Pharmacophore overlays

Planned content:

• Render pharmacophore glyphs with standard colors and transparency.

• Combine with pockets or channels in the same scene.

import molsysviewer as mv

v = mv.MolSysView()
v.shapes.add_pharmacophore_features(
    centers=[(0,0,0), (3,0,0), (6,0,0)],
    kinds=["aromatic", "hydrophobic", "hbond_acceptor"],
    alphas=[0.5, 0.4, 0.6],
    tag="ph4-demo",
)
v.show()

<molsysviewer.widget.MolSysViewerWidget object at 0x7b3aa3dabfb0>

What to tweak

• radii: glyph size (single value or per feature).

• directions: optional for arrows/disks; one per feature if needed.

• colors: override standard palette; otherwise defaults per kind.

• alphas: transparency per feature or a single float.

• Combine with pockets or channels in the same scene using tags.