biom.h

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#ifndef _BIOM_H_
#define _BIOM_H_

#include <gamer/gamer_base.h>

#include <gamer/triangle.h>
#include <gamer/tetgen.h>

#if 0
#include <stdio.h>       /* One of 15 ISO-C headers -- get via MALOC */
#include <stdlib.h>      /* One of 15 ISO-C headers -- get via MALOC */
#include <math.h>        /* One of 15 ISO-C headers -- get via MALOC */
#include <time.h>        /* One of 15 ISO-C headers -- get via MALOC */
#include <string.h>      /* One of 15 ISO-C headers -- get via MALOC */
#include <sys/times.h>   /* System-dependent; include in .c file via MALOC */
#include <sys/stat.h>    /* System-dependent; include in .c file via MALOC */
#include <memory.h>      /* System-dependent; include in .c file via MALOC */
#endif

// critical parameters for mesh generation

#define IsoValue          2.5      

#define BLOBBYNESS        -0.2f    

#define DIM_SCALE         1.99   

#define CoarsenRate       0.1666   

#define MIN_VOLUME        333333   

#define SphereRatio       40

#define MaxVal               999999
#define MaxAtom              10

// Other definitions and data structures

#define PIE              3.14159265358979f 

#define IndexVect(i,j,k) ((k)*xdim*ydim + (j)*xdim + (i))
#define IndexVect1(i,j,k) ((k)*xdim1*ydim1 + (j)*xdim1 + (i))

#define max(x, y)        ((x>y) ? (x):(y))

#define min(x, y)        ((x<y) ? (x):(y))

#define _LITTLE_ENDIAN   1

typedef struct {
  float x;   
  float y;   
}FLT2VECT;

typedef struct {
  float x;   
  float y;   
  float z;   
}FLTVECT;

typedef struct {
  double x;   
  double y;   
  double z;   
}DBLVECT;

typedef struct {
  int a;   
  int b;   
  int c;   
}INT3VECT;

typedef struct {
  int a;   
  int b;   
  int c;   
  int d;   
}INT4VECT;

typedef struct {
  int nv;   
  int nf;   
  float avglen;   
  float min[3];   
  float max[3];   
  FLTVECT *vertex;   
  INT3VECT *face;   
  INT3VECT *neighbor;   
}SurFaceMesh;

typedef struct {
  int nv;   
  int nf;   
  FLTVECT *vertex;   
  INT4VECT *face;   
  INT4VECT *neighbor;   
}TeTraMesh;


typedef struct SamplePoint SPNT;
struct SamplePoint{
  float x;   
  float y;   
  float z;   
  SPNT *next;   
};


typedef struct NeighborPoint3 NPNT3;
struct NeighborPoint3{
  int a;   
  int b;   
  int c;   
  NPNT3 *next;   
};


typedef struct NeighborPoint2 NPNT2;
struct NeighborPoint2{
  int a;   
  int b;   
  NPNT2 *next;   
};

typedef struct {
  float x;   
  float y;   
  float z;   
  float radius;   
}ATOM;


typedef struct {
  float x1;   
  float y1;   
  float z1;   
  float x2;   
  float y2;   
  float z2;   
  float x3;   
  float y3;   
  float z3;   
}EIGENVECT;


typedef struct {
  unsigned short *x; 
  unsigned short *y; 
  unsigned short *z; 
  int *seed;         
  float *dist;       
  int size;          
}MinHeapS;


typedef struct{
  float seedx;       
  float seedy;       
  float seedz;       
  int atom[MaxAtom]; 
}SEEDS;


NPNT3** CreateNeigborList(SurFaceMesh*);
void GetMinMaxAnglesSurfaceOnly(SurFaceMesh* ,float*, float*, int*, int*, int, int);
void RefineSurfaceMesh(SurFaceMesh*&, NPNT3**&);
void ReadActiveSiteFile(char*, unsigned int&, ATOM*&, unsigned int*&, float*&);
bool SmoothMesh(SurFaceMesh*, NPNT3**, unsigned int, unsigned int, unsigned int, bool);
void NormalSmoothMesh(SurFaceMesh*, NPNT3**);
char CoarseMesh(SurFaceMesh*, NPNT3**,unsigned int*, float, float, float, float);
void DestroyNeigborlist(NPNT3**, unsigned int);
void AssignActiveSites(SurFaceMesh*, ATOM*, unsigned int, unsigned int*, unsigned int*);
void CorrectNormals(SurFaceMesh*);

void ReadSurfMeshFile(char*, bool, char*, SurFaceMesh*&, int&);
//void ReadActiveSiteFile(char*, unsigned int&, ATOM*&, unsigned int*&, float*&);
void ReadActiveSiteFile(char*, unsigned int&, ATOM*&, unsigned int*&);
void ReadRawiv(int *, int *, int *, float **, char *,float *, float *);
void ReadMeshOFF(char*, SurFaceMesh*&);
void WriteMesh3OFF(SurFaceMesh *, FILE *);
void SurfaceExtract(TeTraMesh *, SurFaceMesh *);
float PDB2Volume(char *, float **, int *, int *, int *,float *, float *, ATOM **,int *,char);
void MarchingCube(int, int, int, float *, float, float, SurFaceMesh **,SPNT **);
void MergeSurfaceMesh(SurFaceMesh *,SurFaceMesh *,SurFaceMesh *);
void GenerateSphereMesh(int, SurFaceMesh **);
void ReadPDB(char *,int *, ATOM **, float [], float []);
void PDB2Mesh(int, ATOM *, float [], float [], SurFaceMesh **);

#endif /* _BIOM_H_ */

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