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Documentation Index

Fetch the complete documentation index at: https://docs.revilico.bio/llms.txt

Use this file to discover all available pages before exploring further.

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Why Use Compound Design?

Compound Design is Revilico’s interactive molecular structure editor, enabling medicinal chemists and computational scientists to draw, edit, and export chemical structures directly within the platform. New compound ideas can be sketched from scratch, existing structures modified for analog design, and the resulting SMILES exported immediately to docking, property prediction, or generative chemistry engines without leaving the Revilico environment.
Compound Design Interface

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Background

Structure drawing is a core activity in drug discovery, from initial hit design through lead optimization. Having a drawing tool integrated directly with computational engines eliminates the friction of exporting from a standalone editor, converting file formats, and re-uploading. Compound Design uses the Ketcher chemical structure editor, a browser-based drawing tool that produces valid SMILES, MOL, and SDF output and supports the full range of organic chemistry including stereochemistry, isotope labels, R-groups, and query atoms.

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Interface

Left toolbar (drawing tools):
  • Bond drawing tools: single, double, triple bonds and aromatic ring
  • Atom selection and movement tools
  • Text and label tools
  • Stereo bond tools (wedge, dash)
  • R-group and S-group tools
  • Reaction arrow tools
  • Chain and template tools
Right atom palette: The quick-access atom palette on the right side of the canvas provides single-click placement for the most common elements in medicinal chemistry: H, C, N, O, S, P, F, Cl, Br, I. Bottom ring template bar: Pre-built ring templates are available at the bottom of the canvas for common ring systems: cyclopentane, cyclohexane, benzene, cyclopentadiene, cycloheptane, cyclooctane, and fused ring starters. Top toolbar:
  • File operations: new, open, save, copy, paste, delete
  • Undo and redo (also available via Ctrl+Z / Ctrl+Y)
  • Zoom in and out
  • Analysis tools: calculate properties, check structure
  • 3D view toggle
  • Atom map and R-group label tools
  • Mode selector (Molecules / Reactions)

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Workflow

  1. Draw a structure using the bond and atom tools, or open an existing structure file
  2. Edit substituents, ring systems, stereochemistry, and functional groups using the drawing tools
  3. Use the mode selector to switch between molecule drawing and reaction scheme drawing
  4. Export the structure as SMILES for use in any Revilico engine input, or save as MOL/SDF for downstream file-based workflows

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Running the Engine

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Inputs

InputDescription
New structureDraw from scratch using the on-canvas tools
Existing fileOpen a MOL, SDF, or SMILES file from local disk or Data Engineering

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Outputs

  • SMILES: Canonical SMILES string for direct copy-paste into any Revilico engine
  • MOL/SDF file: 2D structure file for download or export to file-based workflows
  • Reaction SMILES: For reaction scheme mode, outputs a reaction SMILES string