Initial commit

.editorconfig

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+root = true
+
+[*]
+charset = utf-8
+indent_style = tab
+indent_size = 4
+insert_final_newline = true
+end_of_line = lf
+
+[*.{yml,yaml}]
+indent_style = space
+indent_size = 2

.github/.templateMarker

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+KOLANICH/python_project_boilerplate.py

.github/dependabot.yml

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+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "daily"
+    allow:
+      - dependency-type: "all"

.github/workflows/CI.yml

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+name: CI
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+jobs:
+  build:
+    runs-on: ubuntu-22.04
+    steps:
+      - name: typical python workflow
+        uses: KOLANICH-GHActions/typical-python-workflow@master
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}

.gitignore

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+__pycache__
+*.pyc
+*.pyo
+./mol2scad.py.egg-info
+./build
+./dist
+./.eggs
+*.mol
+*.sdf
+*.scad

.gitlab-ci.yml

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+image: registry.gitlab.com/kolanich-subgroups/docker-images/fixed_python:latest
+#image: registry.gitlab.com/kolanich-subgroups/docker-images/python_graal_docker:latest
+
+variables:
+  DOCKER_DRIVER: overlay2
+  SAST_ANALYZER_IMAGE_TAG: latest
+  SAST_DISABLE_DIND: "true"
+  SAST_CONFIDENCE_LEVEL: 5
+  CODECLIMATE_VERSION: latest
+
+include:
+  - template: SAST.gitlab-ci.yml
+  - template: Code-Quality.gitlab-ci.yml
+
+build:
+  tags:
+    - shared
+  stage: build
+  variables:
+    GIT_DEPTH: "1"
+    PYTHONUSERBASE: ${CI_PROJECT_DIR}/python_user_packages
+
+  cache:
+    paths:
+      - $PYTHONUSERBASE
+      - ./molFiles
+
+  before_script:
+    - export PATH="$PATH:$PYTHONUSERBASE/bin" # don't move into `variables`
+    - mkdir ./molFiles || true;
+    - wget -nc -O ./molFiles/CuPc.sdf https://webbook.nist.gov/cgi/cbook.cgi?Str3File=C147148 || true
+    - wget -nc -O ./molFiles/DCM.sdf https://webbook.nist.gov/cgi/cbook.cgi?Str3File=C75092 || true
+    - mkdir ./scad
+  script:
+    - python3 setup.py bdist_wheel
+    - pip3 install --upgrade --user --pre ./dist/*.whl
+    - coverage run -a --source=mol2scad mol2scad.py ./molFiles/CuPc.sdf >./scad/CuPc.scad
+    - coverage run -a --source=mol2scad mol2scad.py ./molFiles/DCM.sdf > ./scad/DCM.scad
+    - cp ./util.scad ./scad/
+    - coverage report -m
+    - coverage xml
+  coverage: /^TOTAL(?:\s*\d+){4}\s(\d+%).+/
+  artifacts:
+    paths:
+      - dist
+      - scad
+    reports:
+      #junit: ./rspec.xml
+      cobertura: ./coverage.xml

Code_Of_Conduct.md

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+No codes of conduct!

MANIFEST.in

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+include UNLICENSE
+include *.md
+include tests
+include .editorconfig

