Command-Line Interface

PFASGroups ships a command-line tool available as both halogengroups and pfasgroups (aliases for the same entry point).

Installation makes the command available in your shell after:

pip install PFASGroups
# or: pip install -e .

Quick example:

# Parse a SMILES and list detected groups
pfasgroups parse "CCCC(F)(F)F"

# Generate a 116-column fingerprint (F only) and print as CSV
pfasgroups fingerprint --format csv "CCCC(F)(F)F" "FC(F)(F)C(=O)O"

# List all 116 built-in groups
pfasgroups list-groups

Synopsis

halogengroups <command> [options] [smiles ...]

Commands:
  parse          Parse SMILES and identify halogen groups
  fingerprint    Generate group fingerprints
  list-groups    List all available halogen groups
  list-paths     List available component SMARTS types

parse

Identify halogen groups in one or more SMILES strings.

halogengroups parse [options] [smiles ...]

Positional arguments

smiles    One or more SMILES strings (quoted if they contain spaces)

Options

-i, --input FILE          Read SMILES from file (one per line)
-o, --output FILE         Write results to FILE (default: stdout)
--format {json,csv}       Output format (default: json)
--pretty                  Pretty-print JSON
--halogens H [H ...]      Filter components by halogen(s): F Cl Br I
--saturation {per,poly}   Filter by saturation level
--form {alkyl,cyclic}     Filter by molecular form
--no-component-metrics    Skip all graph-theory metrics (fastest mode)
--limit-effective-graph-resistance N
                          Only compute effective resistance for components
                          with fewer than N atoms (0 = disable; omit = always)
--groups-file FILE        Custom halogen groups JSON file
--component_smarts-file FILE
                          Custom component SMARTS JSON file

Examples

# Single SMILES
halogengroups parse "FC(F)(F)C(F)(F)C(=O)O"

# Multiple SMILES, pretty-printed JSON
halogengroups parse --pretty \
    "FC(F)(F)C(F)(F)C(=O)O" \
    "FC(F)(F)C(F)(F)S(=O)(=O)O"

# Fluorine-only, perfluorinated alkyl components
halogengroups parse --halogens F --saturation per --form alkyl \
    "FC(F)(F)C(F)(F)C(=O)O"

# All four halogens
halogengroups parse --halogens F Cl Br I \
    "ClC(Cl)(Cl)C(Cl)(Cl)C(=O)O"

# From file, CSV output
halogengroups parse --input smiles.txt --output results.csv --format csv

# Skip graph metrics (fastest)
halogengroups parse --no-component-metrics "FC(F)(F)C(F)(F)C(=O)O"

# Compute resistance only for small components
halogengroups parse --limit-effective-graph-resistance 100 \
    "FC(F)(F)C(F)(F)C(=O)O"

# Custom group file
halogengroups parse --groups-file my_groups.json "FC(F)(F)C(F)(F)C(=O)O"

JSON output structure

[
  {
    "smiles": "FC(F)(F)C(F)(F)C(=O)O",
    "matches": [
      {
        "group_id": 1,
        "group_name": "Perfluoroalkyl carboxylic acids",
        "match_count": 1,
        "components": [
          {
            "size": 3,
            "SMARTS": "Perfluoroalkyl",
            "branching": 1.0,
            "smarts_centrality": 0.5
          }
        ]
      }
    ]
  }
]

CSV output columns

smiles, group_id, group_name, match_count, component_sizes

fingerprint

Generate halogen-group fingerprints suitable for machine learning.

halogengroups fingerprint [options] [smiles ...]

Positional arguments

smiles    One or more SMILES strings

Options

-i, --input FILE               Read SMILES from file
-o, --output FILE              Write output to FILE (default: stdout)
-g, --groups SPEC              Group selection as range "1-28" or
                               comma-separated "1,2,3" (default: all)
-f, --format {vector,dict,sparse,detailed,int}
                               Fingerprint representation (default: vector)
--count-mode {binary,count,max_chain}
                               Encoding mode (default: binary)
--halogens H [H ...]           Halogens to include (default: F)
--output-format {json,csv}     File format (default: json)
--pretty                       Pretty-print JSON

Examples

# Binary vector (default)
halogengroups fingerprint "FC(F)(F)C(F)(F)C(=O)O"

# Dictionary representation
halogengroups fingerprint --format dict "FC(F)(F)C(F)(F)C(=O)O"

# OECD groups only (IDs 1–28)
halogengroups fingerprint --groups 1-28 "FC(F)(F)C(F)(F)C(=O)O"

# Count mode
halogengroups fingerprint --count-mode count "FC(F)(F)C(F)(F)C(=O)O"

# Multi-halogen stacked fingerprint (116 × 4 = 464 columns)
halogengroups fingerprint --halogens F Cl Br I "FC(F)(F)C(F)(F)C(=O)O"

# From file, save to CSV
halogengroups fingerprint --input smiles.txt \
    --output fps.csv --output-format csv

list-groups

List all available halogen groups and their definitions.

halogengroups list-groups [options]

Options

-o, --output FILE   Write to FILE (default: stdout)
--pretty            Pretty-print JSON (default: true)

Example output (excerpt)

[
  {
    "id": 1,
    "name": "Perfluoroalkyl carboxylic acids",
    "alias": "PFCA",
    "componentSmarts": "Perfluoroalkyl",
    "componentSaturation": "per",
    "componentHalogens": "F",
    "componentForm": "alkyl"
  },
  {
    "id": 6,
    "name": "Perfluoroalkyl sulfonic acids",
    "alias": "PFSA"
  }
]

Examples

# Print to console
halogengroups list-groups

# Save to file
halogengroups list-groups --output groups.json

list-paths

List available component SMARTS types (path/component definitions).

halogengroups list-paths [options]

Options

-o, --output FILE   Write to FILE (default: stdout)

Example output (excerpt)

{
  "Perfluoroalkyl": {
    "component": "[C;X4;H0](F)(F)!@!=!#[C;X4;H0](F)(F)",
    "end": "[C;X4;H0](F)(F)F",
    "halogen": "F",
    "form": "alkyl",
    "saturation": "per"
  },
  "Polyfluoroalkyl": {
    "component": "[C;X4;H1](F)!@!=!#[C;X4](F)",
    "end": "[C;X4;H1](F)F",
    "halogen": "F",
    "form": "alkyl",
    "saturation": "poly"
  }
}

Global Options

These options can be placed before any sub-command:

--groups-file FILE            Custom halogen groups JSON
--component_smarts-file FILE  Custom component SMARTS JSON

Environment

The CLI uses the Python environment in which PFASGroups is installed. To use a specific environment:

# conda
conda activate chem
halogengroups parse "FC(F)(F)C(F)(F)C(=O)O"

# direct Python invocation
python -m PFASGroups.cli parse "FC(F)(F)C(F)(F)C(=O)O"

Performance Tips

For large input files:

# Skip graph metrics (5–10× faster for large molecules)
halogengroups parse --no-component-metrics --input big_file.smi \
    --output results.json

# Skip effective graph resistance for molecules with > 50 atoms
halogengroups parse --limit-effective-graph-resistance 50 \
    --input big_file.smi --output results.json

See the Benchmarking page for timing data.

See Also

  • Quickstart — Python API quick start

  • Core API — parse_smiles, generate_fingerprint reference

  • Customization — using custom groups and path files with the CLI