CLI Reference

Installation

Pre-built Binaries

sci-form-x86_64-unknown-linux-gnu — Linux x86_64
sci-form-x86_64-apple-darwin — macOS Intel
sci-form-aarch64-apple-darwin — macOS Apple Silicon
sci-form-x86_64-pc-windows-msvc.exe — Windows x86_64
sci-form-aarch64-unknown-linux-gnu — Linux ARM64

Build from Source

bash

cargo install sci-form-cli

Commands

`embed`

Generate a 3D conformer for a single SMILES.

sci-form embed <SMILES> [OPTIONS]

Options:

Option	Default	Description
`-s, --seed <N>`	`42`	RNG seed
`-f, --format <FMT>`	`json`	Output format: `json`, `xyz`, `sdf`

Examples:

bash

sci-form embed "CCO"                # JSON
sci-form embed "c1ccccc1" -f xyz    # XYZ
sci-form embed "CC(=O)O" -f sdf -s 123

JSON output:

json

{
  "smiles": "CCO",
  "num_atoms": 9,
  "coords": [0.123, 0.456, 0.789, ...],
  "elements": [6, 6, 8, 1, 1, 1, 1, 1, 1],
  "bonds": [[0, 1, "SINGLE"], [1, 2, "SINGLE"], ...],
  "error": null,
  "time_ms": 2.34
}

`batch`

Process multiple SMILES from a file.

sci-form batch <FILE> [OPTIONS]

Options:

Option	Default	Description
`-s, --seed <N>`	`42`	RNG seed
`-f, --format <FMT>`	`json`	Output format: `json`, `xyz`, `sdf`
`-t, --threads <N>`	`0`	Number of threads (`0` = auto)

Input file format: One SMILES per line (name optional):

CCO ethanol
c1ccccc1 benzene
CC(=O)O acetic_acid

Examples:

bash

sci-form batch molecules.smi
sci-form batch molecules.smi -f xyz -t 8
cat molecules.smi | sci-form batch /dev/stdin
sci-form batch molecules.smi > conformers.json

`parse`

Parse SMILES and return molecular graph info (no 3D generation).

sci-form parse <SMILES>

bash

sci-form parse "c1ccccc1"

Output:

json

{
  "num_atoms": 12,
  "num_bonds": 12,
  "elements": [6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1],
  "bonds": [[0, 1, "AROMATIC"], ...]
}

`charges`

Compute Gasteiger-Marsili partial charges.

sci-form charges <SMILES>

bash

sci-form charges "CCO"

Output:

json

{
  "charges": [-0.387, -0.042, -0.228, 0.123, ...],
  "iterations": 6,
  "total_charge": 0.0
}

`eht`

Run Extended Hückel Theory calculation.

sci-form eht <ELEMENTS_JSON> <COORDS_JSON> [OPTIONS]

Options:

Option	Default	Description
`-k`	`1.75`	Wolfsberg-Helmholtz constant (0 = default 1.75)

bash

sci-form eht "[6,1,1,1,1]" "[0,0,0,1,0,0,0,1,0,0,0,1]" --k 1.75

`population`

Mulliken & Löwdin population analysis.

sci-form population <ELEMENTS_JSON> <COORDS_JSON>

`dipole`

Compute molecular dipole moment (Debye).

sci-form dipole <ELEMENTS_JSON> <COORDS_JSON>

`esp`

Compute electrostatic potential on a 3D grid.

sci-form esp <ELEMENTS_JSON> <COORDS_JSON> [OPTIONS]

Option	Default	Description
`--spacing`	`0.5`	Grid spacing in Å
`--padding`	`3.0`	Padding beyond molecule in Å

`dos`

Compute density of states.

sci-form dos <ELEMENTS_JSON> <COORDS_JSON> [OPTIONS]

Option	Default	Description
`--sigma`	`0.3`	Broadening width in eV
`--e-min`	`-30.0`	Energy window min in eV
`--e-max`	`5.0`	Energy window max in eV
`-n`	`500`	Grid points

`rmsd`

Compute RMSD between two coordinate sets (Kabsch alignment).

sci-form rmsd <COORDS_JSON> <REFERENCE_JSON>

`uff`

Compute UFF force field energy.

sci-form uff <SMILES> <COORDS_JSON>

bash

sci-form uff "CCO" "[...]"

