oned_screen run Command Help

Command: $SCHRODINGER/oned_screen run

usage: oned_screen run [-h] -query <qfile> -screen <source>
                       [Screening Options]
                       [Hit Treatment Options]
                       [Job Control Options]

Optional Arguments:
  -h, --help          Show this message and exit.

Required Arguments:
  -query <qfile>      File containing one or more query structures. Supported
                      formats are SMILES, SMILES-CSV, Maestro, SD and Phase
                      hypothesis (.phypo). If a single query is supplied, hits
                      are returned in <jobname>-hits.csv.gz, where <jobname>
                      is derived from <qfile>. If multiple queries are
                      supplied, hits are returned in the files
                      <jobname>_<n>-hits.csv.gz, where <n> runs from 1 to the
                      number of queries.
  -screen <source>    1D data file (.1dbin) to screen, or list file (.list)
                      containing the names of the 1D data files to screen,
                      with one name per line. Use of multiple data files
                      containing no more than 50 million rows apiece is
                      strongly recommended to achieve the fastest multi-CPU
                      screens. Absolute paths must be provided if -nocopy is
                      supplied.

Screening Options:
  [-norm {1,2,3,4}] [-filter <min>]

  -norm {1,2,3,4}     Similarity normalization scheme. For query A and
                      screening structure B, similarity is computed as
                      O(A,B)/norm(A,B), where O(A,B) is the overlap between A
                      and B, and norm(A,B) is a function of the self-overlaps
                      O(A,A) and O(B,B): 1->max{O(A,A), O(B,B)},
                      2->min{O(A,A), O(B,B)}, 3->O(A,A), 4->O(B,B) (default:
                      1).
  -filter <min>       Filter out molecules whose similarities fall below
                      <min>. The default is to apply no filter.

Hit Treatment Options:
  [-nosort | -keep <maxhits> [-fraction <f>] [-catgz] [-limit <maxrows>]]

  -nosort             Output hits in the order they are screened. The default
                      is to sort hits by decreasing similarity to the query.
  -keep <maxhits>     Cap the number of sorted hits per query at <maxhits>
                      (default: 1000). Must not exceed 4294967295.
  -fraction <f>       Cap the number of sorted hits per subjob (and per query)
                      at <f>*<maxhits>. For example, -keep 1000000 -fraction
                      0.25 would result in a maximum of 250,000 hits per
                      subjob. While this means only the first 250,000 hits in
                      the combined set are guaranteed to be optimal, the
                      remaining 750,000 are likely to be near optimal if the
                      number of subjobs is sufficiently large and high-
                      similarity hits are uniformly distributed over the
                      subjobs. Furthermore, the time required to post-process
                      hits could be reduced by as much as 75%. The default
                      fraction is 1.0.
  -catgz              Write intermediate file of concatenated hits in
                      compressed format. The resulting file is about half as
                      large, but concatenation is about 3 times slower. Note
                      that the final hits returned by the job are always
                      compressed.
  -limit <maxrows>    Limit on the number of rows held in memory when sorting
                      hits (default: 1000000). Increasing this limit is
                      strongly recommended when requesting more than
                      10,000,000 hits.

Job Control Options:
  [-HOST <host>[:<n>]] [-TMPDIR <tmpdir>] [-JOBNAME <jobname>] [-nocopy]
  [-NJOBS <njobs>]

  -HOST <host>[:<n>]  Run job remotely on the indicated host entry. Include
                      :<n> to distribute the job over <n> CPUs.
  -TMPDIR <tmpdir>    Store temporary job files in <tmpdir>.
  -JOBNAME <jobname>  Override default job name.
  -nocopy             Do not copy source or destination 1D data files between
                      the local host and job host. 1D data file names must
                      include an absolute path that exists on the job host and
                      on all compute nodes of that host.
  -NJOBS <njobs>      Divide the overall job into <njobs> subjobs.