidget): The widget to work on.
atomic_numbers (numpy.ndarray/list): Integer atomic numbers for determining atomic size.
particle_size (float): A scale factor for the atomic size.
colors (numpy.ndarray/list): A per-atom list of HTML or hex color codes.
Returns:
(nglview.NGLWidget): The modified widget.
"""
for n, num in enumerate(atomic_numbers):
view.add_spacefill(
selection=[n],
radius_type="vdw",
radius=_atomic_number_to_radius(num, scale=particle_size),
color=colors[n],
)
return view
def _scalars_to_hex_colors(
scalar_field: np.ndarray,
start: float | None = None,
end: float | None = None,
cmap=None,
):
"""
Convert scalar values to hex codes using a colormap.
Args:
scalar_field (numpy.ndarray/list): Scalars to convert.
start (float): Scalar value to map to the bottom of the colormap (values below are clipped). (Default is
None, use the minimal scalar value.)
end (float): Scalar value to map to the top of the colormap (values above are clipped). (Default is
None, use the maximal scalar value.)
cmap (matplotlib.cm): The colormap to use. (Default is None, which gives a blue-red divergent map.)
Returns:
(list): The corresponding hex codes for each scalar value passed in.
"""
from matplotlib.colors import rgb2hex
if start is None:
start = np.amin(scalar_field)
if end is None:
end = np.amax(scalar_field)
interp = interp1d([start, end], [0, 1])
remapped_field = interp(np.clip(scalar_field, start, end)) # Map field onto [0,1]
if cmap is None:
try:
from seaborn import diverging_palette
except ImportError:
print(
"The package seaborn needs to be installed for the plot3d() function!"
)
cmap = diverging_palette(245, 15, as_cmap=True) # A nice blue-red palette
return [
rgb2hex(cmap(scalar)[:3]) for scalar in remapped_field
] # The slice gets RGB but leaves alpha
def _get_orientation(view_plane: np.ndarray) -> np.ndarray:
"""
A helper method to plot3d, which generates a rotation matrix from the input `view_plane`, and returns a
flattened list of len = 16. This flattened list becomes the input argument to `view.contol.orient`.
Args:
view_plane (numpy.ndarray/list): A Nx3-array/list (N = 1,2,3); the first 3d-component of the array
specifies which plane of the system to view (for example, [1, 0, 0], [1, 1, 0] or the [1, 1, 1] planes),
the second 3d-component (if specified, otherwise [1, 0, 0]) gives the horizontal direction, and the
third component (if specified) is the vertical component, which is ignored and calculated internally.
The orthonormality of the orientation is internally ensured, and therefore is not required in the
function call.
Returns:
(list): orientation tensor
"""
if len(np.array(view_plane).flatten()) % 3 != 0:
raise ValueError(
"The shape of view plane should be (N, 3), where N = 1, 2 or 3. Refer docs for more info."
)
view_plane = np.array(view_plane).reshape(-1, 3)
rotation_matrix = np.roll(np.eye(3), -1, axis=0)
rotation_matrix[: len(view_plane)] = view_plane
rotation_matrix /= np.linalg.norm(rotation_matrix, axis=-1)[:, np.newaxis]
rotation_matrix[1] -= (
np.dot(rotation_matrix[0], rotation_matrix[1]) * rotation_matrix[0]
) # Gran-Schmidt
rotation_matrix[2] = np.cross(
rotation_matrix[0], rotation_matrix[1]
) # Specify third axis
if np.isclose(np.linalg.det(rotation_matrix), 0):
return np.eye(
3
) # view_plane = [0,0,1] is the default view of NGLview, so we do not modify it
return np.roll(
rotation_matrix / np.linalg.norm(rotation_matrix, axis=-1)[:, np.newaxis],
2,
axis=0,
).T
def _get_flattened_orientation(
view_plane: np.ndarray, distance_from_camera: float
) -> list:
"""
A helper method to plot3d, which generates a rotation matrix from the input `view_plane`, and returns a
flattened list of len = 16. This flattened list becomes the input argument to `view.contol.orient`.
Args:
view_plane (numpy.ndarray/list): A Nx3-array/list (N = 1,2,3); the first 3d-component of the array
specifies which plane of the system to view (for example, [1, 0, 0], [1, 1, 0] or the [1, 1, 1] planes),
the second 3d-component (if specified, otherwise [1, 0, 0]) gives the horizontal direction, and the
third component (if specified) is the vertical component, which is ignored and calculated internally.
The orthonormality of the orientation is internally ensured, and therefore is not required in the
function call.
distance_from_camera (float): Distance of the camera from the structure. Higher = farther away.
Returns:
(list): Flattened list of len = 16, which is the input argument to `view.contol.orient`
"""
if distance_from_camera <= 0:
raise ValueError("´distance_from_camera´ must be a positive float!")
flattened_orientation = np.eye(4)
flattened_orientation[:3, :3] = _get_orientation(view_plane)
return (distance_from_camera * flattened_orientation).ravel().tolist()