CLI Usage

The molprint CLI has two subcommands: fp for computing fingerprints, and search for similarity search.

`molprint fp` — compute fingerprints

Reads a molecule file, computes fingerprints, and writes a chemfp-compatible FPS file.

molprint fp --input molecules.smi --output molecules.fps

Options

Flag	Default	Description
`--input` / `-i`	required	Input file (`.smi`, `.sdf`, `.sdf.gz`)
`--output` / `-o`	required	Output FPS file path
`--fp-type` / `-t`	`morgan`	Fingerprint type: `morgan` or `maccs`
`--radius` / `-r`	`2`	Morgan radius (ignored for MACCS)
`--nbits` / `-n`	`2048`	Bit width for Morgan (ignored for MACCS)

Examples

# Default: Morgan ECFP4, 2048 bits
molprint fp --input molecules.smi --output molecules.fps

# MACCS-166 structural keys
molprint fp --input molecules.smi --fp-type maccs --output maccs.fps

# Morgan ECFP6, 4096 bits, from SDF
molprint fp --input molecules.sdf --radius 3 --nbits 4096 --output ecfp6.fps

# Gzip-compressed SDF (auto-detected by extension)
molprint fp --input chembl.sdf.gz --output chembl.fps

Input formats

File format is detected from the extension:

.smi — SMILES file, one molecule per line. Format: SMILES<tab>ID or bare SMILES. If no ID is given, a sequential mol1, mol2, ... ID is assigned.
.sdf — MDL V2000 SDF. The molecule name (first line of the mol block) is used as the ID.
.sdf.gz — gzip-compressed SDF, read transparently via flate2.

Output format

The output is a chemfp-compatible FPS v1 file:

#FPS1
#type=Morgan nbits=2048
#radius=2
#software=molprint/0.1.0
<hex_fingerprint>\t<id>
<hex_fingerprint>\t<id>
...

Fingerprints are encoded as lowercase hexadecimal, least-significant byte first (chemfp convention).

Progress output

The CLI prints a progress summary to stderr when done:

Processed 10000 molecules in 0.14s (71428 mol/s)

`molprint search` — similarity search

Searches a fingerprint database for molecules similar to a query.

molprint search --query "c1ccccc1" --db molecules.fps --threshold 0.4

Options

Flag	Default	Description
`--query` / `-q`	required	Query as a SMILES string
`--db` / `-d`	required	FPS database file path
`--threshold`	`0.7`	Tanimoto threshold for filtering
`--top-k` / `-k`	`10`	Return top-k results

How threshold and top-k interact

If --top-k is non-zero (the default is 10), a top-k search is performed and then results below --threshold are filtered out.
To get all results above a threshold without a hard top-k cap, set --top-k 0.

Examples

# All compounds with Tanimoto >= 0.4 to benzene (no top-k cap)
molprint search --query "c1ccccc1" --db molecules.fps --threshold 0.4 --top-k 0

# Top 20 most similar, filtered to Tanimoto >= 0.7
molprint search --query "c1ccccc1" --db molecules.fps --top-k 20

# Top 5 most similar (no threshold filter)
molprint search --query "c1ccccc1" --db molecules.fps --top-k 5 --threshold 0.0

Output format

Tab-separated id<tab>similarity, sorted by descending score:

CHEMBL123    0.8500
CHEMBL456    0.7800
CHEMBL789    0.7200

The fingerprint type (morgan/maccs) and parameters (radius, nbits) are read from the FPS header automatically, so the query fingerprint is computed with the same settings as the database.