Daylight v4.9
Release Date: 1 February 2008


sdcluster - perform scaffold-directed clustering

Unix Synopsis

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


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).


-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.
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.
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.

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



Daylight License

programs: cluster

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