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DOG: Docking Geometrically two molecules.

Reference:

M. Petitjean,
Solving the Geometric Docking Problem for Planar and Spatial Sets,
Internet Electron. J. Mol. Des. 2002,1[4],185-192.
http://www.biochempress.com
 
Author email: petitjean@itodys.jussieu.fr

DOG reads the cartesian coordinates of two molecules, then translates
and rotates the molecule 2 for docking with the molecule 1.
A pairwise correspondence between two equal length ranges of atoms is
input.
When each of the two molecules is a single nucleotidic strand in
PDB/NDB format, the pairwise correspondence is defined from the
atom-pairs enabling potential hydrogen bonds.

The two input molecules should be concatenated into a single file
prior execution.


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

INPUT  FORMAT:
  CAS : Reserved for internal purposes
  HIN : Hyperchem-type files
  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)
  BIO : Biosym (MSI) files
  ISU : Reserved for internal purposes

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

OUTPUT MOLEC FILE NAME: name of the output file containing the optimally
  translated and rotated molecule 2

IMOL1: sequential position number of molecule 1 in the input molecules file

IMOL2: sequential position number of molecule 2 in the input molecules file

INI1: first atom in molecule 1 to be paired (if the NUCLEO flag is set to N)
  or: first nucleotidic base to be analyzed (if the NUCLEO flag is set to Y)

INI2: first atom in molecule 2 to be paired (if the NUCLEO flag is set to N)
  or: first nucleotidic base to be analyzed (if the NUCLEO flag is set to Y)

LENGTH: number of input atom pairs or number of base pairs to be analyzed.
  Atoms INI1 to INI1-1+LENGTH are paired with atoms INI2 to INI2-1+LENGTH,
  or,
  bases INI1 to INI1-1+LENGTH are paired with bases INI2 to INI2-1+LENGTH
  for atom labeling analysis.

NUCLEO:
 Entering Y activates the automatic detection of potential hydrogen bonds
            from atom labeling analysis, provided that the format is PDB.
            3 atom pairs are included in the pairwise correspondence
            for the CG or GC base pairs, and 2 atom pairs are included
            for the AT, TA, AU or UA base pairs.
            When the K-th base pair {INI1-1+K, INI2-1+K} is mismatched,
            no atom-pair is included in the pairwise atomic correspondence.
 Entering N desactivates the option.
            The default option is Y when the selected format is PDB.
            The option is set to N when a format other than PDB is selected.


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

The variance of the population of the squared distances defined by
the input pairs, and the optimal translation and rotation.
(translation is done prior rotation).

The coordinates of the optimally docked atom-pairs.

The new coordinates of the optimally translated and rotated molecule 2
are written in a separate file.

Remarks:
-------

The number of atoms is currently limited to 15000 for each molecule.
The source has to be recompiled to read larger molecules.

Connectivity and charges are not used.
No relevant initial orientation is needed before docking.

The geometric docking algorithm looks like the RMS algorithm used
for spatial alignments, except that the minimized quantity is the
variance of the squared distances rather than the mean.

When less than 7 atom-pairs are read, the problem is underdetermined,
and numerical instabilities appear.

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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