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GRD: Computation of the Radius and Diameter of a chemical graph

Reference:

M. Petitjean, Applications of the Radius-Diameter Diagram to
the Classification of Topological and Geometrical Shapes of
Chemical Compounds, J.Chem.Inf.Comput.Sci. 1992,32[4],331-337

Author email: petitjean.chiral@gmail.com

GRD reads the connection table of the molecule.
It computes the radius R and the diameter D and the shape index
(D-R)/R, of each component of the molecular graph.


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 the molecule

Enter Y to suppress the hydrogens before calculation.
Entering N or a blank line means that the hydrogens are kept.


Output results:
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For each component:

  DIAMETER: the graph distance D of the longest atom-pair, or,
    in other words, the length of the longest chain.

  RADIUS: the radius R of the graph, i.e. the total number of
    concentric layers around the center of the graph, or,
    in other words, the excentricity of the center.
    This center (not unique, in general), is defined as the atom
    having a minimal excentricity (see below).

  THE SHAPE COEFFICIENT : (D-R)/R. In general, D varies from R to 2R.
    A zero value is returned for R=0 (occurs only for isolated atoms).

For the whole molecule:

The list of the N pairs (icomp(i), exc(i)), i=1,N, where N is the
number of atoms, icomp(i) is the number of the component where the
atom i is found (icomp(i)=1 for any atom i when there is only one
component), and exc(i) is the excentricity of the atom i, i.e. the
number of concentric layers of atoms around i.


Remarks:
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The number of atoms is currently limited to 50000 for each molecule.
The source has to be recompiled to read larger molecules.

The file formats BIO, ISU, PDB, and XYZ are recognized, but no bond
is generated, so that all output values are zero.

R and D are defined in 3D and can be computed by the RADI freeware.

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