restructure

.gitignore

@@ -8,3 +8,4 @@
 paper/paper.html
 paper/paper.log
 paper/paper.pdf
+/py/src/democapsid.egg-info

CITATION.cff

@@ -3,102 +3,37 @@
 
 cff-version: 1.2.0
 title: >-
-  democapsid
-message: 'If you use this software, please cite it as below.'
+    democapsid
+message: "If you use this software, please cite it as below."
 type: software
 authors:
-  - given-names: Daniel
-    family-names: Negrón
-    email: [email protected]
-    affiliation: George Mason University
-    orcid: 'https://orcid.org/0000-0002-6123-2441'
-identifiers:
-  - type: doi
-    value: 10.1101/2020.12.02.408252
-    description: The bioRxiv preprint of the paper.
-repository-code: 'https://github.com/dnanto/democapsid'
-url: 'https://github.com/dnanto/democapsid/capsid.html'
-abstract: >-
-  This work implements Caspar-Klug Theory to
-  generate high-quality, vectorized capsid cartoons 
-  in the browser and is the first online tool that 
-  provides comprehensive style customization,
-   geometry, and SVG export of icosahedra and nets
-  with different lattice structures.
-keywords:
-  - virus
-  - capsid
-  - caspar-klug
-  - moody
-  - icosahedron
-  - prolate
-  - oblate
-  - elongated 
-  - lattice
-  - 2D
-  - 3D
-  - svg
-  - biology
-  - graphics
-  - render
-  - projection
-  - perspective
-  - publication
-  - figure
-  - demoscene
-license: MIT
-preferred-citation:
-  type: article
-  authors:
     - given-names: Daniel
       family-names: Negrón
       email: [email protected]
       affiliation: George Mason University
-      orcid: 'https://orcid.org/0000-0002-6123-2441'
-  doi: 10.1101/2020.12.02.408252
-  journal: bioRxiv
-  abstract: >-
+      orcid: "https://orcid.org/0000-0002-6123-2441"
+identifiers:
+    - type: doi
+      value: 10.1101/2020.12.02.408252
+      description: The bioRxiv preprint of the paper.
+repository-code: "https://github.com/dnanto/democapsid"
+url: "https://github.com/dnanto/democapsid/capsid.html"
+abstract: >-
     This work implements Caspar-Klug Theory to
     generate high-quality, vectorized capsid cartoons 
     in the browser and is the first online tool that 
     provides comprehensive style customization,
      geometry, and SVG export of icosahedra and nets
     with different lattice structures.
-    Motivation Few online services exist for rendering
-    high-quality viral capsid figures compatible with
-    common productivity software to develop effective
-    infographics in the field of virology.
-
-
-    Results The capsid.js library renders class I viral
-    capsids within an online application that
-    parameterizes style options, perspectives, and
-    lattice patterns with SVG export.
-
-
-    Availability This project is actively developed on
-    GitHub (https://github.com/dnanto/capsid),
-    distributed under the MIT License, hosted on GitHub
-    Pages, and runs on modern browsers
-    (https://dnanto.github.io/capsid/capsid.html).
-
-
-    Supplementary information Supplementary data are
-    available on GitHub.
-  month: 12
-  title: >-
-    Vectorized Capsid Rendering in the Browser with
-    Capsid.js
-  year: 2021
-  keywords:
+keywords:
     - virus
     - capsid
     - caspar-klug
     - moody
     - icosahedron
     - prolate
     - oblate
-    - elongated 
+    - elongated
     - lattice
     - 2D
     - 3D
@@ -110,4 +45,69 @@ preferred-citation:
     - perspective
     - publication
     - figure
-    - demoscene
+    - demoscene
+license: MIT
+preferred-citation:
+    type: article
+    authors:
+        - given-names: Daniel
+          family-names: Negrón
+          email: [email protected]
+          affiliation: George Mason University
+          orcid: "https://orcid.org/0000-0002-6123-2441"
+    doi: 10.1101/2020.12.02.408252
+    journal: bioRxiv
+    abstract: >-
+        This work implements Caspar-Klug Theory to
+        generate high-quality, vectorized capsid cartoons 
+        in the browser and is the first online tool that 
+        provides comprehensive style customization,
+         geometry, and SVG export of icosahedra and nets
+        with different lattice structures.
+        Motivation Few online services exist for rendering
+        high-quality viral capsid figures compatible with
+        common productivity software to develop effective
+        infographics in the field of virology.
+
+
+        Results The capsid.js library renders class I viral
+        capsids within an online application that
+        parameterizes style options, perspectives, and
+        lattice patterns with SVG export.
+
+
+        Availability This project is actively developed on
+        GitHub (https://github.com/dnanto/capsid),
+        distributed under the MIT License, hosted on GitHub
+        Pages, and runs on modern browsers
+        (https://dnanto.github.io/capsid/capsid.html).
+
+
+        Supplementary information Supplementary data are
+        available on GitHub.
+    month: 12
+    title: >-
+        Vectorized Capsid Rendering in the Browser with
+        Capsid.js
+    year: 2021
+    keywords:
+        - 2D
+        - 3D
+        - biology
+        - capsid
+        - caspar-klug
+        - demoscene
+        - elongated
+        - figure
+        - graphics
+        - icosahedron
+        - lattice
+        - oblate
+        - perspective
+        - projection
+        - prolate
+        - publication
+        - render
+        - svg
+        - virology
+        - virus

