Addon

.gitignore

@@ -4,6 +4,7 @@
 .vscode/settings.json
 *.pyc
 *.Rproj
+*.zip
 ~*.xlsx
 paper/paper.html
 paper/paper.log

blender/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 - 2024, Daniel Antonio Negrón (dnanto/remaindeer)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

blender/README.md

@@ -0,0 +1,29 @@
+# addon
+
+[![Blender 3.0.0](https://img.shields.io/badge/blender-3.0.0-%23f4792b.svg)]()
+
+Calculate meshes for icosahedral virus capsids.
+
+## Installation
+
+1. Download [latest version](https://github.com/dnanto/democapsid) of blendocapsid.
+2. From Blender: Edit > Preferences
+3. Select the 'Add-ons tab' and click 'Install' in the upper right.
+4. Navigate to the zip file and click 'Install Add-on from File'
+
+## Contributing
+
+Have a bug fix or a new feature you'd like to see? Send it on over! Please make sure you create an issue that addresses your fix/feature so we can discuss the contribution.
+
+1. Fork this repo!
+2. Create your feature branch: `git checkout -b features/fix-bug`
+3. Commit your changes: `git commit -m 'Fixes the following...'`
+4. Push the branch: `git push origin features/fix-bug`
+5. Submit a pull request.
+6. Create an [issue]().
+
+## License
+
+MIT
+
+See the [license](./LICENSE) document for the full text.

blender/blendocapsid/__init__.py

@@ -0,0 +1,45 @@
+bl_info = {
+    'name': 'blendocapsid',
+    'author': 'Daniel Antonio Negrón',
+    'version': (0, 0, 1),
+    'blender': (3, 0, 0),
+    'location': 'Objects > Add Capsid Mesh',
+    'description': 'Calculate meshes for icosahedral virus capsids with democapsid.',
+    'warning': '',
+    'wiki_url': 'https://github.com/dnanto/democapsid',
+    'support': 'COMMUNITY',
+    'category': 'Add Mesh'
+}
+
+__version__ = '.'.join(map(str, bl_info['version']))
+
+
+# Handle Reload Scripts
+
+if 'reload' in locals():
+    import importlib as il
+    il.reload(reload)
+    reload.all()
+
+import blendocapsid.reload as reload
+
+
+def register():
+    from . import patch
+    patch.add_local_modules_to_path()
+
+    from blendocapsid import operators, panels
+
+    operators.register()
+    panels.register()
+
+
+def unregister():
+    from blendocapsid import operators, panels
+
+    operators.unregister()
+    panels.unregister()
+
+
+if __name__ == '__main__':
+    register()

