Clustering Steps

The basic steps are as follows:

  1. (IF data is in MOL format:) Convert the MOLfile to Daylight TDT format with "mol2tdt". This is a contributed program at $DY_ROOT/contrib/src/applics/convert/molfiles/mol2tdt.c You have to compile the program with:
           cd DY_ROOT/contrib/src
           cd DY_ROOT/contrib/src/applics/convert/molfiles
           make mol2tdt
    There may be a newer version of the program at our ftp site, directory /var/spool/ftp/pub/contrib/src, filename "mol2smi.c".
  2. Fingerprint (fingerprint program) the TDT file.
  3. Compute nearest neighbors (nearneighbors).
  4. Use jpscan to predict clustering results and select clustering parameters.
  5. Cluster with chosen parameters (jarpat).
  6. Add variances to clusters (listclusters -v).
  7. (Optionally) display clustering results with showclusters.
  8. Create a Daylight database (datatypes database and regular database). (Use thormake or sthorman.) See Creating a Daylight Database for guidance.
  9. Load database with datafiles. Use output of fingerprint program plus output of listclusters program (2 loads, merging). (thorload or sthorman).
  10. Load pool (merlinload or sthorman) to view with Merlin.
This is a brief description of the process. Please refer to the Daylight Administration manual for more guidance, and the Daylight Theory manual (Thor/Merlin especially), and the Clustering manual.

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