.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.41.2.
.TH RDKIT2FPS "1" "May 2013" "rdkit2fps 1.1p1" "User Commands"
.SH NAME
rdkit2fps \- rdkit2fps
.SH DESCRIPTION
usage: rdkit2fps [\-h] [\-\-fpSize INT] [\-\-RDK] [\-\-minPath INT] [\-\-maxPath INT]
.IP
[\-\-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 ...]]
.PP
Generate FPS fingerprints from a structure file using RDKit
.SS "positional arguments:"
.TP
filenames
input structure files (default is stdin)
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-fpSize\fR INT
number of bits in the fingerprint (applies to RDK,
Morgan, topological torsion, and atom pair
fingerprints (default=2048)
.TP
\fB\-\-id\-tag\fR NAME
tag name containing the record id (SD files only)
.TP
\fB\-\-in\fR FORMAT
input structure format (default guesses from filename)
.TP
\fB\-o\fR FILENAME, \fB\-\-output\fR FILENAME
save the fingerprints to FILENAME (default=stdout)
.TP
\fB\-\-errors\fR {strict,report,ignore}
how should structure parse errors be handled?
(default=strict)
.SS "RDKit topological fingerprints:"
.TP
\fB\-\-RDK\fR
generate RDK fingerprints (default)
.TP
\fB\-\-minPath\fR INT
minimum number of bonds to include in the subgraph
(default=1)
.TP
\fB\-\-maxPath\fR INT
maximum number of bonds to include in the subgraph
(default=7)
.TP
\fB\-\-nBitsPerHash\fR INT
number of bits to set per path (default=4)
.TP
\fB\-\-useHs\fR 0|1
include information about the number of hydrogens on
each atom (default=1)
.SS "RDKit Morgan fingerprints:"
.TP
\fB\-\-morgan\fR
generate Morgan fingerprints
.TP
\fB\-\-radius\fR INT
radius for the Morgan algorithm (default=2)
.TP
\fB\-\-useFeatures\fR 0|1
use chemical\-feature invariants (default=0)
.TP
\fB\-\-useChirality\fR 0|1
include chirality information (default=0)
.TP
\fB\-\-useBondTypes\fR 0|1
include bond type information (default=1)
.SS "RDKit Topological Torsion fingerprints:"
.TP
\fB\-\-torsions\fR
generate Topological Torsion fingerprints
.TP
\fB\-\-targetSize\fR INT
number of bits in the fingerprint (default=4)
.SS "RDKit Atom Pair fingerprints:"
.TP
\fB\-\-pairs\fR
generate Atom Pair fingerprints
.TP
\fB\-\-minLength\fR INT
minimum bond count for a pair (default=1)
.TP
\fB\-\-maxLength\fR INT
maximum bond count for a pair (default=30)
.SS "166 bit MACCS substructure keys:"
.TP
\fB\-\-maccs166\fR
generate MACCS fingerprints
.SS "881 bit substructure keys:"
.TP
\fB\-\-substruct\fR
generate ChemFP substructure fingerprints
.SS "ChemFP version of the 166 bit RDKit/MACCS keys:"
.TP
\fB\-\-rdmaccs\fR
generate 166 bit RDKit/MACCS fingerprints
.PP
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:
.TP
File Type
Valid FORMATs (use gz if compressed)
.HP
\fB\-\-\-\-\-\-\-\-\-\fR      \fB\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\-\fR
.TP
SMILES
smi, ism, can, smi.gz, ism.gz, can.gz
.TP
SDF
sdf, mol, sd, mdl, sdf.gz, mol.gz, sd.gz, mdl.gz