CLI

Installation

Download prebuilt binaries from GitHub Releases, or build from source:

cargo install sci-form-cli

Commands

embed — Single molecule

Generate a 3D conformer for one SMILES string.

sci-form embed "CCO" --format xyz

Option	Default	Description
--seed, -s	42	RNG seed for reproducibility
--format, -f	json	Output format: json, xyz, sdf

JSON output (default):

$ sci-form embed "CCO"
{
  "smiles": "CCO",
  "num_atoms": 9,
  "coords": [0.123, -0.456, ...],
  "elements": [6, 6, 8, 1, 1, 1, 1, 1, 1],
  "bonds": [[0, 1, "SINGLE"], ...],
  "error": null,
  "time_ms": 12.3
}

XYZ output:

$ sci-form embed "CCO" -f xyz
9
CCO
 C     0.764735     0.013411    -0.082862
 C    -0.718153     0.048620     0.089507
 O    -1.168543    -0.490543     1.323891
 ...

SDF output:

$ sci-form embed "CCO" -f sdf > ethanol.sdf

batch — Multiple molecules

Process many molecules from a file or stdin.

# From file
sci-form batch -i molecules.smi -o output.sdf -f sdf -t 8

# From stdin
cat molecules.smi | sci-form batch -f xyz > output.xyz

# No output file → stdout
sci-form batch -i molecules.smi -f json

Option	Default	Description
--input, -i	stdin	Input file (one SMILES per line)
--output, -o	stdout	Output file
--seed, -s	42	RNG seed
--threads, -t	0 (auto)	Number of threads
--format, -f	json	Output format: json, xyz, sdf

parse — SMILES analysis

Parse a SMILES string and show molecular structure (no 3D generation).

$ sci-form parse "c1ccccc1" | jq .
{
  "num_atoms": 12,
  "num_bonds": 12,
  "smiles": "c1ccccc1"
}

info — Version

$ sci-form info
sci-form 0.1.0

Exit Codes

Code	Meaning
0	Success
1	Conformer generation failed

Pipeline Examples

# Generate SDF file from SMILES list
sci-form batch -i ligands.smi -o conformers.sdf -f sdf -t 8

# Pipe through jq to extract coordinates
sci-form embed "CCO" | jq '.coords | [range(0; length; 3)] | map(. as $i | [input[$i], input[$i+1], input[$i+2]])'

# Count embed failures in a batch
sci-form batch -i molecules.smi | jq '[.[] | select(.error != null)] | length'