diff options
Diffstat (limited to 'io_mesh_pdb/import_pdb.py')
| -rw-r--r-- | io_mesh_pdb/import_pdb.py | 144 |
1 files changed, 116 insertions, 28 deletions
diff --git a/io_mesh_pdb/import_pdb.py b/io_mesh_pdb/import_pdb.py index d007603f..cf559d91 100644 --- a/io_mesh_pdb/import_pdb.py +++ b/io_mesh_pdb/import_pdb.py @@ -25,7 +25,7 @@ # # Start of project : 2011-08-31 by Clemens Barth # First publication in Blender : 2011-11-11 -# Last modified : 2011-12-26 +# Last modified : 2011-12-30 # # Acknowledgements: Thanks to ideasman, meta_androcto, truman, kilon, # dairin0d, PKHG, Valter, etc @@ -35,8 +35,10 @@ import bpy import io import math import os +import copy from math import pi, cos, sin from mathutils import Vector, Matrix +from copy import copy # These are variables, which contain the name of the PDB file and # the path of the PDB file. @@ -207,10 +209,12 @@ class CLASS_atom_pdb_atom(object): # This is the class, which stores the two atoms of one stick. class CLASS_atom_pdb_stick(object): - __slots__ = ('atom1', 'atom2') - def __init__(self, atom1, atom2): + __slots__ = ('atom1', 'atom2', 'number', 'dist') + def __init__(self, atom1, atom2, number, dist): self.atom1 = atom1 self.atom2 = atom2 + self.number = number + self.dist = dist # ----------------------------------------------------------------------------- @@ -492,7 +496,9 @@ def DEF_atom_pdb_radius_sticks(radius, how): return True -# This reads a custom data file. +# ----------------------------------------------------------------------------- +# The custom data file + def DEF_atom_pdb_custom_datafile(path_datafile): if path_datafile == "": @@ -560,7 +566,9 @@ def DEF_atom_pdb_custom_datafile(path_datafile): def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith, Ball_radius_factor,radiustype,Ball_distance_factor, - use_sticks,use_sticks_color,Stick_sectors,Stick_diameter,put_to_center, + use_sticks,use_sticks_color,use_sticks_smooth, + use_sticks_bonds,Stick_dist, + Stick_sectors,Stick_diameter,put_to_center, use_camera,use_lamp,path_datafile): # The list of all atoms as read from the PDB file. @@ -849,10 +857,34 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith, atom1 = atom_list[0] # For all the other atoms in the list do: - for each_atom in atom_list[1:]: - - # The second, third, ... partner atom - atom2 = each_atom + for atom2 in atom_list[1:]: + + if use_sticks_bonds == True: + number = atom_list[1:].count(atom2) + if number == 2 or number == 3: + basis_list = list(set(atom_list[1:])) + + if len(basis_list) > 1: + basis1 = (all_atoms[atom1-1].location + - all_atoms[basis_list[0]-1].location) + basis2 = (all_atoms[atom1-1].location + - all_atoms[basis_list[1]-1].location) + plane_n = basis1.cross(basis2) + + dist_n = (all_atoms[atom1-1].location + - all_atoms[atom2-1].location) + dist_n = dist_n.cross(plane_n) + dist_n = dist_n / dist_n.length + else: + dist_n = Vector((0,0,0)) + elif number > 3: + number = 1 + dist_n = None + else: + dist_n = None + else: + number = 1 + dist_n = None # Note that in a PDB file, sticks of one atom pair can appear a # couple of times. (Only god knows why ...) @@ -869,7 +901,7 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith, # If the stick is not yet registered (FLAG_BAR == False), then # register it! if FLAG_BAR == False: - all_sticks.append(CLASS_atom_pdb_stick(atom1,atom2)) + all_sticks.append(CLASS_atom_pdb_stick(atom1,atom2,number,dist_n)) Number_of_sticks += 1 j += 1 @@ -1169,27 +1201,79 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith, continue sticks_list = [] for stick in all_sticks: - dv = all_atoms[stick.atom1-1].location - all_atoms[stick.atom2-1].location - n = dv / dv.length - if atom_type[0] == all_atoms[stick.atom1-1].name: - location = all_atoms[stick.atom1-1].location - name = "_" + all_atoms[stick.atom1-1].name - material = all_atoms[stick.atom1-1].material - sticks_list.append([name, location, dv, material]) - if atom_type[0] == all_atoms[stick.atom2-1].name: - location = all_atoms[stick.atom1-1].location - n * dl * int(math.ceil(dv.length / (2.0 * dl))) - name = "_" + all_atoms[stick.atom2-1].name - material = all_atoms[stick.atom2-1].material - sticks_list.append([name, location, dv, material]) + + for repeat in range(stick.number): + + atom1 = copy(all_atoms[stick.atom1-1].location) + atom2 = copy(all_atoms[stick.atom2-1].location) + + dist = Stick_diameter * Stick_dist + + if stick.number == 2: + if repeat == 0: + atom1 += (stick.dist * dist) + atom2 += (stick.dist * dist) + if repeat == 1: + atom1 -= (stick.dist * dist) + atom2 -= (stick.dist * dist) + + if stick.number == 3: + if repeat == 0: + atom1 += (stick.dist * dist) + atom2 += (stick.dist * dist) + if repeat == 2: + atom1 -= (stick.dist * dist) + atom2 -= (stick.dist * dist) + + dv = atom1 - atom2 + n = dv / dv.length + if atom_type[0] == all_atoms[stick.atom1-1].name: + location = atom1 + name = "_" + all_atoms[stick.atom1-1].name + material = all_atoms[stick.atom1-1].material + sticks_list.append([name, location, dv, material]) + if atom_type[0] == all_atoms[stick.atom2-1].name: + location = atom1 - n * dl * int(math.ceil(dv.length / (2.0 * dl))) + name = "_" + all_atoms[stick.atom2-1].name + material = all_atoms[stick.atom2-1].material + sticks_list.append([name, location, dv, material]) + sticks_all_lists.append(sticks_list) else: sticks_list = [] for stick in all_sticks: - dv = all_atoms[stick.atom1-1].location - all_atoms[stick.atom2-1].location - n = dv / dv.length - location = all_atoms[stick.atom1-1].location - material = stick_material - sticks_list.append(["", location, dv, material]) + + if stick.number > 3: + stick.number = 1 + + for repeat in range(stick.number): + + atom1 = copy(all_atoms[stick.atom1-1].location) + atom2 = copy(all_atoms[stick.atom2-1].location) + + dist = Stick_diameter * Stick_dist + + if stick.number == 2: + if repeat == 0: + atom1 += (stick.dist * dist) + atom2 += (stick.dist * dist) + if repeat == 1: + atom1 -= (stick.dist * dist) + atom2 -= (stick.dist * dist) + if stick.number == 3: + if repeat == 0: + atom1 += (stick.dist * dist) + atom2 += (stick.dist * dist) + if repeat == 2: + atom1 -= (stick.dist * dist) + atom2 -= (stick.dist * dist) + + dv = atom1 - atom2 + n = dv / dv.length + location = atom1 + material = stick_material + sticks_list.append(["", location, dv, material]) + sticks_all_lists.append(sticks_list) @@ -1238,8 +1322,12 @@ def DEF_atom_pdb_main(use_mesh,Ball_azimuth,Ball_zenith, current_layers = bpy.context.scene.layers stick_cylinder = DEF_atom_pdb_build_stick(Stick_diameter, dl, Stick_sectors) stick_cylinder.active_material = stick[3] - stick_cylinder.parent = new_mesh + + if use_sticks_smooth == True: + for face in stick_cylinder.data.faces: + face.use_smooth = True + stick_cylinder.parent = new_mesh new_mesh.dupli_type = 'FACES' atom_object_list.append(new_mesh) |