sdcluster

Daylight v4.9
Release Date: 1 February 2008

Name

sdcluster - perform scaffold-directed clustering

Unix Synopsis

sdcluster [options] in.tdt [out.tdt]

Description

sdcluster parses a small-sized list of SMILES and partitions the input SMILES into clusters with significant scaffolds.

The input file must be a SMILES file that may include space-separated names.

Default output is to stdout. The output is in TDT format and is compatible with listclusters and showclusters. The clusters are designated with the CL<> datatype. The TDT output also includes the SMARTS representation of the scaffold (which may contain more than one fragment) and a minimum coverage value for each cluster, attached to the first TDT in each cluster (like kmodes).

Options

-MIN_COVERAGE <number>

Sets the minimum coverage (scalar value between 0.00 and 1.0) for any molecule in a cluster with the default at 0.3.

-MAX_FP_PATH_SIZE <number>

Sets the maximum fingerprint path length with a potential range of 0 to 19. The default is 19.

-MIN_FP_PATH_SIZE <number>

Sets the minimum fingerprint path length with a potential range of 0 to 19. The default is O.

TOPO_OPTION [DX_CSS_DEFAULT|DX_CSS_SIMPLE_TOPOLOGY]

Sets topology to full or simple, i.e., no ring bond counts used. The default is full (DX_CSS_DEFAULT).

-SKIP_RECORDS <number>

Sets the number of records in the input file to skip. The default value is 0.

-DO_RECORDS <number>

Sets the number of records from the input file to be processed. The default is 10,000.

-SHOW_ERRORLEVEL [ALL|NOTE|WARNING|ERROR|FATAL]

Sets minimum level for errors to be reported along with more serious errors. Possible values are:

     NOTE|ALL  Might be of interest but not an error 
     WARNING   Something abnormal; may require attention
     ERROR     Requested operation cannot be carried out
     FATAL     Serious error; program cannot continue

Default is ERROR which shows this level and above.

-HELP [TRUE|FALSE]

Prints the help message. Default is FALSE. Setting -HELP to TRUE or using -h prints the help message to stout.

-VERSION [TRUE|FALSE]

Prints the program version. Default is FALSE. Setting -VERSION to TRUE prints the program version to stout.

Return Value

Returns 0 to its environment on success, or 1 on error, in which case a diagnostic message is printed:

Files

$DY_ROOT/bin/sdcluster

Daylight License

programs: cluster