prettymol

Quick start

Prerequisites

• pixi. Manages the environment.
• Blender the core viz engine.

Up and running

git clone https://github.com/zachcp/prettymol &&  cd prettymol

pixi run remove  # removes Blender's python
pixi run jupyter # starts Blender AND IPYTHON

Complete Minimal Example

import bpy
import mathutils
from IPython.display import Image, display
from dataclasses import replace, fields
from prettymol import draw, load_pdb,  StructureSelector, Repltools
from prettymol import BSDFPrincipled, CartoonStyle, SpheresStyle, SurfaceStyle

# Load and process structure
structure = load_pdb("7xbu")
polymer = StructureSelector(structure).amino_acids().get_selection()
ligand = StructureSelector(structure).resname("MYN").get_selection()

# repl helpers including managing the view
rt = Repltools()
rt.clear()

# Create materials and customize them. Here I am setting the emisssion and color
surface_material =  BSDFPrincipled()
cartoon_material =  BSDFPrincipled()
sticks_material =  replace(
        BSDFPrincipled(),
        **{'base_color': [0.15, 1, 0.15, 1],
           "emission_strength": 1,
           "emission_color": [0.15, 1, 0.15, 1]})

# Draw fn takes an  AtomArray; a Style; and as Material
draw(structure, CartoonStyle(), cartoon_material)
draw(ligand, SpheresStyle(), sticks_material)
# draw2(structure, styles.SurfaceStyle(), surface_material)
rt.auto_view()

# Render and view
bpy.context.scene.render.filepath = '/tmp/output.png'
bpy.ops.render.render(use_viewport=True, write_still=True)
display(Image('/tmp/output.png'))