[Bf-extensions-cvs] SVN commit: /data/svn/bf-extensions [2703] trunk/py/scripts/addons/ io_mesh_pdb: removing this PDB importer in preparation to replace with a re-written one which supports more file types
Campbell Barton
ideasman42 at gmail.com
Thu Dec 1 20:57:28 CET 2011
Revision: 2703
http://projects.blender.org/scm/viewvc.php?view=rev&root=bf-extensions&revision=2703
Author: campbellbarton
Date: 2011-12-01 19:57:27 +0000 (Thu, 01 Dec 2011)
Log Message:
-----------
removing this PDB importer in preparation to replace with a re-written one which supports more file types
Removed Paths:
-------------
trunk/py/scripts/addons/io_mesh_pdb/__init__.py
trunk/py/scripts/addons/io_mesh_pdb/import_pdb.py
Deleted: trunk/py/scripts/addons/io_mesh_pdb/__init__.py
===================================================================
--- trunk/py/scripts/addons/io_mesh_pdb/__init__.py 2011-12-01 19:55:32 UTC (rev 2702)
+++ trunk/py/scripts/addons/io_mesh_pdb/__init__.py 2011-12-01 19:57:27 UTC (rev 2703)
@@ -1,132 +0,0 @@
-# ##### 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 #####
-
-# <pep8-80 compliant>
-
-bl_info = {
- "name": "Import/Export: PDB format",
- "author": "Mariusz Maximus & Jong89",
- "version": (0, 9, 0),
- "blender": (2, 6, 0),
- "api": 35616,
- "location": "File > Import/Export > PDB",
- "description": "Import PDB files",
- "warning": "",
- "wiki_url": "http://blenderartists.org/forum/showthread.php?t=194336",
- "tracker_url": "http://blenderartists.org/forum/showthread.php?t=194336",
- "category": "Import-Export"}
-
-# @todo write the wiki page
-
-# To support reload properly, try to access a package var,
-# if it's there, reload everything
-if "bpy" in locals():
- import imp
- if "import_pdb" in locals():
- imp.reload(import_pdb)
-
-
-import bpy
-from bpy.props import (StringProperty,
- BoolProperty,
- IntProperty,
- FloatProperty,
- )
-
-from bpy_extras.io_utils import ImportHelper
-
-
-class ImportPDB(bpy.types.Operator, ImportHelper):
- """Import from PDB file format (.pdb)"""
- bl_idname = 'import_scene.pdb'
- bl_label = 'Import PDB'
- bl_options = {'REGISTER', 'UNDO'}
-
- filename_ext = ".pdb"
- filter_glob = StringProperty(default="*.pdb", options={'HIDDEN'})
-
- filepath = StringProperty(
- name="File Path",
- description="Filepath used for importing the PDB file",
- maxlen=1024,
- )
- multi_models = BoolProperty(
- name="Import all models",
- description="Import all alternative structures listed in file",
- default=False,
- )
- multimers = BoolProperty(
- name="Import Biomolecules",
- description="Import all file-listed biomolecules and multimers, "
- "disable to import default biomolecule with "
- "all chains",
- default=False,
- )
- retain_alts = BoolProperty(
- name="Retain Alternative Atoms",
- description="Select to retain alternative atoms. "
- "Some PDB files label coordinates of entries "
- "in multiple models as alternates",
- default=False,
- )
- atom_subdivisions = IntProperty(
- name="Atom Subdivisions",
- description="Number of icosphere subdivisions for the atoms",
- min=1, max=6,
- default=3,
- )
- atom_size = FloatProperty(
- name="Atom Size",
- description="Multiplier for the van der Waals radius of the atoms",
- min=0.0, max=5.0,
- default=1.0,
- )
- scene_scale = FloatProperty(
- name="Scene Scale Factor",
- description="Number of Blender units equivalent to 1 angstrom",
- min=0.0, max=10.0,
- default=1.0,
- )
-
- def execute(self, context):
- from . import import_pdb
- keywords = self.as_keywords(ignore=("filter_glob", ))
- import_pdb.load_pdb(context, **keywords)
- return {'FINISHED'}
-
- def invoke(self, context, event):
- wm = context.window_manager
- wm.fileselect_add(self)
- return {'RUNNING_MODAL'}
-
-
-def menu_func(self, context):
- self.layout.operator(ImportPDB.bl_idname, text='Protein Databank (.pdb)')
-
-
-def register():
- bpy.utils.register_module(__name__)
- bpy.types.INFO_MT_file_import.append(menu_func)
-
-
-def unregister():
- bpy.utils.unregister_module(__name__)
- bpy.types.INFO_MT_file_import.remove(menu_func)
-
-if __name__ == '__main__':
- register()
Deleted: trunk/py/scripts/addons/io_mesh_pdb/import_pdb.py
===================================================================
--- trunk/py/scripts/addons/io_mesh_pdb/import_pdb.py 2011-12-01 19:55:32 UTC (rev 2702)
+++ trunk/py/scripts/addons/io_mesh_pdb/import_pdb.py 2011-12-01 19:57:27 UTC (rev 2703)
@@ -1,496 +0,0 @@
-# ##### 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 #####
-
-# <pep8 compliant>
-
-# TODO, currently imported names are assumed to make valid blender names
-# this is _not_ assured, so we should use a reliable dict mapping.
