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CSR: The Combined SDM/RMS Algorithm for spatial alignment of two molecules.

Reference:

M. Petitjean, Interactive Maximal Common 3D Substructure Searching
with the Combined SDM/RMS Algorithm, Comput. Chem. 1998,22[6],463-465).

Author email: petitjean@itodys.jussieu.fr

CSR reads the cartesian coordinates of two molecules, then optimally rotates and
translates the molecule 2 onto the molecule 1 to find the maximal common 3D motif.

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
  rotated and translated 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

ITERMX: maximum number of iterations; recommended value: about 200 for
  small molecules (<100at.), about 2000 for a hundred to a thousand atoms,
  and 20000 for larger molecules

CUT-OFF DIST:
  This parameter does NOT affect the results. It saves space and time.
  As a rule of thumb, this value should be roughly near a bondlength.
  E.g. about 1.5 to 2 for small inorganic molecules, 0.9 to 1.2 for full
  proteins, 4 to 5 for C-alpha protein backbones).


Output results:
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The size N of the common 3D motif, and the r.m.s. between the N pairs
of atoms, followed by the one-to-one correspondence between the N atoms
of molecule 1 and the N atoms of molecule 2.

The new coordinates of the optimally rotated and translated molecule 2.


Remarks:
-------

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

To operate on C-alpha protein backbones, the other atoms should be
removed prior execution.

The computing time is roughly proportional to the product n1*n2 of
the number of atoms of the two molecules, and proportional to the
number of iterations (reading and writing files not included).

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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