Created
January 28, 2015 22:49
-
-
Save anonymous/5fd2e6edf75b99765100 to your computer and use it in GitHub Desktop.
test
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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]} | |
colors = { | |
'C': [.1, .1, .1], 'CA': [.4, 1, .14], 'N': [.24, .41, .7], 'O': [.46, .1, .1], | |
'S': [1, .75, .17], 'P': [1, .37, .05], 'FE': [1, .5, 0], 'MG': [.64, 1, .05], | |
'ZN': [.32, .42, 1], 'CU': [1, .67, 0], 'NA': [.8, .48, 1], 'K': [.72, .29, 1], | |
'CL': [.1, 1, .6], 'MN': [.67, .6, 1], 'H': [.9, .9, .9], 'F': [.27, .8, .21]} | |
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(2, 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) | |
# make material and assign to child as active material. | |
mat = bpy.data.materials.new('bb_material_' + atom_type) | |
mat.use_nodes = True | |
mat.use_fake_user = True # usually handy | |
tcol = colors[atom_type] + [1.0] | |
node = mat.node_tree.nodes['Diffuse BSDF'] | |
node.inputs[0].default_value = tcol | |
obj_child_repr.active_material = mat | |
# attach the child to the parent object's vertices | |
obj.dupli_type = 'VERTS' | |
obj_child_repr.parent = obj | |
def set_autosmooth(obj): | |
mesh = obj.data | |
smooth_states = [True] * len(mesh.polygons) | |
mesh.polygons.foreach_set('use_smooth', smooth_states) | |
mesh.update() | |
set_autosmooth(obj_child_repr) |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment