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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Classes
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...
struct	EIGENVECT
	Other data structure EIGENVECT. More...
struct	MinHeapS
	Other data structure MinHeapS. More...
struct	SEEDS
	Other data structure SEEDS. More...
Defines
#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.
Typedefs
typedef struct SamplePoint	SPNT
	Other data structure SPNT.
typedef struct NeighborPoint3	NPNT3
	Other data structure NPNT3.
typedef struct NeighborPoint2	NPNT2
	Other data structure NPNT2.
Functions
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 **)

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Detailed Description

Some parameter/datatype definitions.

Author:

Zeyun Yu (zeyun.yu@gmail.com)

Note:

None

Version:

Id

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

Attention:

 *
 * 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
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
 * 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
 * 
 *