Molecule_builder.txt

import bpy
import json

from math import acos
from mathutils import Vector

def draw_molecule(molecule):
    
    radii = { 'C': 70, 'N': 71, 'O': 66, 'bond': 20, 'S': 105, 'H':31, 'P':107}
    for key in radii.keys():
        radii[key] *= 0.4/30
    """Draw a molecule to blender."""
    for atom in molecule["atoms"]:
        
        if atom["element"][0] in bpy.data.materials.keys():
            if atom["element"][0] in radii.keys():
                s=radii[atom["element"][0]]
            else:
                s=3.0
                
            bpy.ops.mesh.primitive_uv_sphere_add(scale=(s,s,s), location=atom["location"])
            bpy.ops.object.shade_smooth()
            bpy.context.active_object.data.materials.append(bpy.data.materials[atom["element"][0]])
        else:
            if atom["element"][0] in radii.keys():
                s=radii[atom["element"][0]]
            else:
                s=2.0
            bpy.data.materials.new(atom["element"][0])
            bpy.ops.mesh.primitive_uv_sphere_add(scale=(s,s,s), location=atom["location"])
            bpy.ops.object.shade_smooth()
            bpy.context.active_object.data.materials.append(bpy.data.materials[atom["element"][0]])
                       
    for bond in molecule["bonds"]:
        
        if not 'bond' in bpy.data.materials.keys():
            bpy.data.materials.new('bond')

        # Extracting locations
        first_loc = molecule["atoms"][bond["atoms"][0]]["location"]
        second_loc = molecule["atoms"][bond["atoms"][1]]["location"]

        # Useful values
        diff = tuple([c2-c1 for c2, c1 in zip(first_loc, second_loc)])
        center = tuple([(c2+c1)/2 for c2, c1 in zip(first_loc, second_loc)])
        magnitude = pow(sum([(c2-c1)**2
                        for c1, c2 in zip(first_loc, second_loc)]), 0.5)

        # Euler rotation calculation, (Vector from mathutils, acos from math)
        Vaxis = Vector(diff).normalized()
        Vobj = Vector((0,0,1))
        angle_x = Vobj.angle(Vector((0,1,0))*Vaxis.y + Vector((0,0,1))*Vaxis.z)
    
        # Specify locations of each bond in every scenario
        if bond["order"] == 1:
            trans = [[0] * 3]
        elif bond["order"] == 2:
            trans = [[0.1  * x for x in Vobj],
                [-0.1 * x for x in Vobj]]
        elif bond["order"] == 3:
            trans = [[0] * 3, [0.2 * x for x in Vobj],
                [-0.2 * x for x in Vobj]]
        # Draw bonds
        for tran in trans:
            bpy.ops.mesh.primitive_cylinder_add(radius=0.1, depth=magnitude,location=center)
            bpy.ops.object.shade_smooth()
            bpy.context.active_object.data.materials.append(bpy.data.materials['bond'])
            bpy.context.object.rotation_mode = 'QUATERNION'
            bpy.context.object.rotation_quaternion = Vaxis.to_track_quat('Z','Y')
            bpy.ops.transform.translate(value=tran)

with open("D:/Blender Tutorials/phosphate-deoxyribose.json") as in_file:
    MolA = json.load(in_file)
draw_molecule(MolA)