simsearch command-line options

The following comes from simsearch --help:

usage: simsearch [-h] [-k K_NEAREST] [-t THRESHOLD] [--alpha ALPHA]
                 [--beta BETA] [--queries QUERIES] [--NxN] [--query QUERY]
                 [--hex-query HEX_QUERY] [--query-id QUERY_ID]
                 [--query-format FORMAT] [--target-format FORMAT]
                 [--query-type STRING] [--id-tag NAME]
                 [--errors {strict,report,ignore}] [-R NAME=VALUE]
                 [--delimiter {tab,whitespace,to-eol,space}] [--has-header]
                 [-o FILENAME] [--out FORMAT]
                 [--include-empty | --no-include-empty]
                 [--empty-target-id EMPTY_TARGET_ID]
                 [--empty-score EMPTY_SCORE] [--precision N] [-c]
                 [-b BATCH_SIZE] [--scan] [--memory] [--no-mmap] [--times]
                 [--version] [--license-check]

Search an FPS or FPB file for similar fingerprints

positional arguments:
  target_filename       target filename

  -h, --help            show this help message and exit
  -k K_NEAREST, --k-nearest K_NEAREST
                        select the k nearest neighbors (use 'all' for all
  -t THRESHOLD, --threshold THRESHOLD
                        minimum similarity score threshold
  --alpha ALPHA         Tversky alpha parameter (default: 1.0)
  --beta BETA           Tversky beta parameter (default: the value of --alpha)
  --queries QUERIES, -q QUERIES
                        filename containing the query fingerprints
  --NxN                 use the targets as the queries, and exclude the self-
                        similarity term
  --query QUERY         query as a structure record (default format: 'smi')
  --hex-query HEX_QUERY
                        query in hex
  --query-id QUERY_ID   id for the query or hex-query (default: 'Query1'
  --query-format FORMAT, --in FORMAT
                        input query format (default uses the file extension,
                        else 'fps')
  --target-format FORMAT
                        input target format (default uses the file extension,
                        else 'fps')
  --query-type STRING   fingerprint type string if the queries are structures
                        (default: use the target fingerprint type)
  --id-tag NAME         tag containing the record id if --query-format is an
                        SD file)
  --errors {strict,report,ignore}
                        how should structure parse errors be handled?
  -R NAME=VALUE         specify a reader argument
  --delimiter {tab,whitespace,to-eol,space}
                        delimiter style for SMILES and InChI files. Alias for
                        '-R delimiter=VALUE'.
  --has-header          Skip the first line of a SMILES or InChI file Alias
                        for '-R has_header=1'
  -o FILENAME, --output FILENAME
                        output filename (default is stdout)
  --out FORMAT          Output format. One of 'chemfp', 'csv', or 'tsv'
                        (default: based on filename, or 'chemfp')
  --include-empty, --no-include-empty
                        In csv or tsv output, include a line for queries with
                        no hits (the default) (default: True)
  --empty-target-id EMPTY_TARGET_ID
                        In csv or tsv output, the target id for a query with
                        no hits (default: '*')
  --empty-score EMPTY_SCORE
                        In csv or tsv output, the score for a query with no
                        hits (default: 'NaN')
  --precision N         Number of digits in Tanimoto score (default: based on
                        the fingerprint size)
  -c, --count           report counts
  -b BATCH_SIZE, --batch-size BATCH_SIZE
                        batch size
  --scan                scan the file to find matches (low memory overhead)
  --memory              build and search an in-memory data structure (faster
                        for multiple queries)
  --no-mmap             don't use mmap to read uncompressed FPB files. May
                        give better performance on networked file systems, at
                        the expense of higher memory use.
  --times               report load and execution times to stderr
  --version             show program's version number and exit
  --license-check       Check the license and report results to stdout.