ReadMe.md

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+mol2scad.py [![Unlicensed work](https://raw.githubusercontent.com/unlicense/unlicense.org/master/static/favicon.png)](https://unlicense.org/)
+===============
+~~[![GitLab Build Status](https://gitlab.com/KOLANICH/mol2scad.py/badges/master/pipeline.svg)](https://gitlab.com/KOLANICH/mol2scad.py/pipelines/master/latest)~~
+~~![GitLab Coverage](https://gitlab.com/KOLANICH/mol2scad.py/badges/master/coverage.svg)~~
+[![Libraries.io Status](https://img.shields.io/librariesio/github/KOLANICH/mol2scad.py.svg)](https://libraries.io/github/KOLANICH/mol2scad.py)
+[![Code style: antiflash](https://img.shields.io/badge/code%20style-antiflash-FFF.svg)](https://codeberg.org/KOLANICH-tools/antiflash.py)
+
+This tool converts `mol` and `sdf` files into OpenSCAD files showing a 3D model of a molecule. Either run it in this folder or copy `util.scad` to the folder with generated files. Also you will need [scad-utils](https://github.com/OskarLinde/scad-utils.git) either installed or put in the same dir.
+
+Requirements
+------------
+* [`mollusk`](https://github.com/georglind/mollusk) ![License](https://img.shields.io/github/license/georglind/mollusk.svg) - `mol` (and `sdf`) file parser
+* [`webcolors`](https://github.com/ubernostrum/webcolors) [![PyPi Status](https://img.shields.io/pypi/v/webcolors.svg)](https://pypi.python.org/pypi/webcolors) [![CI Build Status](https://github.com/ubernostrum/webcolors/workflows/CI/badge.svg)](https://github.com/ubernostrum/webcolors/actions?query=workflow%3ACI) ![License](https://img.shields.io/github/license/ubernostrum/webcolors.svg) - colors
+* [`SolidPython`](https://github.com/SolidCode/SolidPython) [![PyPi Status](https://img.shields.io/pypi/v/plumbum.svg)](https://pypi.python.org/pypi/solid) [![CircleCI Build Status](https://circleci.com/gh/SolidCode/SolidPython.svg?style=shield)](https://circleci.com/gh/SolidCode/SolidPython) ![License](https://img.shields.io/github/license/SolidCode/SolidPython.svg) - OpenSCAD AST
+* `mendeleev` [![PyPi Status](https://img.shields.io/pypi/v/mendeleev.svg)](https://pypi.org/pypi/mendeleev) - chemical elements database
+* [`plumbum`](https://github.com/tomerfiliba/plumbum) [![PyPi Status](https://img.shields.io/pypi/v/plumbum.svg)](https://pypi.org/pypi/plumbum)
+  [![CI Build Status](https://github.com/tomerfiliba/plumbum/workflows/CI/badge.svg)](https://github.com/tomerfiliba/plumbum/actions)
+  [![Coveralls Coverage](https://coveralls.io/repos/tomerfiliba/plumbum/badge.svg?branch=master&service=github)](https://coveralls.io/github/tomerfiliba/plumbum?branch=master)
+ ![License](https://img.shields.io/github/license/tomerfiliba/plumbum.svg) - for command line interface

UNLICENSE

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+This is free and unencumbered software released into the public domain.
+
+Anyone is free to copy, modify, publish, use, compile, sell, or
+distribute this software, either in source code form or as a compiled
+binary, for any purpose, commercial or non-commercial, and by any
+means.
+
+In jurisdictions that recognize copyright laws, the author or authors
+of this software dedicate any and all copyright interest in the
+software to the public domain. We make this dedication for the benefit
+of the public at large and to the detriment of our heirs and
+successors. We intend this dedication to be an overt act of
+relinquishment in perpetuity of all present and future rights to this
+software under copyright law.
+
+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 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.
+
+For more information, please refer to <https://unlicense.org/>