blender/blendocapsid/operators.py

@@ -0,0 +1,72 @@
+import bpy
+
+
+class CapsidMesh(bpy.types.Operator):
+    """Add icosahedral capsid mesh."""
+    bl_idname = "object.add_mesh"
+    bl_label = "Add Capsid Mesh"
+    bl_options = {"REGISTER", "UNDO"}
+    axis_items = [
+        ("2", "2", "two-fold axial symmetry", 2),
+        ("3", "3", "three-fold axial symmetry", 3),
+        ("5", "5", "five-fold axial symmetry", 5)
+    ]
+    tile_items = [
+        (key, key, f"{key} lattice", idx)
+        for idx, key in enumerate((pfx + ele for pfx in ("", "dual") for ele in ("hex", "trihex", "snubhex", "rhombitrihex")), start=1)
+    ]
+    mode_items = [
+        ("ico", "ico", "render icosahedral mesh", 1),
+        ("tri", "tri", "render triangular Caspar-Klug meshes", 2)
+    ]
+
+    h: bpy.props.IntProperty(name="h", description="the h Caspar-Klug parameter", default=1, min=0)
+    k: bpy.props.IntProperty(name="k", description="the k Caspar-Klug parameter", default=0, min=0)
+    H: bpy.props.IntProperty(name="H", description="the H Caspar-Klug parameter", default=1, min=0)
+    K: bpy.props.IntProperty(name="K", description="the K Caspar-Klug parameter", default=0, min=0)
+    a: bpy.props.EnumProperty(name="a", description="the axial symmetry", items=axis_items, default=axis_items[2][3])
+    R: bpy.props.FloatProperty(name="R", description="the hexagonal lattice unit circumradius", default=1, min=0)
+    t: bpy.props.EnumProperty(name="t", description="the hexagonal lattice unit tile", items=tile_items, default=tile_items[0][3])
+    s: bpy.props.FloatProperty(name="s", description="the sphericity value", default=0, min=-1, max=1)
+    m: bpy.props.EnumProperty(name="mode", description="the render mode", items=mode_items, default=mode_items[0][3])
+    iter: bpy.props.IntProperty(name="iter", description="the iteration number for numerical methods", default=100, min=1)
+    tol: bpy.props.FloatProperty(name="tol", description="the machine epsilon for numerical methods", default=1E-15, min=0)
+
+    def execute(self, context):
+        from blendocapsid.modules.democapsid.democapsid import (calc_ckm,
+                                                                calc_ico,
+                                                                calc_lattice)
+
+        m, a, s = self.m, int(self.a), self.s
+        ckp = (self.h, self.k, self.H, self.K)
+        lat = calc_lattice(self.t, self.R)
+
+        if m == "ico":
+            meshes = calc_ico(ckp, lat, a=a, s=s, iter=self.iter, tol=self.tol)
+        elif m == "tri":
+            meshes = calc_ckm(ckp, lat)
+
+        for i, mesh in enumerate(meshes[1:], start=1):
+            collection = bpy.data.collections.new(f"face-{i}")
+            bpy.context.scene.collection.children.link(collection)
+            for j, polygon in enumerate(mesh, start=1):
+                mesh = bpy.data.meshes.new(name=f"polygon_msh[{i},{j}]")
+                mesh.from_pydata(*polygon, [])
+                mesh.validate(verbose=True)
+                obj = bpy.data.objects.new(f"polygon_obj-[{i},{j}]", mesh)
+                collection.objects.link(obj)
+
+        return {"FINISHED"}
+
+
+def menu_func(self, context):
+    self.layout.operator(CapsidMesh.bl_idname)
+
+
+def register():
+    bpy.utils.register_class(CapsidMesh)
+    bpy.types.VIEW3D_MT_object.append(menu_func)
+
+
+def unregister():
+    bpy.utils.unregister_class(CapsidMesh)

blender/blendocapsid/panels.py

@@ -0,0 +1,9 @@
+import bpy
+
+
+def register():
+    """Register classes, types, etc."""
+
+
+def unregister():
+    """Unregister classes, types, etc."""

blender/blendocapsid/patch.py

@@ -0,0 +1,12 @@
+import os
+import sys
+
+
+def add_local_modules_to_path():
+    """Add local modules directory to system path. This is done so the
+    addon can find it's dependencies."""
+    modules_dir = os.path.join(os.path.dirname(__file__), 'modules')
+    modules_dir = os.path.abspath(modules_dir)
+
+    if modules_dir not in sys.path:
+        sys.path.append(modules_dir)

blender/blendocapsid/reload.py

@@ -0,0 +1,16 @@
+import blendocapsid
+
+
+def all():
+    import importlib as il
+
+    # Reload package
+    il.reload(blendocapsid)
+
+    # Reload operators subpackage
+    il.reload(blendocapsid.operators)
+
+    # Reload panels subpackage
+    il.reload(blendocapsid.panels)
+
+    print('blendocapsid: Reload finished.')

blender/makefile

@@ -0,0 +1,8 @@
+.PHONY: dist clean
+
+dist:
+	python package.py
+
+clean:
+	rm -rf ./dist
+	find . -name "*.pyc" -delete

