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DIVCF: Reads N conformers of a molecule, then retains only K of them
       as representative ones (K .le. N), in order to reduce the
       redundancy in the conformational space.

Reference:

J.E. Meslamani, F. Andre, M. Petitjean
J. Chem. Inf. Model. 2009, 49[2], 330-337.
DOI: 10.1021/ci800275k

mailto: petitjean.chiral@gmail.com


DIVCF reads the N sets of cartesian coordinates of the molecule,
then computes the (N*N) array of minimized RMS distances between them.
This array of non euclidean distances is submitted to a hierarchical
ascending classification with the MCG (Modified Clustering Gain)
as the stop criterion, which gives K clusters of conformers.
The K mean points of the clusters are the K retained conformers.


Input data and parameters:
-------------------------

INPUT  FORMAT:
  BIO : Biosym (MSI) files
  CAS : Reserved for internal purposes
  HIN : Hyperchem-type files
  ISU : Reserved for internal purposes
  MDL : Cambridge Crystallographic Model files
  ML2 : SYBYL Mol2 files
  PDB : Protein Data Bank or Nucleic Acid Data Bank files
        (only HEADER, ATOM, ENDMDL and END records are recognized)
  SDF : Symyx Mol/SDF files
        (data between 'M  END' and '$$$$' are treated as comments)
  XYZ : n+2 lines. Line 1: n; line 2: free comment,
        Next n lines: label or atomic symbol, x, y, z
        (separator: spaces; no tabulation allowed).

INPUT  MOLEC FILE NAME: name of the input file containing both molecules

OUTPUT MOLEC FILE NAME: name of the output file containing the
     K retained conformers.

(S,C,A): indicates the linkage mode for the hierarchical clustering:
     Entering S sets the single linkage mode
     Entering C sets the complete linkage mode (default)
     Entering A sets the quadratic average linkage mode


Output results:
--------------

The file containing the K retained conformers.

The global mean conformer, among the K retained ones.

The dispersion between clusters, i.e. the square root of the
quadratic mean distance (in the RMS sense) of the K retained
conformers around the global mean conformer.


Remarks:
-------

The maximal number of input conformers is 2000.
The number of atoms is currently limited to 15000 for each molecule.
The source has to be recompiled to read more.

The generated file containing the output moved molecule 2 is empty for
CAS, MDL and BIO formats, and the message "EERCO2 = 1" is displayed.

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