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"
}

charges — Gasteiger-Marsili partial charges

$ sci-form charges "CCO"
{
  "charges": [-0.032, 0.081, -0.329, ...],
  "total_charge": 0.0,
  "iterations": 8
}

eht — Extended Hückel Theory

Compute EHT electronic structure from atomic numbers and coordinates.

sci-form eht "[6,8,1,1,1,1,1,1,1]" "[0.76,0.01,-0.08,-0.72,0.05,0.09,...]" --k 1.75

Option	Default	Description
--k	1.75	Wolfsberg-Helmholz parameter

population — Mulliken & Löwdin analysis

sci-form population "[6,8,1,1,1,1,1,1,1]" "[0.76,0.01,-0.08,...]"
# Output: mulliken_charges, lowdin_charges, homo_energy, lumo_energy, gap

dipole — Molecular dipole moment

sci-form dipole "[6,8,1,1,1,1,1,1,1]" "[0.76,0.01,-0.08,...]"
# Output: magnitude (Debye), vector [x, y, z]

esp — Electrostatic potential grid

sci-form esp "[6,8,1,1,1,1,1,1,1]" "[...]" --spacing 0.5 --padding 3.0

Option	Default	Description
--spacing	0.5	Grid spacing (Å)
--padding	3.0	Padding around molecule (Å)

dos — Density of states

sci-form dos "[6,8,1,1,1,1,1,1,1]" "[...]" --sigma 0.3 --e-min -30 --e-max 5 -n 500

Option	Default	Description
--sigma	0.3	Gaussian broadening (eV)
--e-min	-30.0	Energy range minimum (eV)
--e-max	5.0	Energy range maximum (eV)
-n	500	Number of grid points

rmsd — RMSD alignment

Compute RMSD between two coordinate sets (flat arrays).

sci-form rmsd "[0.1,0.2,0.3,...]" "[0.15,0.22,0.31,...]"
# Output: {"rmsd": 0.034, "aligned_coords": [...]}

uff — UFF force field energy

sci-form uff "CCO" "[0.76,0.01,-0.08,...]"
# Output: {"energy": 12.3}  (kcal/mol)

sasa — Solvent-accessible surface area

sci-form sasa "[6,8,1,1,1,1,1,1,1]" "[...]" --probe-radius 1.4
# Output: total_sasa (ų), per_atom_sasa

ani — ANI neural network potential

ANI-2x supports H, C, N, O, F, S, Cl.

sci-form ani "[6,8,1,1,1,1,1,1,1]" "[0.76,0.01,-0.08,...]"
# Output: energy (eV), forces per atom

hf3c — Hartree-Fock 3c calculation

Minimal-basis HF with D3 dispersion, gCP counterpoise, and SRB short-range corrections.

sci-form hf3c "[6,8,1,1,1,1,1,1,1]" "[0.76,0.01,-0.08,...]"
# Output: energy, hf_energy, d3_energy, gcp_energy, srb_energy, orbital_energies, converged

stereo — Stereochemistry analysis

Detect R/S stereocenters, E/Z double bonds, atropisomeric axes, and helical chirality.

$ sci-form stereo "C(F)(Cl)(Br)I"
{
  "stereocenters": [{"atom_index": 0, "configuration": "R", ...}],
  "double_bonds": [],
  "n_stereocenters": 1,
  "n_double_bonds": 0
}

# With 3D coordinates for geometric assignment
sci-form stereo "C/C=C/C" --coords "[...]"

solvation — Solvation energy

Non-polar (SASA-based) solvation, optionally with Generalized Born electrostatics.

# Non-polar only
sci-form solvation "[8,1,1]" "[0,0,0,0.757,0.586,0,-0.757,0.586,0]"

# With GB electrostatic solvation (provide charges)
sci-form solvation "[8,1,1]" "[...]" --charges "[-0.8,0.4,0.4]"

sssr — Ring perception

Smallest Set of Smallest Rings (Horton's algorithm).

$ sci-form sssr "c1ccc2ccccc2c1"   # naphthalene
{
  "rings": [[0,1,2,3,4,9], [4,5,6,7,8,9]],
  "ring_size_histogram": {"6": 2}
}

ecfp — ECFP fingerprints

Extended-Connectivity Fingerprints (Morgan algorithm).

sci-form ecfp "CCO" --radius 2 --n-bits 2048
# Output: {n_bits, on_bits, radius, raw_features}

tanimoto — Fingerprint similarity

Compute Tanimoto similarity between two SMILES.

$ sci-form tanimoto "c1ccccc1" "Cc1ccccc1"
{"tanimoto": 0.714}

cell — Create unit cell

sci-form cell --a 5.43 --b 5.43 --c 5.43 --alpha 90 --beta 90 --gamma 90
# Output: volume, lattice vectors, fractional ↔ Cartesian matrices

assemble — Framework assembly

Build MOF/COF crystal structures from topology and building blocks.

sci-form assemble --topology pcu --metal 30 --geometry octahedral --a 10.0
# Output: num_atoms, elements, coordinates, unit cell, space group

Option	Default	Description
--topology	required	pcu, dia, sql
--metal	required	Atomic number of metal node
--geometry	required	linear, trigonal, tetrahedral, square_planar, octahedral
--a	required	Lattice parameter a (Å)
--supercell	1	Supercell expansion factor

info — Version

$ sci-form info
sci-form 0.9.1

Exit Codes

Code	Meaning
0	Success
1	Invalid SMILES or embedding failure
2	I/O error

Pipeline Examples

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

# Filter only successful embeddings
sci-form batch -i molecules.smi | jq -c 'select(.error == null)'

# Batch statistics
sci-form batch -i molecules.smi | jq -s '{total:length, success:[.[]|select(.error==null)]|length}'

# Embed → PM3 pipeline (using coordinate extraction with jq)
COORDS=$(sci-form embed "CCO" | jq -c '.coords')
ELEMS=$(sci-form embed "CCO" | jq -c '.elements')

# Parallel batch with GNU Parallel
cat huge.smi | parallel -j8 --pipe -N100 sci-form batch /dev/stdin > results.json

# Stereochemistry analysis of all molecules
sci-form batch -i molecules.smi | jq -r '.smiles' | while read smi; do
  sci-form stereo "$smi"
done

# Fingerprint similarity matrix
sci-form tanimoto "c1ccccc1" "CCO"
sci-form tanimoto "c1ccccc1" "CC(=O)O"