`sasa`

Compute solvent-accessible surface area.

sci-form sasa <ELEMENTS_JSON> <COORDS_JSON> [OPTIONS]

Option	Default	Description
`--probe-radius`	`1.4`	Probe radius in Å

`ani`

Run ANI ML potential calculation.

sci-form ani <ELEMENTS_JSON> <COORDS_JSON>

`hf3c`

Run HF-3c quantum calculation.

sci-form hf3c <ELEMENTS_JSON> <COORDS_JSON>

`cell`

Create a unit cell and show parameters.

sci-form cell [OPTIONS]

Option	Default	Description
`--a`, `--b`, `--c`	(required)	Lattice parameters in Å
`--alpha`, `--beta`, `--gamma`	`90.0`	Lattice angles in degrees

bash

sci-form cell --a 5.43 --b 5.43 --c 5.43

`assemble`

Assemble a framework crystal structure.

sci-form assemble [OPTIONS]

Option	Default	Description
`--topology`	`pcu`	Framework topology
`--metal`	`30`	Metal atomic number
`--geometry`	`octahedral`	Coordination geometry
`--a`	`10.0`	Lattice parameter Å
`--supercell`	`1`	Replication factor

bash

sci-form assemble --topology pcu --metal 30 --geometry octahedral --a 10.0

`info`

Display build and feature information.

bash

sci-form info

Output includes: version, compiled features (parallel, etc.), supported platforms.

`stereo`

Analyze stereochemistry: CIP priorities, R/S, E/Z.

sci-form stereo <SMILES> [OPTIONS]

Options:

Option	Description
`--coords <JSON>`	Flat coordinate array as JSON string (enables 3D R/S and E/Z assignment)

bash

sci-form stereo "C(F)(Cl)(Br)I"
sci-form stereo "C/C=C/C" --coords "[$(sci-form embed 'C/C=C/C' | jq '.coords')]"

Output:

json

{
  "stereocenters": [
    { "atom_index": 0, "element": 6, "priorities": [1,2,3,4], "configuration": "R" }
  ],
  "double_bonds": [],
  "n_stereocenters": 1,
  "n_double_bonds": 0
}

`solvation`

Compute GB/SA solvation energy.

sci-form solvation <ELEMENTS_JSON> <COORDS_JSON> [OPTIONS]

Arguments:

ELEMENTS_JSON — Atomic numbers as JSON array, e.g. "[8,1,1]"
COORDS_JSON — Flat coordinates as JSON array (Å)

Options:

Option	Default	Description
`--charges <JSON>`	Gasteiger auto	Per-atom charges as JSON array
`--probe-radius <F>`	`1.4`	Probe radius in Å
`--solvent-dielectric <F>`	`78.5`	Solvent dielectric constant
`--nonpolar-only`	—	Skip GB, return only non-polar SASA term

bash

# Using SMILES pipeline
RESULT=$(sci-form embed "CCO")
ELEM=$(echo "$RESULT" | jq '.elements')
COORDS=$(echo "$RESULT" | jq '.coords')
sci-form solvation "$ELEM" "$COORDS"

Output:

json

{
  "nonpolar_energy_kcal_mol": 0.72,
  "electrostatic_energy_kcal_mol": -3.45,
  "total_energy_kcal_mol": -2.73,
  "total_sasa": 187.4
}

`sssr`

Perceive the Smallest Set of Smallest Rings.