TODO.md

@@ -0,0 +1,4 @@
+-   [ ] comments/documentation
+-   [ ] python package
+-   [ ] R package
+-   [ ] Blender addo

py/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/README.rst

@@ -0,0 +1,6 @@
+==========
+democapsid
+==========
+
+
+Calculate meshes for icosahedral virus capsids.

democapsid/pyproject.toml → py/pyproject.toml

@@ -11,7 +11,7 @@ authors = [
 maintainers = [
   { name="Daniel Antonio Negrón", email="[email protected]" },
 ]
-description = "This package includes methods to calculate the coordinates of viral capsids."
+description = "Calculate meshes for icosahedral virus capsids."
 readme = "README.md"
 license = {text = "MIT License"}
 requires-python = ">=3.9.11"

py/src/democapsid/__init__.py

@@ -0,0 +1,7 @@
+#!/usr/bin/env python3
+
+"""Top-level package for democapsid."""
+
+__author__ = """Daniel Antonio Negrón"""
+__email__ = '[email protected]'
+__version__ = '0.0.1'

py/src/democapsid/__main__.py

@@ -0,0 +1,24 @@
+#!/usr/bin/env python3
+
+import sys
+from functools import partial
+
+from .cli import parse_args
+from .democapsid import calc_ckm, calc_ckv, calc_ico, calc_lattice, cylinderize
+
+args = parse_args(sys.argv[1:])
+h, k, H, K, s, R, t, c = args.h, args.k, args.H, args.K, args.symmetry, args.radius, args.tile, args.sphericity
+
+lattice = calc_lattice(t, R)
+ckv = calc_ckv(h, k, H, K, lattice[0])
+ckm = calc_ckm(ckv, lattice)
+
+if args.mode == "ico":
+    inflater = spherize if h == H and k == K else partial(cylinderize, s=s)
+    meshes = calc_ico(ckv, ckm, s, c, inflater)
+
+print("x", "y", "z", "face", "polygon", "point", sep="\t")
+for i, mesh in enumerate(meshes[1:], start=1):
+    for j, polygon in enumerate(mesh, start=1):
+        for k, point in enumerate(polygon[0], start=1):
+            print(*point, i, j, k, sep="\t")

