#include "dist.h"

int TheMethod ;

void SaveAtomVertices(int n,atom_record * a, vertex *v1, vertex *v2)
{}

void LoopOverNeighbors
(atom_record *atom,neibour_descr *neibours,int neibour_count)
{}

main(int argc,char **argv)
{
  SAY_HI_FIRST ;
  CITATION ;
  char * types_file = STRG_AFTER_OPT_W_ENV("types-file","data/NucProt.atom-defs.dat") ;
  char * res_file = STRG_AFTER_OPT_W_ENV("residue-file","data/NucProt.resi-defs.dat") ;
  char * vol_file = STRG_AFTER_OPT_W_ENV("stdvols","data/NucProt.stdvol258.dat") ;
  fprintf(stderr,"Expecting atoms definitions to be in %s (types_file)\n",types_file);
  fprintf(stderr,"Expecting residue definitions to be in %s (res_file)\n",res_file);
  initial_residues(types_file,res_file,0);
  STDERR("Initialization is DONE");

  /* WriteAtomTypes(); */

  {
    file_records *f = open_and_read_pdb(STRG_AFTER_OPT_W_ENV("i","in.pdb"),0);
    int n = f->atomnum;
    atom_record ** P = f->atoms;
    double packeff ;
    int ii;
    double surf_thresh = DoubleAfterOption(argc,argv,"SurfThresh",3.0);

    STDERR("Option [-probe X.X] is set by default to 1.4 A by can be set to X.X") ;
    calculate_surface(f,DoubleAfterOption(argc,argv,"probe",1.4));

    STDERR("Surface Calculation is DONE");
    STDERR("Option [-method X] is set by default to 4 but can be set to X") ;
    STDERR("The methods are 1 for Normal Voronoi (bisection), 2 for Richards' Method B");
    STDERR("3 for Radical Plane, and 4 for Simplified Method B");
    NN_Calculate_Volumes(f,
			 (int) DoubleAfterOption(argc,argv,"method",4), 
			 DoubleAfterOption(argc,argv,"VolMaxDist",64),
			 DoubleAfterOption(argc,argv,"DistCheck",8.5));

    STDERR("Volume Calculation is DONE");

    COPY_ATOM_VECTS_1TO2(P,surface,P,x,n);
    COPY_ATOM_VECTS_1TO2(P,volume,P,y,n);

    fprintf(stderr,"Expecting standard volumes to be in %s (vol_file)\n",vol_file);
    STDERR("About to read this file NOW (might crash if it is not there!)");
    read_standard_volumes (vol_file);
    RefVToB(f);
    COPY_ATOM_VECTS_1TO2(P,b,P,x,n);
    CovVDWRadiiToOccB(f);
    STDERR("Internally rearranging data vectors: X=ref-vol Y=volume Z=z Occ=Covalent-Radius B=VDW-Radius Surf=surface volume=volume\n");

    { 
      char * fieldnames = 
	"number_\tresnum\tchain\tresname\tatname\ttypenum\ttypenam\tcovrad\tvdwrad\tsurface\tvolume\trefvol\tpackeff\tgoodbad\n";
      
      if (OPT("no-field-names")) {
	fprintf(stderr,fieldnames);
      } else {
	fprintf(stdout,fieldnames);
      }
    }
    
    for (ii=0; ii<f->atomnum; ii++) {
      atom_record * a = f->atoms[ii];
      if (a->chain == ' ') { a->chain='.' ; }
      printf("%7d\t%7d\t%1c\t",a->number,a->resnum,a->chain);
      printf("%5s\t%5s\t%4d\t%5s\t",
	     a->resname,a->name,
	     a->definition->type_index, 
	     atom_type_name(a->definition->type_index));
      printf("%7.3f\t",a->occ);       /* Covalent Radius */
      printf("%7.3f\t",a->b);         /* VDW Radius */
      printf("%7.3f\t",a->surface);         /* Surface */
      printf("%7.3f\t",a->volume);    /* Volume */
      /* printf("%7.3f\t",a->y);    */     /* Volume */
      printf("%7.3f\t",a->x);   /* Ref. Volume */
      if (a->x > 0 && a->volume > 0) {
	packeff = a->volume/a->x ;
      } else {
	packeff = -1;
      }
      printf("%7.3f\t",packeff); /* Relative Packing Eff. */

      if (a->volume <= 0) {
	printf("bad");
      } else if (a->surface > surf_thresh) {
	printf("possible");
      } else if (a->surface > .00001) {
	printf("[OK]");
      } else {
	printf ("[GOOD]");
      }
      printf ("\n");
    }
  }
}