blender/package.py

@@ -0,0 +1,88 @@
+"""Packages the blendocapsid and dependency"""
+import importlib
+import os
+import re
+import zipfile
+
+import blendocapsid
+
+ignored_directories = (
+    '__pycache__',
+    '.DS_Store'
+)
+
+
+def gather_files(basedir, arc_prefix=''):
+    """Walk the given directory and return a sequence of filepath, archive name
+    pairs.
+
+    Args:
+        basedir: The directory to start the walk
+
+        arc_prefix: A path to join to the front of the relative (to basedir)
+            file path
+
+    Returns:
+        A sequence of (filepath, archive name) pairs
+    """
+    results = []
+
+    for path, subdirectories, files in os.walk(basedir):
+        if os.path.basename(path) in ignored_directories:
+            continue
+
+        for file in files:
+            relative_path = os.path.join(path, file)
+            full_path = os.path.abspath(relative_path)
+            arcname = os.path.relpath(full_path, os.path.dirname(basedir))
+            arcname = os.path.join(arc_prefix, arcname)
+
+            results.append((full_path, arcname))
+
+    return results
+
+
+def get_required_modules():
+    """Parse the requirements.txt file to determine dependencies.
+
+    Returns:
+        A sequence of module names
+    """
+    with open('requirements.txt') as file:
+        data = file.read()
+        modules = data.split('\n')
+        pattern = '([A-Za-z0-9]+)(?:[<=>]+.*\n)?'
+
+        def get_module_name(s):
+            result = re.search(pattern, s)
+
+            if result:
+                return result.group()
+
+        modules = [get_module_name(s) for s in modules if s]
+
+        return modules
+
+
+def run():
+    try:
+        os.mkdir('dist')
+
+    except FileExistsError:
+        pass
+
+    zip_entries = gather_files('blendocapsid')
+
+    for module in get_required_modules():
+        module = importlib.import_module(module)
+        zip_entries += gather_files(os.path.dirname(module.__file__), os.path.join('blendocapsid', 'modules'))
+
+    filename = f'blendocapsid-{blendocapsid.__version__}.zip'
+    filepath = os.path.abspath(os.path.join('dist', filename))
+    with zipfile.ZipFile(filepath, 'w') as dist_zip:
+        for filename, arcname in zip_entries:
+            dist_zip.write(filename, arcname)
+
+
+if __name__ == '__main__':
+    run()

blender/requirements.txt

@@ -0,0 +1 @@
+democapsid @ git+https://github.com/dnanto/democapsid.git#egg=democapsid&subdirectory=py

js/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 - 2024, Daniel Antonio Negrón (dnanto/remaindeer)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

py/src/democapsid/__main__.py

@@ -3,7 +3,7 @@
 import sys
 
 from .cli import parse_args
-from .democapsid import calc_ckm, calc_ckv, calc_ico, calc_lattice, cylinderize
+from .democapsid import calc_ckm, calc_ico, calc_lattice
 
 args = parse_args(sys.argv[1:])
 h, k, H, K, a, R, t, s, m = (getattr(args, key) for key in "h,k,H,K,a,R,t,s,m".split(","))

py/src/democapsid/cli.py

@@ -8,16 +8,15 @@ def parse_args(argv):
         description="Calculate meshes for icosahedral virus capsids."
     )
     for ele in "hkHK":
-        parser.add_argument(ele, default=1, type=int, help=f"the {ele} Caspar-Klug parameter")
+        parser.add_argument(ele, type=int, help=f"the {ele} Caspar-Klug parameter")
     choices = (5, 3, 2)
-    parser.add_argument("-a", "-axis", default=choices[0], choices=choices, type=int, help=f"the axial symmetry: {choices}")
+    parser.add_argument("-a", "-axis", default=choices[0], choices=choices, type=int, help="the axial symmetry")
     parser.add_argument("-R", "-radius", default=1, type=int, help="the hexagonal lattice unit circumradius")
-    choices = ("hex", "trihex", "snubhex", "rhombitrihex")
-    choices = (*choices, *("dual" + ele for ele in choices))
+    choices = tuple(pfx + ele for pfx in ("", "dual") for ele in ("hex", "trihex", "snubhex", "rhombitrihex"))
     parser.add_argument("-t", "-tile", default=choices[0], choices=choices, help="the hexagonal lattice unit tile")
     parser.add_argument("-s", "-sphericity", default=0, type=float, help="the sphericity value")
     choices = ("ico", "tri")
     parser.add_argument("-m", "-mode", default=choices[0], choices=choices, help="the render mode")
-    parser.add_argument("-iter", default=100, type=int, help="the number of iterations for numerical methods")
-    parser.add_argument("-tol", default=1E-15, type=float, help="the machine epsilon")
+    parser.add_argument("-iter", default=100, type=int, help="the iteration number for numerical methods")
+    parser.add_argument("-tol", default=1E-15, type=float, help="the machine epsilon for numerical methods")
     return parser.parse_args(argv)