---
name: "rdkit2fps"
section: "1"
platform: "linux"
package: "python-chemfp"
version: "1.1p1-2.1"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/rdkit2fps"
---

# rdkit2fps(1)

rdkit2fps

## NAME

rdkit2fps - rdkit2fps

## DESCRIPTION

usage: rdkit2fps \[-h\] \[--fpSize INT\] \[--RDK\] \[--minPath INT\] \[--maxPath INT\]

-

  \[--nBitsPerHash INT\] \[--useHs 0\|1\] \[--morgan\] \[--radius INT\] \[--useFeatures 0\|1\] \[--useChirality 0\|1\] \[--useBondTypes 0\|1\] \[--torsions\] \[--targetSize INT\] \[--pairs\] \[--minLength INT\] \[--maxLength INT\] \[--maccs166\] \[--substruct\] \[--rdmaccs\] \[--id-tag NAME\] \[--in FORMAT\] \[-o FILENAME\] \[--errors {strict,report,ignore}\] \[filenames \[filenames ...\]\]

Generate FPS fingerprints from a structure file using RDKit

### positional arguments:

- filenames

  input structure files (default is stdin)

### optional arguments:

- **-h**, **--help**

  show this help message and exit

- **--fpSize** INT

  number of bits in the fingerprint (applies to RDK, Morgan, topological torsion, and atom pair fingerprints (default=2048)

- **--id-tag** NAME

  tag name containing the record id (SD files only)

- **--in** FORMAT

  input structure format (default guesses from filename)

- **-o** FILENAME, **--output** FILENAME

  save the fingerprints to FILENAME (default=stdout)

- **--errors** {strict,report,ignore}

  how should structure parse errors be handled? (default=strict)

### RDKit topological fingerprints:

- **--RDK**

  generate RDK fingerprints (default)

- **--minPath** INT

  minimum number of bonds to include in the subgraph (default=1)

- **--maxPath** INT

  maximum number of bonds to include in the subgraph (default=7)

- **--nBitsPerHash** INT

  number of bits to set per path (default=4)

- **--useHs** 0\|1

  include information about the number of hydrogens on each atom (default=1)

### RDKit Morgan fingerprints:

- **--morgan**

  generate Morgan fingerprints

- **--radius** INT

  radius for the Morgan algorithm (default=2)

- **--useFeatures** 0\|1

  use chemical-feature invariants (default=0)

- **--useChirality** 0\|1

  include chirality information (default=0)

- **--useBondTypes** 0\|1

  include bond type information (default=1)

### RDKit Topological Torsion fingerprints:

- **--torsions**

  generate Topological Torsion fingerprints

- **--targetSize** INT

  number of bits in the fingerprint (default=4)

### RDKit Atom Pair fingerprints:

- **--pairs**

  generate Atom Pair fingerprints

- **--minLength** INT

  minimum bond count for a pair (default=1)

- **--maxLength** INT

  maximum bond count for a pair (default=30)

### 166 bit MACCS substructure keys:

- **--maccs166**

  generate MACCS fingerprints

### 881 bit substructure keys:

- **--substruct**

  generate ChemFP substructure fingerprints

### ChemFP version of the 166 bit RDKit/MACCS keys:

- **--rdmaccs**

  generate 166 bit RDKit/MACCS fingerprints

This program guesses the input structure format based on the filename extension. If the data comes from stdin, or the extension name us unknown, then use "--in" to change the default input format. The supported format extensions are:

- File Type

  Valid FORMATs (use gz if compressed)

**---------**      **------------------------------------**

- SMILES

  smi, ism, can, smi.gz, ism.gz, can.gz

- SDF

  sdf, mol, sd, mdl, sdf.gz, mol.gz, sd.gz, mdl.gz