py/src/democapsid/cli.py

@@ -0,0 +1,21 @@
+#!/usr/bin/env python3
+
+def parse_args(argv):
+    from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser
+    parser = ArgumentParser(
+        prog="democapsid",
+        formatter_class=ArgumentDefaultsHelpFormatter,
+        description="Calculate meshes for icosahedral virus capsids."
+    )
+    for ele in "hkHK":
+        parser.add_argument(ele, default=1, type=int, help=f"the {ele} lattice parameter")
+    choices = (5, 3, 2)
+    parser.add_argument("-symmetry", default=choices[0], type=int, help=f"the axial symmetry: {choices}")
+    parser.add_argument("-radius", default=1, type=int, help="the hexagonal lattice unit radius")
+    choices = ("hex", "trihex", "snubhex", "rhombitrihex")
+    choices = (*choices, *("dual" + ele for ele in choices))
+    parser.add_argument("-tile", default=choices[0], help="the hexagonal lattice unit tile")
+    parser.add_argument("-sphericity", default=0, type=float, help="the sphericity value")
+    choices = ("ico", "net")
+    parser.add_argument("-mode", default=choices[0], help="the sphericity value")
+    return parser.parse_args(argv)

democapsid/src/democapsid.py → py/src/democapsid/democapsid.py

@@ -1,23 +1,17 @@
 #!/usr/bin/env python3
 
 import sys
-from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser
-from itertools import chain
 from functools import partial
+from itertools import chain
 
 import numpy as np
 
-try:
-    import bpy
-except ImportError:
-    pass
-
-
 SQRT2 = np.sqrt(2)
 SQRT3 = np.sqrt(3)
 SQRT5 = np.sqrt(5)
 PHI = (1 + SQRT5) / 2
 
+
 ICO_CONFIG = (
     (),
     (),
@@ -561,63 +555,3 @@ def calc_ico(ckv, ckm, s, c, inflater):
             M = np.transpose(np.apply_along_axis(roro, 1, coors[v_idx,], t=i * (2 * np.pi) / s)) @ A
             meshes.append([([inflater(M @ point, coors, c) for point in vertices], edges) for vertices, edges in ckm[t_idx]])
     return meshes
-
-
-def parse_args(argv):
-    parser = ArgumentParser(formatter_class=ArgumentDefaultsHelpFormatter)
-    for ele in "hkHK":
-        parser.add_argument(ele, default=1, type=int, help=f"the {ele} lattice parameter")
-    choices = (5, 3, 2)
-    parser.add_argument("-symmetry", default=choices[0], type=int, help=f"the axial symmetry: {choices}")
-    parser.add_argument("-radius", default=1, type=int, help="the hexagonal lattice unit radius")
-    choices = ("hex", "trihex", "snubhex", "rhombitrihex")
-    choices = (*choices, *("dual" + ele for ele in choices))
-    parser.add_argument("-tile", default=choices[0], help="the hexagonal lattice unit tile")
-    parser.add_argument("-sphericity", default=0, type=float, help="the sphericity value")
-    choices = ("ico", "net")
-    parser.add_argument("-mode", default=choices[0], help="the sphericity value")
-    return parser.parse_args(argv)
-
-
-def main(argv):
-    args = parse_args(argv[1:])
-    h, k, H, K, s, R, t, c = args.h, args.k, args.H, args.K, args.symmetry, args.radius, args.tile, args.sphericity
-
-    lattice = calc_lattice(t, R)
-    ckv = calc_ckv(h, k, H, K, lattice[0])
-    ckm = calc_ckm(ckv, lattice)
-
-    if args.mode == "ico":
-        inflater = spherize if h == H and k == K else partial(cylinderize, s=s)
-        meshes = calc_ico(ckv, ckm, s, c, inflater)
-    else:
-        meshes = ckm
-
-    if "bpy" in sys.modules:
-        for obj in bpy.data.objects:
-            bpy.data.objects.remove(obj, do_unlink=True)
-
-        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)
-    else:
-        print("x", "y", "z", "face", "polygon", "point", sep="\t")
-        for i, mesh in enumerate(meshes[1:], start=1):
-            for j, polygon in enumerate(mesh, start=1):
-                for k, point in enumerate(polygon[0], start=1):
-                    print(*point, i, j, k, sep="\t")
-
-    return 0
-
-
-if __name__ == "__main__":
-    if "bpy" in sys.modules:
-        main(["capsid", "1", "1", "1", "2", "-symmetry", "5", "-sphericity", "0"])
-    else:
-        sys.exit(main(sys.argv))