--- name: chem-vis description: Generate 2D structure images and interactive 3D viewers from chemical names or SMILES. Supports PNG\/SVG output for 2D and 3Dmol.js HTML viewers for 3D conformers. license: MIT --- # Chemical Visualization Skill ## Overview Generate publication-quality 2D molecular structure images and interactive 3D conformer viewers from chemical names, SMILES, or InChI strings. Needs network access to `*.nih.gov` servers to access PubChem for common names like caffeine, testosterone, estrogen, etc. Much of the code was generated by Claude, with careful validation, error fixing, and OPSIN integration by Geoff Hutchison. ## Quick Start ```bash # 2D structure image python scripts\/chem_2d.py "caffeine" --output caffeine.png # 3D interactive viewer python scripts\/chem_3d.py "caffeine" --output caffeine.html # Both at once python scripts\/chem_vis.py "caffeine" --both --output-dir .\/caffeine\/ ``` ## Dependencies ```bash pip install rdkit pubchempy py2opsin --break-system-packages ``` ## Scripts | Script | Purpose | |--------|---------| | `chem_2d.py` | Generate 2D structure images (PNG\/SVG) | | `chem_3d.py` | Generate 3D conformer viewers (HTML) | | `chem_vis.py` | Unified CLI for both | | `common.py` | Shared utilities (name resolution, etc.) | --- ## 2D Structure Images Generate static images of molecular structures. ### Usage ```bash python scripts\/chem_2d.py "aspirin" --output aspirin.png python scripts\/chem_2d.py "CCO" --input-type smiles --output ethanol.svg --format svg python scripts\/chem_2d.py "glucose" --width 400 --height 400 --output glucose.png ``` ### Options | Option | Description | Default | |--------|-------------|---------| | `--input-type`, `-t` | Input: `name`, `smiles`, `inchi` | `name` | | `--output`, `-o` | Output file path | `molecule.png` | | `--format`, `-f` | Output: `png`, `svg` | `png` | | `--width`, `-W` | Width in pixels | 300 | | `--height`, `-H` | Height in pixels | 300 | | `--kekulize`, `-k` | Show Kekulé structure | False | | `--show-atom-numbers`, `-n` | Display atom indices | False | | `--highlight-atoms` | Atom indices to highlight | None | ### Python API ```python from scripts.chem_2d import chemical_to_image, batch_convert # Single molecule chemical_to_image("caffeine", "caffeine.png", width=400, height=400) # Batch conversion chemicals = ["aspirin", "ibuprofen", "acetaminophen"] results = batch_convert(chemicals, output_dir=".\/structures\/", format="svg") ``` --- ## 3D Conformer Viewers Generate interactive HTML viewers with 3Dmol.js. ### Usage ```bash python scripts\/chem_3d.py "dopamine" --output dopamine.html python scripts\/chem_3d.py "CCO" --input-type smiles --style ballstick --output ethanol.html python scripts\/chem_3d.py "serotonin" --embed --output serotonin_widget.html ``` ### Options | Option | Description | Default | |--------|-------------|---------| | `--input-type`, `-t` | Input: `name`, `smiles` | `name` | | `--output`, `-o` | Output file path | `molecule_3d.html` | | `--width`, `-W` | Viewer width (px) | 500 | | `--height`, `-H` | Viewer height (px) | 400 | | `--style`, `-s` | Style: `stick`, `sphere`, `line`, `ballstick` | `stick` | | `--conformers`, `-c` | Conformers to sample | 10 | | `--no-optimize` | Skip MMFF optimization | False | | `--no-controls` | Hide interactive buttons | False | | `--embed` | Output snippet without HTML wrapper | False | ### Embed Mode Use `--embed` to generate a snippet for inserting into existing web pages: ```bash python scripts\/chem_3d.py "aspirin" --embed --output aspirin_widget.html ``` The parent page must load 3Dmol.js: ```html