MLP_mod.py

# kdArrange

import bpy
from collections import defaultdict


''' 
[x] step 01: first store atoms as {element_name: [co,..], } 
[ ] step 02: generate singular ordered mesh by adding vertices 
             in clumps of element types. (H,H,H,H,H,H,O,O,O,O,O,O..)
[ ] step 03: track start and end index for each element into mapper_obj
[ ] step 04: get surface mesh.
[ ] step 05: for every vertex on surface mesh find closest
             vertex in proxy_ob, and MLP value

'''

# step 01
# attrs = [a for a in dir(o) if a.startswith('bb2')]
attrs = [
    'bb2_objectType',
    'bb2_outputOptions',
    'bb2_pdbID',
    'bb2_pdbPath',
    'bb2_subID',
    'BBInfo'
]

proxy_obj = defaultdict(list)
nstr = '_4GE.001'
objs = bpy.data.objects[nstr].children
count = 0
for o in objs:
    
    if count > 120:
        break

    for a in attrs:
        print(a, ':', getattr(o, a))

    # coincides and is a relatively fast lookup
    element_name = o.active_material.name

    co = o.location[:]
    proxy_obj[element_name].append(co)
    count += 1
    
# step 03

mapper_obj = {}
verts = []

for key in sorted(proxy_obj.keys()):
    start = len(verts)
    verts.extend(proxy_obj[key])
    end = len(verts)-1
    mapper_obj[key] = (start, end)

# print(mapper_obj)
# {'C': (0, 97), 'N': (98, 124), 'O': (125, 153)}


# step 02

mesh = bpy.data.meshes.new("mesh_name")
mesh.from_pydata(verts, edges=[], faces=[])
mesh.update()

obj = bpy.data.objects.new("obj_name", mesh)

scene = bpy.context.scene
scene.objects.link(obj)

#