biom.h File Reference

Some parameter/datatype definitions. More...

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

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struct  FLT2VECT
 Other data structure FLT2VECT (float). More...
struct  FLTVECT
 Other data structure FLTVECT (float). More...
struct  DBLVECT
 Other data structure DBLVECT (double float). More...
struct  INT3VECT
 Other data structure INT3VECT (int). More...
struct  INT4VECT
 Other data structure INT4VECT (int). More...
struct  SurFaceMesh
 Other data structure SurFaceMesh (for surface meshes). More...
struct  TeTraMesh
 Other data structure TeTraMesh (for tetrahedral meshes). More...
struct  SamplePoint
 Other data structure SamplePoint. More...
struct  NeighborPoint3
 Other data structure NeighborPoint3. More...
struct  NeighborPoint2
 Other data structure NeighborPoint2. More...
struct  ATOM
 Other data structure ATOM. More...
 Other data structure EIGENVECT. More...
struct  MinHeapS
 Other data structure MinHeapS. More...
struct  SEEDS
 Other data structure SEEDS. More...


#define IsoValue   2.5
 Isovalue used in the Marching Cube method.
#define BLOBBYNESS   -0.2f
 Blurring blobyness used in conversion from PDB/PQR to 3D volumes.
#define DIM_SCALE   1.99
 Discretization rate of 3D volumes.
#define CoarsenRate   0.1666
 Coarsening Rate in surface post-processing.
#define MIN_VOLUME   333333
 The minimal volumes (in voxels) of islands to be removed.
#define SphereRatio   40
 The size of the bounding sphere (= object size X the following rate).
#define MaxVal   999999
#define MaxAtom   10
#define PIE   3.14159265358979f
 Other definition.
#define IndexVect(i, j, k)   ((k)*xdim*ydim + (j)*xdim + (i))
 Other definition.
#define IndexVect1(i, j, k)   ((k)*xdim1*ydim1 + (j)*xdim1 + (i))
#define max(x, y)   ((x>y) ? (x):(y))
 Other definition.
#define min(x, y)   ((x<y) ? (x):(y))
 Other definition.
#define _LITTLE_ENDIAN   1
 Other definition.


typedef struct SamplePoint SPNT
 Other data structure SPNT.
typedef struct NeighborPoint3 NPNT3
 Other data structure NPNT3.
typedef struct NeighborPoint2 NPNT2
 Other data structure NPNT2.


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 *&)
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 **)

Detailed Description

Some parameter/datatype definitions.

Zeyun Yu (
biom.h,v 1.18 2010/07/13 13:37:01 fetk Exp

 * GAMER = < Geometry-preserving Adaptive MeshER >
 * Copyright (C) 2007-2010 -- Michael Holst and Zeyun Yu
 * This library is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public
 * License as published by the Free Software Foundation; either
 * version 2.1 of the License, or (at your option) any later version.
 * This library is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * Lesser General Public License for more details.
 * You should have received a copy of the GNU Lesser General Public
 * License along with this library; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

Generated on Mon Aug 9 11:14:24 2010 for GAMER by  doxygen 1.5.6