Pharmacophore overlay#

Goal

  • Render pharmacophore glyphs with standard colors/transparency.

  • Combine with pockets or channels in the same scene.

Code sketch

import molsysviewer as mv

v = mv.MolSysView()
v.show()
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.write_html("_static/views/pharmacophore_overlay.html")

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.

Embed the exported view

from molsysviewer.thirds.jupyter import load_html_in_notebook
load_html_in_notebook("_static/views/pharmacophore_overlay.html")