Pockets & blobs#

Planned content:

Build Gaussian pocket surfaces from alpha-spheres with multi-iso and color maps.
Pocket blobs with iso thresholds and smoothing.
Export a static view: MolSysView.write_html("_static/views/pockets.html").

Pocket surface from alpha-spheres#

Goal

Build a Gaussian pocket surface from alpha-sphere centers/radii.
Show multiple iso levels with distinct colors/alphas.
Export a static view for the docs.

import molsysviewer as viewer

centers = [(0,0,0), (3,0,0), (1.5,2,0)]
radii = [2.0, 1.8, 1.2]

view = viewer.MolSysView()
view.shapes.add_pocket_surface(
    atom_indices=[0],
    iso_levels=[0.08, 0.15],
    iso_colors=[0x44CCFF, 0x003366],
    grid={"resolution": 1.0, "smoothness": 1.0},
    tag="pocket-surface",
)
view.show()

What to tweak

atom_indices: real atom ids defining the pocket region; used for positioning/clipping.
grid: resolution, smoothness, radius_offset control the Gaussian field.
iso_levels/iso_colors/iso_alphas: multiple surfaces from one field.
clip_plane or mouth_atom_indices if you need clipping at openings.
tag: group related shapes for selective clear.

Pocket blob (Gaussian field)#

Goal

Generate a volumetric blob from alpha-spheres with custom iso thresholds and smoothing.
Support multiple iso levels/colors/alphas.

v = mv.MolSysView()
v.shapes.add_pocket_blob(
    centers=[(0,0,0), (3,0,0), (1.5,2,0)],
    radii=[2.0, 1.8, 1.2],
    iso_levels=[0.08, 0.15],
    iso_colors=[0x44CCFF, 0x003366],
    iso_alphas=[0.35, 0.5],
    smoothing=1.0,
    tag="pocket-blob",
)
v.show()

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[6], line 2
      1 v = mv.MolSysView()
----> 2 v.shapes.add_pocket_blob(
      3     centers=[(0,0,0), (3,0,0), (1.5,2,0)],
      4     radii=[2.0, 1.8, 1.2],
      5     iso_levels=[0.08, 0.15],
      6     iso_colors=[0x44CCFF, 0x003366],
      7     iso_alphas=[0.35, 0.5],
      8     smoothing=1.0,
      9     tag="pocket-blob",
     10 )
     11 v.show()

File ~/repos@uibcdf/molsysviewer/molsysviewer/shapes/__init__.py:99, in ShapesManager.add_pocket_blob(self, *args, **kwargs)
     94 def add_pocket_blob(
     95     self,
     96     *args,
     97     **kwargs,
     98 ):
---> 99     return self.blobs.add_pocket_blob(*args, **kwargs)

TypeError: PocketBlobs.add_pocket_blob() got an unexpected keyword argument 'iso_levels'

What to tweak

smoothing: higher → smoother field, lower → sharper.
iso_levels/iso_colors/iso_alphas: multiple surfaces from one field.
radius_scale: scale radii before computing the field.
color_map and values: color per center via a numeric property.
tag: group blobs for selective clear.