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import bpy | |
import bmesh | |
from collections import defaultdict | |
''' Aliases and variables and constants ''' | |
meshes = bpy.data.meshes | |
objects = bpy.data.objects | |
scene = bpy.context.scene | |
filepath = r'C:\Users\dealga\Documents\GitHub\BioBlender\Test_molecules\02_4IHV_dsDNA.pdb' | |
# index 0 is visual, 1 is for game engine (i think..) | |
scale_cov = { | |
'C': [1.1, 0.6], 'CA': [0.99, 0.6], 'N': [1.07, 0.6], 'O': [1.04, 0.6], | |
'S': [1.46, 0.6], 'P': [1.51, 0.6], 'FE': [0.64, 0.6], 'MG': [0.65, 0.6], | |
'ZN': [0.74, 0.6], 'CU': [0.72, 0.6], 'NA': [0.95, 0.6], 'K': [1.33, 0.6], | |
'CL': [1.81, 0.6], 'MN': [0.46, 0.6], 'H': [0.53, 0.3], 'F': [1.36, 0.6]} | |
scalex = 0.2 | |
scaley = 0.2 | |
scalez = 0.2 | |
''' Handle PDB import ''' | |
def import_pdb(filepath): | |
atom_dict = defaultdict(list) | |
def inspect_line_by_line(pdb_file): | |
for line in pdb_file: | |
# protein data line: pdl | |
pdl = line.strip() | |
if not pdl.startswith('ATOM'): | |
continue | |
values = pdl.split() | |
x, y, z = values[6:9] | |
xyz = (float(x) * scalex, float(y) * scaley, float(z) * scalez) | |
atom_type = values[-1] | |
atom_dict[atom_type].append(xyz) | |
def pdb_import_intermediate(): | |
with open(filepath) as pdb_file: | |
inspect_line_by_line(pdb_file) | |
pdb_import_intermediate() | |
return atom_dict | |
atom_dict = import_pdb(filepath) | |
''' Handle mesh construction ''' | |
def pydata_from_bmesh(bm): | |
v = [v.co[:] for v in bm.verts] | |
e = [[i.index for i in e.verts] for e in bm.edges[:]] | |
p = [[i.index for i in p.verts] for p in bm.faces[:]] | |
return v, e, p | |
def create_icospehere(subdiv, d): | |
bm = bmesh.new() | |
bmesh.ops.create_icosphere(bm, subdivisions=subdiv, diameter=d) | |
v, e, p = pydata_from_bmesh(bm) | |
bm.free() | |
return v, e, p | |
for atom_type, verts in atom_dict.items(): | |
''' parent ''' | |
# generate a new mesh, ever atom of certain type goes into the same mesh | |
mesh = meshes.new('atoms_' + atom_type) | |
mesh.from_pydata(verts, [], []) | |
mesh.update() | |
# create an object to assign the mesh data to | |
obj = objects.new('atoms_' + atom_type, mesh) | |
scene.objects.link(obj) | |
''' child ''' | |
# create a donor mesh (child) to represent each of these atoms | |
# this mesh is duplicated onto each vertex of the atoms_* parent mesh | |
diameter = scale_cov[atom_type][0] * scalex # unified | |
verts, edges, faces = create_icospehere(3, diameter) | |
mesh = meshes.new('repr_atom_' + atom_type) | |
mesh.from_pydata(verts, [], faces) | |
mesh.update() | |
# child must be an object too | |
obj_child_repr = objects.new('repr_atoms_' + atom_type, mesh) | |
scene.objects.link(obj_child_repr) | |
# attach the child to the parent object's vertices | |
obj.dupli_type = 'VERTS' | |
obj_child_repr.parent = obj |
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