sci-form sssr <SMILES>

bash

sci-form sssr "c1ccc2ccccc2c1"  # naphthalene

Output:

json

{
  "rings": [
    { "atoms": [0,1,2,3,4,5], "size": 6, "is_aromatic": true },
    { "atoms": [4,5,6,7,8,9], "size": 6, "is_aromatic": true }
  ],
  "ring_size_histogram": { "6": 2 }
}

`ecfp`

Compute an ECFP fingerprint.

sci-form ecfp <SMILES> [OPTIONS]

Options:

Option	Default	Description
`--radius <N>`	`2`	Morgan radius (ECFP4 = 2, ECFP6 = 3)
`--n-bits <N>`	`2048`	Bit-vector size

bash

sci-form ecfp "c1ccccc1"
sci-form ecfp "c1ccccc1" --radius 3 --n-bits 1024

Output:

json

{
  "n_bits": 2048,
  "on_bits": [42, 317, 891, ...],
  "radius": 2,
  "density": 0.0137
}

`tanimoto`

Compute Tanimoto similarity between two molecules.

sci-form tanimoto <SMILES1> <SMILES2> [OPTIONS]

Options:

Option	Default	Description
`--radius <N>`	`2`	ECFP radius
`--n-bits <N>`	`2048`	Bit-vector size

bash

sci-form tanimoto "c1ccccc1" "Cc1ccccc1"

Output:

json

{ "tanimoto": 0.583, "smiles1": "c1ccccc1", "smiles2": "Cc1ccccc1" }

Output Formats

JSON

Default format. Returns the full ConformerResult as compact JSON.

XYZ

Standard XYZ format for molecular viewers (Avogadro, VESTA, VMD):

9
CCO seed=42
C    0.123   0.456   0.789
O    1.234   0.567   0.890
...

SDF

MDL Structure Data File format. Compatible with RDKit, OpenBabel, MarvinSuite.

Exit Codes

Code	Meaning
`0`	Success
`1`	Invalid SMILES or embedding failure
`2`	File not found or I/O error

Pipeline Examples

Filter successful results

bash

sci-form batch molecules.smi | jq -c 'select(.error == null)'

Get batch statistics

bash

sci-form batch molecules.smi | jq -s '{
  total: length,
  success: [.[] | select(.error == null)] | length,
  avg_time_ms: ([.[] | .time_ms] | add / length)
}'

Convert batch to XYZ

bash

sci-form batch molecules.smi -f xyz > all_conformers.xyz

Compute charges for all molecules in a file

bash

while read smiles; do
  sci-form charges "$smiles"
done < molecules.smi | jq -s '.'

Parallel processing with GNU Parallel

bash

cat huge_set.smi | parallel -j8 --pipe -N100 sci-form batch /dev/stdin > results.json

CLI Reference ​

Installation ​

Pre-built Binaries ​

Build from Source ​

Commands ​

embed ​

batch ​

parse ​

charges ​

eht ​

population ​

dipole ​

esp ​

dos ​

rmsd ​

uff ​

sasa ​

ani ​

hf3c ​

cell ​

assemble ​

info ​

stereo ​

solvation ​

sssr ​

ecfp ​

tanimoto ​

Output Formats ​

JSON ​

XYZ ​

SDF ​

Exit Codes ​

Pipeline Examples ​

Filter successful results ​

Get batch statistics ​

Convert batch to XYZ ​

Compute charges for all molecules in a file ​

Parallel processing with GNU Parallel ​

CLI Reference

Installation

Pre-built Binaries

Build from Source

Commands

`embed`

`batch`

`parse`

`charges`

`eht`

`population`

`dipole`

`esp`

`dos`

`rmsd`

`uff`

`sasa`

`ani`

`hf3c`

`cell`

`assemble`

`info`

`stereo`

`solvation`

`sssr`

`ecfp`

`tanimoto`

Output Formats

JSON

XYZ

SDF

Exit Codes

Pipeline Examples

Filter successful results

Get batch statistics

Convert batch to XYZ

Compute charges for all molecules in a file

Parallel processing with GNU Parallel