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Diffstat (limited to 'io_mesh_pdb/__init__.py')
| -rw-r--r-- | io_mesh_pdb/__init__.py | 574 |
1 files changed, 574 insertions, 0 deletions
diff --git a/io_mesh_pdb/__init__.py b/io_mesh_pdb/__init__.py new file mode 100644 index 00000000..69046b84 --- /dev/null +++ b/io_mesh_pdb/__init__.py @@ -0,0 +1,574 @@ +# ##### BEGIN GPL LICENSE BLOCK ##### +# +# This program is free software; you can redistribute it and/or +# modify it under the terms of the GNU General Public License +# as published by the Free Software Foundation; either version 2 +# of the License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software Foundation, +# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. +# +# ##### END GPL LICENSE BLOCK ##### + +bl_info = { + "name": "PDB Atomic Blender", + "description": "Loading and manipulating atoms from PDB files", + "author": "Clemens Barth", + "version": (1,0), + "blender": (2,6), + "api": 31236, + "location": "File -> Import -> PDB (.pdb), Panel: View 3D - Tools", + "warning": "", + "wiki_url": "http://development.root-1.de/Atomic_Blender.php", + "tracker_url": "http://projects.blender.org/tracker/" + "index.php?func=detail&aid=29226&group_id=153&atid=468", + "category": "Import-Export" +} + + +import bpy +from bpy_extras.io_utils import ImportHelper +from bpy.props import (StringProperty, + BoolProperty, + EnumProperty, + IntProperty, + FloatProperty) + + +# TODO, allow reload +from . import import_pdb + +# ----------------------------------------------------------------------------- +# GUI + +# The panel, which is loaded after the file has been +# chosen via the menu 'File -> Import' +class CLASS_atom_pdb_panel(bpy.types.Panel): + bl_label = "PDB - Atomic Blender" + #bl_space_type = "PROPERTIES" + #bl_region_type = "WINDOW" + #bl_context = "physics" + # This could be also an option ... : + bl_space_type = "VIEW_3D" + bl_region_type = "TOOL_PROPS" + + # This 'poll thing' has taken 3 hours of a hard search and understanding. + # I explain it in the following from my point of view: + # + # Before this class is entirely treaten (here: drawing the panel) the + # poll method is called first. Basically, some conditions are + # checked before other things in the class are done afterwards. If a + # condition is not valid, one returns 'False' such that nothing further + # is done. 'True' means: 'Go on' + # + # In the case here, it is verified if the ATOM_PDB_FILEPATH variable contains + # a name. If not - and this is the case directly after having started the + # script - the panel does not appear because 'False' is returned. However, + # as soon as a file has been chosen, the panel appears because + # ATOM_PDB_FILEPATH contains a name. + # + # Please, correct me if I'm wrong. + @classmethod + def poll(self, context): + if import_pdb.ATOM_PDB_FILEPATH == "": + return False + else: + return True + + def draw(self, context): + layout = self.layout + scn = bpy.context.scene + + row = layout.row() + row.label(text="Custom data file") + row = layout.row() + col = row.column() + col.prop(scn, "atom_pdb_datafile") + col.operator("atom_pdb.datafile_apply") + row = layout.row() + col = row.column(align=True) + col.prop(scn, "atom_pdb_PDB_file") + + layout.separator() + + row = layout.row() + col = row.column(align=True) + col.prop(scn, "use_atom_pdb_mesh") + col.prop(scn, "atom_pdb_mesh_azimuth") + col.prop(scn, "atom_pdb_mesh_zenith") + + + col = row.column(align=True) + col.label(text="Scaling factors") + col.prop(scn, "atom_pdb_scale_ballradius") + col.prop(scn, "atom_pdb_scale_distances") + row = layout.row() + col = row.column() + col.prop(scn, "use_atom_pdb_sticks") + col = row.column(align=True) + col.prop(scn, "atom_pdb_sticks_sectors") + col.prop(scn, "atom_pdb_sticks_radius") + + row = layout.row() + row.prop(scn, "use_atom_pdb_center") + + row = layout.row() + col = row.column() + col.prop(scn, "use_atom_pdb_cam") + col.prop(scn, "use_atom_pdb_lamp") + col = row.column() + col.operator("atom_pdb.button_reload") + + # TODO, use lanel() instead + col.prop(scn, "atom_pdb_number_atoms") + + layout.separator() + + row = layout.row() + row.operator("atom_pdb.button_distance") + row.prop(scn, "atom_pdb_distance") + layout.separator() + + row = layout.row() + row.label(text="All changes concern:") + row = layout.row() + row.prop(scn, "atom_pdb_radius_how") + + row = layout.row() + row.label(text="1. Change type of radii") + row = layout.row() + row.prop(scn, "atom_pdb_radius_type") + + row = layout.row() + row.label(text="2. Change atom radii in pm") + row = layout.row() + row.prop(scn, "atom_pdb_radius_pm_name") + row = layout.row() + row.prop(scn, "atom_pdb_radius_pm") + + row = layout.row() + row.label(text="3. Change atom radii by scale") + row = layout.row() + col = row.column() + col.prop(scn, "atom_pdb_radius_all") + col = row.column(align=True) + col.operator( "atom_pdb.radius_all_bigger" ) + col.operator( "atom_pdb.radius_all_smaller" ) + + if bpy.context.mode == 'EDIT_MESH': + + layout.separator() + row = layout.row() + row.operator( "atom_pdb.separate_atom" ) + + +class CLASS_atom_pdb_IO(bpy.types.PropertyGroup): + + def Callback_radius_type(self, context): + scnn = bpy.context.scene + import_pdb.DEF_atom_pdb_radius_type( + scnn.atom_pdb_radius_type, + scnn.atom_pdb_radius_how, + ) + + def Callback_radius_pm(self, context): + scnn = bpy.context.scene + import_pdb.DEF_atom_pdb_radius_pm( + scnn.atom_pdb_radius_pm_name, + scnn.atom_pdb_radius_pm, + scnn.atom_pdb_radius_how, + ) + + # In the file dialog window + scn = bpy.types.Scene + scn.use_atom_pdb_cam = BoolProperty( + name="Camera", default=False, + description="Do you need a camera?") + scn.use_atom_pdb_lamp = BoolProperty( + name="Lamp", default=False, + description = "Do you need a lamp?") + scn.use_atom_pdb_mesh = BoolProperty( + name = "Mesh balls", default=False, + description = "Do you want to use mesh balls instead of NURBS?") + scn.atom_pdb_mesh_azimuth = IntProperty( + name = "Azimuth", default=32, min=0, + description = "Number of sectors (azimuth)") + scn.atom_pdb_mesh_zenith = IntProperty( + name = "Zenith", default=32, min=0, + description = "Number of sectors (zenith)") + scn.atom_pdb_scale_ballradius = FloatProperty( + name = "Balls", default=1.0, min=0.0, + description = "Scale factor for all atom radii") + scn.atom_pdb_scale_distances = FloatProperty ( + name = "Distances", default=1.0, min=0.0, + description = "Scale factor for all distances") + scn.use_atom_pdb_center = BoolProperty( + name = "Object to origin", default=True, + description = "Shall the object first put into the global origin " + "before applying the offsets on the left?") + scn.use_atom_pdb_sticks = BoolProperty( + name="Use sticks", default=False, + description="Do you want to display also the sticks?") + scn.atom_pdb_sticks_sectors = IntProperty( + name = "Sector", default=20, min=0, + description="Number of sectors of a stick") + scn.atom_pdb_sticks_radius = FloatProperty( + name = "Radius", default=0.1, min=0.0, + description ="Radius of a stick") + scn.atom_pdb_atomradius = EnumProperty( + name="Type of radius", + description="Choose type of atom radius", + items=(('0', "Pre-defined", "Use pre-defined radius"), + ('1', "Atomic", "Use atomic radius"), + ('2', "van der Waals", "Use van der Waals radius")), + default='0',) + + # In the panel + scn.atom_pdb_datafile = StringProperty( + name = "", description="Path to your custom data file", + maxlen = 256, default = "", subtype='FILE_PATH') + scn.atom_pdb_PDB_file = StringProperty( + name = "Path to file", default="", + description = "Path of the PDB file") + # TODO, remove this property, its used for display only! + scn.atom_pdb_number_atoms = StringProperty(name="", + default="Number", description = "This output shows " + "the number of atoms which have been loaded") + scn.atom_pdb_distance = StringProperty( + name="", default="Distance (A)", + description="Distance of 2 objects in Angstrom") + scn.atom_pdb_radius_how = EnumProperty( + name="", + description="Which objects shall be modified?", + items=(('ALL_ACTIVE',"all active objects", "in the current layer"), + ('ALL_IN_LAYER',"all"," in active layer(s)")), + default='ALL_ACTIVE',) + scn.atom_pdb_radius_type = EnumProperty( + name="Type", + description="Which type of atom radii?", + items=(('0',"predefined", "Use pre-defined radii"), + ('1',"atomic", "Use atomic radii"), + ('2',"van der Waals","Use van der Waals radii")), + default='0',update=Callback_radius_type) + scn.atom_pdb_radius_pm_name = StringProperty( + name="", default="Atom name", + description="Put in the name of the atom (e.g. Hydrogen)") + scn.atom_pdb_radius_pm = FloatProperty( + name="", default=100.0, min=0.0, + description="Put in the radius of the atom (in pm)", + update=Callback_radius_pm) + scn.atom_pdb_radius_all = FloatProperty( + name="Scale", default = 1.05, min=1.0, + description="Put in the scale factor") + + +# Button loading a custom data file +class CLASS_atom_pdb_datafile_apply(bpy.types.Operator): + bl_idname = "atom_pdb.datafile_apply" + bl_label = "Apply" + bl_description = "Use color and radii values stored in a custom file" + + def execute(self, context): + scn = bpy.context.scene + + if scn.atom_pdb_datafile == "": + return {'FINISHED'} + + import_pdb.DEF_atom_pdb_custom_datafile(scn.atom_pdb_datafile) + + for obj in bpy.context.selected_objects: + if len(obj.children) != 0: + child = obj.children[0] + if child.type == "SURFACE" or child.type == "MESH": + for element in ATOM_PDB_ELEMENTS: + if element.name in obj.name: + child.scale = (element.radii[0], + element.radii[0], + element.radii[0]) + child.active_material.diffuse_color = element.color + else: + if obj.type == "SURFACE" or obj.type == "MESH": + for element in ATOM_PDB_ELEMENTS: + if element.name in obj.name: + obj.scale = (element.radii[0], + element.radii[0], + element.radii[0]) + obj.active_material.diffuse_color = element.color + + return {'FINISHED'} + + +# Button for measuring the distance of the active objects +class CLASS_atom_pdb_separate_atom(bpy.types.Operator): + bl_idname = "atom_pdb.separate_atom" + bl_label = "Separate atom" + bl_description = "Separate the atom you have chosen" + + def execute(self, context): + scn = bpy.context.scene + + # Get first all important properties from the atom which the user + # has chosen: location, color, scale + obj = bpy.context.edit_object + name = obj.name + loc_obj_vec = obj.location + scale = obj.children[0].scale + material = obj.children[0].active_material + + # Separate the vertex from the main mesh and create a new mesh. + bpy.ops.mesh.separate() + new_object = bpy.context.scene.objects[0] + # Keep in mind the coordinates <= We only need this + loc_vec = new_object.data.vertices[0].co + + # And now, switch to the OBJECT mode such that we can ... + bpy.ops.object.mode_set(mode='OBJECT', toggle=False) + # ... delete the new mesh including the separated vertex + bpy.ops.object.select_all(action='DESELECT') + new_object.select = True + bpy.ops.object.delete() + + # Create a new atom/vacancy