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POSE: Computes the RMSD between two ligand poses.

Reference of the SDM algorithm:
[1] M. Petitjean; Interactive Maximal Common 3D Substructure Searching
with the Combined SDM/RMS Algorithm. Comput. Chem. 1998, 22[6], 463-465.
[2] M. Petitjean; Three-Dimensional Pattern Recognition from Molecular
Distance Minimization. J. Chem. Inf. Comput. Sci. 1996, 36[5], 1038-1049.
 
Author email: petitjean.chiral@gmail.com

POSE reads the cartesian coordinates of two ligands, then computes
the population of the squared distances between atom-pairs, each pair
having its first member in ligand 1 and its second member in ligand 2.
The list of the pairs is either read or computed.

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


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

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

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

LENGTH: number of atom pairs.
  When LENGTH>0, LENGTH atom-pairs are to be read on the next input line.
       Example: "1 1, 2 5, 6 7, 10 10, 14 3, 3 20, 12 12" means that
       atom 1 of ligand 1 is paired with atom 1 of ligand 2,
       atom 2 of ligand 1 is paired with atom 5 of ligand 2, etc.
  When LENGTH=0, the atom-pairs are implicitely:
       "1 1, 2 2, 3 3, ..., n n", where n is the number of atoms of the
       smaller ligand (i.e. the one with the smallest number of atoms).
  When LENGTH<0, the pairwise correspondence is computed automatically
       with the SDM algorithm.


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

The computed pairwise correspondence, When LENGTH<0.

The population of the squared distances (size: LENGTH).
The mean (and its square root, i.e. the RMSD), the variance,
the standard deviation, the minimal value and the maximal value,
and the median of this population.


Remarks:
-------

The number of atoms is currently limited to 50000 for each ligand.
The source has to be recompiled to read larger molecules.
Neither rotation nor translation is allowed.
For automatic 3D alignments (i.e. with rotation and translation),
please use the CSR freeware.

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