mol2scad.py

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+from mol.parser import parse as parseMol
+import solid as sld
+import mendeleev
+import webcolors
+
+from plumbum import cli
+
+class rot2Vec(sld.OpenSCADObject):
+	def __init__(self, v2, v1=[0, 0, 1]):
+		sld.OpenSCADObject.__init__(self, 'rot2Vec', {"v2":v2, "v1":v1})
+
+def rotByVec(v):
+	return rot2Vec(v)
+
+def convertWebColorToOpenScad(cstr):
+	try:
+		res = webcolors.hex_to_name(cstr)
+	except:
+		res = [c/255 for c in webcolors.hex_to_rgb(cstr)]
+	#res.append(0.5)
+	return res
+
+class singleBond(sld.OpenSCADObject):
+	def __init__(self, l1, l2, centr, length, color1, color2):
+		sld.OpenSCADObject.__init__(self, 'singleBond', {
+			"l1":l1,
+			"l2":l2,
+			"color1": color1,
+			"color2": color2,
+		})
+
+def makeSingleBond(l1, l2, center, length, color1, color2):
+	return singleBond(l1, l2, center, length, convertWebColorToOpenScad(color1), convertWebColorToOpenScad(color2))
+
+class bond(sld.OpenSCADObject):
+	def __init__(self, a1v, a2v, color1, color2, multiplicity=1):
+		sld.OpenSCADObject.__init__(self, 'bond', {
+			"a1v":a1v,
+			"a2v":a2v,
+			"color1": color1,
+			"color2": color2,
+			"multiplicity": multiplicity
+		})
+
+def makeBond(a1v, a2v, color1, color2, multiplicity=1):
+	return bond(a1v, a2v, convertWebColorToOpenScad(color1), convertWebColorToOpenScad(color2), multiplicity=multiplicity)
+
+class module(sld.OpenSCADObject):
+	def __init__(self, **kwargs):
+		sld.OpenSCADObject.__init__(self, 'module', kwargs)
+
+def useOpenScadVariable(obj, vars={}):
+	s=sld.scad_render(obj)
+	for placeholder, replacement in vars.items():
+		s=s.replace('"'+placeholder+'"', replacement)
+	return s
+
+def genScadSource(name, vectors, spieces, bonds, lFact=1, r=1, bondR=None, bondSpacingFactor=3):
+	if not bondR:
+		bondR=0.05*r
+
+	spiecesDescr = {el:mendeleev.element(el) for el in spieces}
+	maxRad=max( (sp.covalent_radius for sp in spiecesDescr.values()) )
+
+	def createElementCall(name, el):
+		class element(sld.OpenSCADObject):
+			def __init__(self, pos):
+				sld.OpenSCADObject.__init__(self, el.name, {"pos":pos})
+		element.__name__=el.name
+		return element
+
+
+	elToScadRemap={elN:createElementCall(elN, sp) for elN, sp in spiecesDescr.items()}
+
+	spiecesChem = [spiecesDescr[el] for el in spieces]
+	spiecesScad = [elToScadRemap[el] for el in spieces]
+
+	def createElementModule(name, sp):
+		elModSrc="module "+sp.name+"(pos=[0,0,0]){"+useOpenScadVariable(
+			sld.translate("%%%positionExprPlaceholder%%%")(
+				sld.color(convertWebColorToOpenScad(sp.cpk_color))(
+					sld.sphere(r*sp.covalent_radius/maxRad)
+				)
+			),
+			{"%%%positionExprPlaceholder%%%": "pos*lFact"}
+		)+"\n}"
+		return elModSrc
+
+	src=[
+		"$fs=0.1;",
+		"r="+str(r)+";",
+		"bondR="+str(bondR)+";",
+		"lFact="+str(lFact)+";",
+		"bondSpacingFactor="+str(bondSpacingFactor)+";",
+		"include <./util.scad>",
+	]
+	src.extend((createElementModule(elN, sp) for elN, sp in spiecesDescr.items()))
+
+	for i, v in enumerate(vectors):
+		src.append(
+			sld.scad_render(
+				spiecesScad[i](v)
+			)
+		)
+
+	for i, (a1, a2, mult) in enumerate(bonds):
+		src.append(
+			sld.scad_render(
+				makeBond(vectors[a1], vectors[a2], spiecesChem[a1].cpk_color, spiecesChem[a2].cpk_color, mult)
+			)
+		)
+	return src
+
+class mol2scadApp(cli.Application):
+	"""Converts .mol and .sdf files into OpenSCAD .scad files, which can be rendered into 3D models."""
+
+	r=cli.SwitchAttr(["radius"], float, default=1., help="A radius of the biggest atom.")
+	bondRFactor=cli.SwitchAttr(["bond-radius-factor"], float, default=0.05, help="A radius of a single bond is this number multiplied by radius of the largest atom.")
+	bondSpacingFactor=cli.SwitchAttr(["bond-spacing-factor"], float, default=3., help="When a bond is multiple its parts are placed on the circumference of the bond radius multiplied by this number.")
+	lFact=cli.SwitchAttr(["l-factor"], float, default=1., help="A factor bond length are multiplied. Useful when atoms overlap and you want to see bonds clearly.")
+
+	def main(self, fileName:cli.ExistingFile):
+		print("\n".join(genScadSource(*parseMol(fileName), lFact=self.lFact, r=self.r, bondR=self.bondRFactor*self.r, bondSpacingFactor=3)))
+
+mol2scadApp.run()

pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.2.0", "wheel", "setuptools_scm[toml]>=3.4.3"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "mol2scad"
+authors = [{name = "KOLANICH"}]
+description = "A tool to render mol and sdf files to OpenSCAD"
+readme = "ReadMe.md"
+keywords = ["mol", "structure data file", "OpenSCAD", "molecule"]
+license = {text = "Unlicense"}
+classifiers = [
+	"Programming Language :: Python",
+	"Programming Language :: Python :: 3",
+	"Development Status :: 4 - Beta",
+	"Environment :: Other Environment",
+	"Intended Audience :: End Users/Desktop",
+	"License :: Public Domain",
+	"Operating System :: OS Independent",
+	"Topic :: Software Development :: Libraries :: Python Modules",
+	"Intended Audience :: Science/Research",
+	"Intended Audience :: Education",
+]
+urls = {Homepage = "https://codeberg.org/KOLANICH-physics/mol2scad.py"}
+requires-python = ">=3.4"
+dependencies = [
+	"webcolors", # @ git+https://github.com/ubernostrum/webcolors.git"
+	"mollusk", # @ git+https://github.com/georglind/mollusk.git"
+	"solid", # @ git+https://github.com/SolidCode/SolidPython.git"
+	"mendeleev",
+	"plumbum # @ git+https://github.com/tomerfiliba/plumbum.git",
+]
+dynamic = ["version"]
+
+[tool.setuptools]
+zip-safe = true
+py-modules = ["mol2scad"]
+include-package-data = false
+
+[tool.setuptools_scm]

util.scad

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+include <scad-utils/linalg.scad>
+
+function normalize(vec) = vec / norm(vec);
+
+function identity3()=[[1,0,0],[0,1,0],[0,0,1]];
+
+module rot2Vec(v2, v1=[0, 0, 1]){
+	v1=v1;
+	v2=normalize(v2);
+
+	ax=cross(v1, v2);
+	c=v1 * v2;
+	ssc = [
+		[0, -ax[2], ax[1]],
+		[ax[2], 0, -ax[0]],
+		[-ax[1], ax[0], 0]
+	];
+
+	m=identity3() + ssc + (ssc*ssc)*(1-c)/(ax*ax);
+	//echo(m);
+	multmatrix(m)
+		children();
+};
+
+module singleBond(l1, l2, color1, color2){
+	union(){
+		color(color2)
+			cylinder(h=l2, r=bondR);
+		translate([0, 0, -l1])
+			color(color1)
+				cylinder(h=l1, r=bondR);
+	}
+};
+
+module bond(a1v, a2v, color1, color2, multiplicity=1){
+	a1v=a1v*lFact;
+	a2v=a2v*lFact;
+	centr=(a2v+a1v)/2;
+	bondVec=normalize(a2v-a1v);
+	//echo(bondVec);
+	l1=norm(centr-a1v);
+	l2=norm(centr-a2v);
+	mOfs=multiplicity%2;
+	bondSpace=bondSpacingFactor*bondR;
+	translate(centr){
+		union(){
+			rot2Vec(bondVec){
+				if (multiplicity>1){
+					for (i = [0: multiplicity-1]){
+						rotate(360/multiplicity*i, [0,0, 1])
+							translate([0, bondSpace, 0])
+								singleBond(l1, l2, color1, color2);
+					};
+				}else{
+					singleBond(l1, l2, color1, color2);
+				};
+			};
+		};
+	};
+};
+