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Plotly change size #132

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Merged
merged 9 commits into from
Feb 9, 2024
Merged

Plotly change size #132

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57e268e
make height available
samwaseda Feb 8, 2024
3e785ed
add doc string
samwaseda Feb 8, 2024
6252efd
Merge branch 'plotly_draw_frame' into plotly_change_size
samwaseda Feb 8, 2024
72217e6
Merge branch 'main' into plotly_change_size
samwaseda Feb 8, 2024
59ce25b
Format black
pyiron-runner Feb 9, 2024
433a464
add warning for height
samwaseda Feb 9, 2024
d7377a4
resolve conflicts
samwaseda Feb 9, 2024
ec4dbbe
satisfy black
samwaseda Feb 9, 2024
0af1b42
set default and correct doc string
samwaseda Feb 9, 2024
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13 changes: 13 additions & 0 deletions structuretoolkit/visualize.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,7 @@ def plot3d(
view_plane=np.array([0, 0, 1]),
distance_from_camera=1.0,
opacity=1.0,
height=None,
):
"""
Plot3d relies on NGLView or plotly to visualize atomic structures. Here, we construct a string in the "protein database"
Expand Down Expand Up @@ -82,6 +83,8 @@ def plot3d(
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",
Expand All @@ -96,6 +99,8 @@ def plot3d(
* 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)
return _plot3d(
structure=structure,
show_cell=show_cell,
Expand Down Expand Up @@ -128,8 +133,11 @@ def plot3d(
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)
return _plot3d_ase(
structure=structure,
show_cell=show_cell,
Expand Down Expand Up @@ -165,6 +173,7 @@ def _plot3d_plotly(
view_plane=np.array([1, 1, 1]),
distance_from_camera=1,
opacity=1,
height=None,
):
"""
Make a 3D plot of the atomic structure.
Expand All @@ -183,6 +192,7 @@ def _plot3d_plotly(
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.
Expand Down Expand Up @@ -227,6 +237,9 @@ def _plot3d_plotly(
fig.update_layout(scene_camera=angle)
fig.update_traces(marker=dict(line=dict(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

Expand Down