# include "dist.h"

# define HELP_STRING "\
                                                                            \n\
Options:                                                                    \n\
-Fixed          = Filename of Fixed  Structure                              \n\
-Moving         = Filename of Moving Structure                              \n\
-Output         = Filename to output (transformed) Moving Structure         \n\
-Selection      = Filename of CA Selections ( '-' = stdin )                 \n\
-VerboseDumpRT  = Print out transformation with rotation angle and axis     \n\
-SimpleDumpRT   = Print out transformation in a simple form                 \n\
-DoTransRot     = Apply transformation to coordinates                       \n\
-SelectAll      = Select All Atoms                                          \n\
-VerifySelect   = Dump the selected atoms for verification                  \n\
-CompareCoordinates = Compare CAs                                           \n\
                                                                            \n\
"
# define HELP_STRING2 "\
Selection File Format :                                                     \n\
  File      = StrucSel-for-fixed StrucSel-for-moving                        \n\
  StrucSel  = { \\n Range [ \\n range] \\n } \\n                            \n\
  Range     = from-integer to-integer chain-char                            \n\
              If chain is '_' or NULL, chain is ' '.                        \n\
Example :                                                                   \n\
  Fixed                                                                     \n\
  {                                                                         \n\
    1      10    A                                                          \n\
    20     30    A                                                          \n\
  }                                                                         \n\
  Moving                                                                    \n\
  {                                                                         \n\
    10     20                                                               \n\
    40     50                                                               \n\
  }                                                                         \n\
                                                                            \n\
Normal Output Format is :                                                   \n\
  Rotation[3,3] \\n Translation[3] \\n RMS[1]                               \n\
"

main(int argc,char ** argv) 
{
  SAY_HI_FIRST;
  CITATION ;
  do_initialization(0,0) ;
  if (OPT("help")) {
    printf(HELP_STRING);
    printf(HELP_STRING2);
  } else {
    char 
      *MovingFileName = StringAfterOption(argc,argv,"Moving", "Moving.pdb"),
      *FixedFileName  = StringAfterOption(argc,argv,"Fixed", "Fixed.pdb"),
      *OutputFileName = StringAfterOption(argc,argv,"Output", NULL);
    file_records
      *Moving = open_and_read_pdb(MovingFileName,0),
      *Fixed  = open_and_read_pdb(FixedFileName,0);
    int nsel1, nsel2 ;
    if (OPT("SelectAll")) {
      FlagOffEverywhere(Fixed,FLAG_1_DESELECT|FLAG_2_DESELECT);
      FlagOffEverywhere(Moving,FLAG_1_DESELECT|FLAG_2_DESELECT);
    } else if (OPT("EquivSelect")) {
      TokenizeData d = {0};
      d.filename = StringAfterOption(argc,argv,"EquivSelect","Selection.txt");
      InitLexer(&d);
      d.whitespace = " -\t\n" ;
      fprintf(stderr,"MyFit.c: EquivSelectCA():  Fixed=%s  Moving=%s\n",FixedFileName,MovingFileName);
      nsel1 = nsel2 = EquivSelectCA(Fixed,Moving,&d);
    } else {
      TokenizeData d = {0};
      d.filename = StringAfterOption(argc,argv,"Selection","Selection.txt");
      InitLexer(&d);
      d.whitespace = " -\t\n" ;
      fprintf(stderr,"[ MyFit.c ] Selection from Fixed  Structure %s\n",FixedFileName);
      nsel1 = NSelectCA(Fixed,&d) ;
      fprintf(stderr,"[ MyFit.c ] Selection from Moving Structure %s\n",MovingFileName);
      nsel2 = NSelectCA(Moving,&d);
      if (nsel1 != nsel2) STDERR("nsel1 != nsel2") ;
    }   
    if (OPT("VerifySelect")) {
      printf("Selected Atoms from Fixed  Structure: \n");
      write_pdb_file(stdout,Fixed,IO_ONLY_SELECTED);
      printf("Selected Atoms from Moving Structure: \n");
      write_pdb_file(stdout,Moving,IO_ONLY_SELECTED);
    }
    
    {
      double ** RotMat = dmatrix(1,3,1,3) ;
      double TVect[4];
      double rms ;

      if (OPT("MyFit")) {
	rms = MyFit(RotMat,TVect,Moving,Fixed);
      } else if (OPT("FindFitTranslationOnly")) {
	IdentityMatrix(RotMat);
	FindFitTranslationOnly(TVect,Moving,Fixed);
	rms = 0;
      } else if (OPT("FitTR")) {
	AllocateNRVect3 TVect2;
	FindFitTranslationOnly(TVect,Moving,Fixed);
	TranslateCoordinates(Moving,TVect);
	rms = MyFit(RotMat,TVect2,Moving,Fixed);
	STDERR("FitTR means doing translation first.");
	fprintf(stderr,
		"The secondary translation, which is ( %6.3f %6.3f %6.3f ), should be (0 0 0)\n",
		TVect2[1],TVect2[2],TVect2[3]);
	TVect2[1]= -TVect[1];
	TVect2[2]= -TVect[2];
	TVect2[3]= -TVect[3];
	TranslateCoordinates(Moving,TVect2);
      }
      if (OPT("SimpleDumpRT"))
	SimpleDumpRT(RotMat,TVect,rms);
      if (OPT("DoTransRot")) {
	if (OPT("FitTR")) {
	  RotateCoordinates(Moving,RotMat);
	  TranslateCoordinates(Moving,TVect);
	} else {
	  TranslateCoordinates(Moving,TVect);
	  RotateCoordinates(Moving,RotMat);
	}
      }
      if (OPT("CompareCoordinates")) {
	double rms2 = CompareCoordinatesSecondToFirst(Fixed,Moving,FLAG_2_DESELECT);
	FTOE(rms2);
      }
    }
    if (OutputFileName) {
      FILE * OutputStream = fopen(OutputFileName,"w");
      if (OPT("WriteOnlySelected")) {
   	write_pdb_file(OutputStream,Moving,IO_ONLY_SELECTED);
      } else {
	write_pdb_file(OutputStream,Moving,0);
      }	  
    }
  }
  exit(0);
}