minimal_pdb_import_to_vertices.py

import bpy
import bmesh

from collections import defaultdict

''' Aliases and variables '''


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'

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 '''


for atom_type, verts in atom_dict.items():

    # assign locations to a new 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)