at the position of the old atom + current_layers=bpy.context.scene.layers + + if "Vacancy" not in name: + if scn.use_atom_pdb_mesh == False: + bpy.ops.surface.primitive_nurbs_surface_sphere_add( + view_align=False, enter_editmode=False, + location=loc_vec+loc_obj_vec, + rotation=(0.0, 0.0, 0.0), + layers=current_layers) + else: + bpy.ops.mesh.primitive_uv_sphere_add( + segments=scn.atom_pdb_mesh_azimuth, + ring_count=scn.atom_pdb_mesh_zenith, + size=1, view_align=False, enter_editmode=False, + location=loc_vec+loc_obj_vec, + rotation=(0, 0, 0), + layers=current_layers) + else: + bpy.ops.mesh.primitive_cube_add( + view_align=False, enter_editmode=False, + location=loc_vec+loc_obj_vec, + rotation=(0.0, 0.0, 0.0), + layers=current_layers) + + new_atom = bpy.context.scene.objects.active + # Scale, material and name it. + new_atom.scale = scale + new_atom.active_material = material + new_atom.name = name + "_sep" + + # Switch back into the 'Edit mode' because we would like to seprate + # other atoms may be (more convinient) + new_atom.select = False + obj.select = True + bpy.context.scene.objects.active = obj + bpy.ops.object.select_all(action='DESELECT') + bpy.ops.object.mode_set(mode='EDIT', toggle=False) + + return {'FINISHED'} + + +# Button for measuring the distance of the active objects +class CLASS_atom_pdb_distance_button(bpy.types.Operator): + bl_idname = "atom_pdb.button_distance" + bl_label = "Measure ..." + bl_description = "Measure the distance between two objects" + + def execute(self, context): + scn = bpy.context.scene + dist = import_pdb.DEF_atom_pdb_distance() + + if dist != "N.A.": + # The string length is cut, 3 digits after the first 3 digits + # after the '.'. Append also "Angstrom". + # Remember: 1 Angstrom = 10^(-10) m + pos = str.find(dist, ".") + dist = dist[:pos+4] + dist = dist + " A" + + # Put the distance into the string of the output field. + scn.atom_pdb_distance = dist + return {'FINISHED'} + + +# Button for increasing the radii of all atoms +class CLASS_atom_pdb_radius_all_bigger_button(bpy.types.Operator): + bl_idname = "atom_pdb.radius_all_bigger" + bl_label = "Bigger ..." + bl_description = "Increase the radii of the atoms" + + def execute(self, context): + scn = bpy.context.scene + import_pdb.DEF_atom_pdb_radius_all( + scn.atom_pdb_radius_all, + scn.atom_pdb_radius_how, + ) + return {'FINISHED'} + + +# Button for decreasing the radii of all atoms +class CLASS_atom_pdb_radius_all_smaller_button(bpy.types.Operator): + bl_idname = "atom_pdb.radius_all_smaller" + bl_label = "Smaller ..." + bl_description = "Decrease the radii of the atoms" + + def execute(self, context): + scn = bpy.context.scene + import_pdb.DEF_atom_pdb_radius_all( + 1.0/scn.atom_pdb_radius_all, + scn.atom_pdb_radius_how, + ) + return {'FINISHED'} + + +# The button for loading the atoms and creating the scene +class CLASS_atom_pdb_load_button(bpy.types.Operator): + bl_idname = "atom_pdb.button_reload" + bl_label = "RELOAD" + bl_description = "Load the structure again" + + def execute(self, context): + scn = bpy.context.scene + + azimuth = scn.atom_pdb_mesh_azimuth + zenith = scn.atom_pdb_mesh_zenith + bradius = scn.atom_pdb_scale_ballradius + bdistance = scn.atom_pdb_scale_distances + radiustype = scn.atom_pdb_atomradius + center = scn.use_atom_pdb_center + sticks = scn.use_atom_pdb_sticks + ssector = scn.atom_pdb_sticks_sectors + sradius = scn.atom_pdb_sticks_radius + cam = scn.use_atom_pdb_cam + lamp = scn.use_atom_pdb_lamp + mesh = scn.use_atom_pdb_mesh + datafile = scn.atom_pdb_datafile + + # Execute main routine an other time ... from the panel + atom_number = import_pdb.DEF_atom_pdb_main( + mesh, azimuth, zenith, bradius, + radiustype, bdistance, sticks, + ssector, sradius, center, cam, lamp, datafile, + ) + scn.atom_pdb_number_atoms = str(atom_number) + " atoms" + + return {'FINISHED'} + + +# This is the class for the file dialog. +class CLASS_LoadPDB(bpy.types.Operator, ImportHelper): + bl_idname = "import_pdb.pdb" + bl_label = "Import PDB" + + filename_ext = ".pdb" + filter_glob = StringProperty(default="*.pdb", options={'HIDDEN'},) + + def draw(self, context): + layout = self.layout + scn = bpy.context.scene + + row = layout.row() + row.prop(scn, "use_atom_pdb_cam") + row.prop(scn, "use_atom_pdb_lamp") + row = layout.row() + col = row.column() + col.prop(scn, "use_atom_pdb_mesh") + col = row.column(align=True) + col.prop(scn, "atom_pdb_mesh_azimuth") + col.prop(scn, "atom_pdb_mesh_zenith") + + row = layout.row() + col = row.column() + col.label(text="Scaling factors") + col = row.column(align=True) + col.prop(scn, "atom_pdb_scale_ballradius") + col.prop(scn, "atom_pdb_scale_distances") + row = layout.row() + col = row.column() + col.prop(scn, "use_atom_pdb_sticks") + col = row.column(align=True) + col.prop(scn, "atom_pdb_sticks_sectors") + col.prop(scn, "atom_pdb_sticks_radius") + + row = layout.row() + row.prop(scn, "use_atom_pdb_center") + + row = layout.row() + row.prop(scn, "atom_pdb_atomradius") + + def execute(self, context): + global ATOM_PDB_ELEMENTS_DEFAULT + global ATOM_PDB_ELEMENTS + + scn = bpy.context.scene + + # This is in order to solve this strange 'relative path' thing. + import_pdb.ATOM_PDB_FILEPATH = bpy.path.abspath(self.filepath) + + scn.atom_pdb_PDB_file = import_pdb.ATOM_PDB_FILEPATH + + azimuth = scn.atom_pdb_mesh_azimuth + zenith = scn.atom_pdb_mesh_zenith + bradius = scn.atom_pdb_scale_ballradius + bdistance = scn.atom_pdb_scale_distances + radiustype = scn.atom_pdb_atomradius + center = scn.use_atom_pdb_center + sticks = scn.use_atom_pdb_sticks + ssector = scn.atom_pdb_sticks_sectors + sradius = scn.atom_pdb_sticks_radius + cam = scn.use_atom_pdb_cam + lamp = scn.use_atom_pdb_lamp + mesh = scn.use_atom_pdb_mesh + datafile = scn.atom_pdb_datafile + + # Execute main routine + atom_number = import_pdb.DEF_atom_pdb_main( + mesh, azimuth, zenith, bradius, + radiustype, bdistance, sticks, + ssector, sradius, center, cam, lamp, datafile) + + scn.atom_pdb_number_atoms = str(atom_number) + " atoms" + + return {'FINISHED'} + + +# The entry into the menu 'file -> import' +def menu_func(self, context): + self.layout.operator(CLASS_LoadPDB.bl_idname, text="PDB (.pdb)") + + +def register(): + bpy.utils.register_class(CLASS_atom_pdb_panel) + bpy.utils.register_class(CLASS_atom_pdb_datafile_apply) + bpy.utils.register_class(CLASS_atom_pdb_IO) + bpy.utils.register_class(CLASS_atom_pdb_load_button) + bpy.utils.register_class(CLASS_atom_pdb_radius_all_bigger_button) + bpy.utils.register_class(CLASS_atom_pdb_radius_all_smaller_button) + bpy.utils.register_class(CLASS_atom_pdb_distance_button) + bpy.utils.register_class(CLASS_atom_pdb_separate_atom) + bpy.utils.register_module(__name__) + bpy.types.INFO_MT_file_import.append(menu_func) + +def unregister(): + bpy.utils.unregister_class(CLASS_atom_pdb_panel) + bpy.utils.unregister_class(CLASS_atom_pdb_datafile_apply) + bpy.utils.unregister_class(CLASS_atom_pdb_IO) + bpy.utils.unregister_class(CLASS_atom_pdb_load_button) + bpy.utils.unregister_class(CLASS_atom_pdb_radius_all_bigger_button) + bpy.utils.unregister_class(CLASS_atom_pdb_radius_all_smaller_button) + bpy.utils.unregister_class(CLASS_atom_pdb_distance_button) + bpy.utils.unregister_class(CLASS_atom_pdb_separate_atom) + bpy.utils.unregister_module(__name__) + bpy.types.INFO_MT_file_import.remove(menu_func) + +if __name__ == "__main__": + + register() |