Water and Ethanol - OpenSCAD generated from chemical SDF files

thingiverse

Molecule structure STL files are created by OpenSCAD, a program generated from "sdf2scad.perl," a Perl script from NCBI PubChem's 3D SDF format files database. Model generator Perl scripts and OpenSCAD subroutines are provided for generating your own chemical files from SDF data or fine-tuning model parameters, requiring Perl and OpenSCAD. The most basic molecule is water (H2O), while ethanol (C2H5OH) serves as another fundamental molecule. More complex molecule models will be uploaded in the future. February 22, 2015: Updated "sdf2scad.scad" and "sdf2scad.perl"; see instructions for details on past updates. On ethanol models, separate "carbon" (black) STL files and "non-carbon" (white) STL files were generated for dual-extruder printers. However, these turned out dirty due to contamination, which is why separate files are not used in the series' other works. Despite this issue, generating separate files is still possible through the script (refer to instructions for details). Refer to "Caffeine and Melatonin" on Thingiverse: http://www.thingiverse.com/thing:690625, a model showcasing two materials with contamination evident when made using dual extrusion, and a single filament caffeine model followed by painting. For 3D printing, scaling of at least x8 is recommended for the "hydrogen bond's strength." This applies to other chemical structures as well; they can be scaled similarly to represent exact compositions. Additionally, users can convert SDF data into STL files through "sdf2scad.perl" (requires Perl) and OpenSCAD format, utilizing "sdf2scad.scad" (need Perl). Refer to the Perl script for limitations. Some CAD/slicer software might require fixing models, so modifications may be necessary. To create larger chemical student models, users can increase $fn or define $fs in the script depending on the atom ball size. To simplify painting models, attempts have been made to separate the model into carbon (black filament) and non-carbon (white filament with paint) parts for dual extruder 3D printers; however, contamination leads to a dirty model appearance. If you generate your own chemical STL files from SDF data using "sdf2scad.perl," you can run OpenSCAD twice. First set "$isc = 0;" to generate the non-carbon part, then "$isc = 1; $isxc = 0" to create carbon parts. February 22, 2015: Adjusted parameters in "sdf2scad.scad" to resolve "non-manifoldness errors," particularly with slicer software.