.. _simsearch:

simsearch command-line options
====================================

The following comes from ``simsearch --help``:

.. code-block:: none

  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]
                   target_filename
  
  Search an FPS or FPB file for similar fingerprints
  
  positional arguments:
    target_filename       target filename
  
  options:
    -h, --help            show this help message and exit
    -k K_NEAREST, --k-nearest K_NEAREST
                          select the k nearest neighbors (use 'all' for all
                          neighbors)
    -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?
                          (default=ignore)
    -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.