-
-import bpy
-
-
-class Element:
- """Element class with properties ([R, G, B], cov_radius, vdw_radius, name)"""
- def __init__(self, color, cov_radius, vdw_radius, name):
- self.color = color
- self.cov_radius = cov_radius
- self.vdw_radius = vdw_radius
- self.name = name
-
-
-class Atom:
- """Atom class with properties (serial, name, altloc, resname,chainid,
- resseq, icode, x, y, z, occupancy, tempfactor, element, charge)"""
-
- def __init__(self, serial, name, altloc, resname, chainid, resseq, icode,
- x, y, z, occupancy, tempfactor, element, charge):
- self.serial = serial
- self.name = name
- self.altloc = altloc
- self.resname = resname
- self.chainid = chainid
- self.resseq = resseq
- self.icode = icode
- self.x = x
- self.y = y
- self.z = z
- self.occupancy = occupancy
- self.tempfactor = tempfactor
- self.element = element
- self.charge = charge
-
-
-# collection of biomolecules based on model
-# all chains in model stored here
-class Model:
- '''Model class'''
- def __init__(self, model_id):
- self.model_id = model_id
- self.atoms = {}
- self.atom_count = 0
- self.vert_list = []
- # Dictionary of {vert index: [list of vertex groups it belongs to]}
- # Now element only
- self.vert_group_index = {}
- # Dictionary of {vertex group: number of group members}
- self.vert_group_counts = {}
- self.chains = {}
-
-
-# new object level class
-class Biomolecule:
- '''Biomolecule'''
- def __init__(self, serial):
- self.serial = serial
- self.atom_count = 0
- self.vert_list = []
- self.vert_group_index = {}
- self.vert_group_counts = {}
- self.chain_transforms = {}
-
-
-# Atom collection
-class Chain:
- '''Chain'''
- def __init__(self, chain_id):
- self.chain_id = chain_id
- self.atoms = {}
-
-# Atomic data from http://www.ccdc.cam.ac.uk/products/csd/radii/
-# Color palatte adapted from Jmol
-# "Element symbol":[[Red, Green, Blue], Covalent radius, van der Waals radius,
-# Element name]
-# Atomic radii are in angstroms (100 pm)
-# Unknown covalent radii are assigned 1.5 A, unknown van der Waals radiii are
-# assigned 2 A,
-
-atom_data = {
- "H" : Element((1.00000, 1.00000, 1.00000), 0.23, 1.09, "Hydrogen" ),
- "HE": Element((0.85098, 1.00000, 1.00000), 1.5 , 1.4 , "Helium" ),
- "LI": Element((0.80000, 0.50196, 1.00000), 1.28, 1.82, "Lithium" ),
- "BE": Element((0.76078, 1.00000, 0.00000), 0.96, 2 , "Beryllium" ),
- "B" : Element((1.00000, 0.70980, 0.70980), 0.83, 2 , "Boron" ),
- "C" : Element((0.56471, 0.56471, 0.56471), 0.68, 1.7 , "Carbon" ),
- "N" : Element((0.18824, 0.31373, 0.97255), 0.68, 1.55, "Nitrogen" ),
- "O" : Element((1.00000, 0.05098, 0.05098), 0.68, 1.52, "Oxygen" ),
- "F" : Element((0.56471, 0.87843, 0.31373), 0.64, 1.47, "Fluorine" ),
- "NE": Element((0.70196, 0.89020, 0.96078), 1.5 , 1.54, "Neon" ),
- "NA": Element((0.67059, 0.36078, 0.94902), 1.66, 2.27, "Sodium" ),
- "MG": Element((0.54118, 1.00000, 0.00000), 1.41, 1.73, "Magnesium" ),
- "AL": Element((0.74902, 0.65098, 0.65098), 1.21, 2 , "Aluminum" ),
- "SI": Element((0.94118, 0.78431, 0.62745), 1.2 , 2.1 , "Silicon" ),
- "P" : Element((1.00000, 0.50196, 0.00000), 1.05, 1.8 , "Phosphorus" ),
- "S" : Element((1.00000, 1.00000, 0.18824), 1.02, 1.8 , "Sulfur" ),
- "CL": Element((0.12157, 0.94118, 0.12157), 0.99, 1.75, "Chlorine" ),
- "AR": Element((0.50196, 0.81961, 0.89020), 1.51, 1.88, "Argon" ),
- "K" : Element((0.56078, 0.25098, 0.83137), 2.03, 2.75, "Potassium" ),
- "CA": Element((0.23922, 1.00000, 0.00000), 1.76, 2 , "Calcium" ),
- "SC": Element((0.90196, 0.90196, 0.90196), 1.7 , 2 , "Scandium" ),
- "TI": Element((0.74902, 0.76078, 0.78039), 1.6 , 2 , "Titanium" ),
- "V" : Element((0.65098, 0.65098, 0.67059), 1.53, 2 , "Vanadium" ),
- "CR": Element((0.54118, 0.60000, 0.78039), 1.39, 2 , "Chromium" ),
- "MN": Element((0.61176, 0.47843, 0.78039), 1.61, 2 , "Manganese" ),
@@ Diff output truncated at 10240 characters. @@
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