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VoxelSeries Class Reference

#include <VoxelSeries.h>

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Detailed Description

Definition at line 5 of file VoxelSeries.h.

Public Member Functions

 VoxelSeries (int sizeX, int sizeY, int sizeZ)
void setVoxel (int x, int y, int z, bool fill)
Voxel getVoxel (int x, int y, int z)
void setVoxelFilled (int x, int y, int z, bool fill)
bool isVoxelFilled (int x, int y, int z)
int getBoundX ()
int getBoundY ()
int getBoundZ ()
void setInternalCavity (int x, int y, int z, bool internalCv)
bool isInternalCavity (int x, int y, int z)
void setSurfaceVoxel (int x, int y, int z, bool surface)
bool isSurfaceVoxel (int x, int y, int z)
void setActiveSite (int x, int y, int z, bool activesite)
bool isActiveSite (int x, int y, int z)
bool isCoreVoxel (int x, int y, int z)
void setBlockedDirectionSize (int x, int y, int z, int blockNumber)
int getBlockedDirectionSize (int x, int y, int z)
void setDirectionalVisibility (int posX, int posY, int posZ, int dirX, int dirY, int dirZ, int visibility)
int getDirectionalVisibility (int posX, int posY, int posZ, int dirX, int dirY, int dirZ)
void setAtomID (int posX, int posY, int posZ, Atom *atom)
Atom * getAtomID (int posX, int posY, int posZ)
Amino_Acid * getResidueID (int posX, int posY, int posZ)
void setGID (int posX, int posY, int posZ, int id)
int getGID (int posX, int posY, int posZ)
void setCtr (int posX, int posY, int posZ, int cnt)
int getCtr (int posX, int posY, int posZ)
void initialize ()
void setType (bool t)
bool getType ()

Public Attributes

float grid_span

Private Attributes

Voxel voxelSrs [VOXELSERIES_X_MAX][VOXELSERIES_Y_MAX][VOXELSERIES_Z_MAX]
int boundX
int boundY
int boundZ
bool type

Constructor & Destructor Documentation

VoxelSeries::VoxelSeries (  int  sizeX,
int  sizeY,
int  sizeZ
) 
 

Definition at line 11 of file VoxelSeries.cpp.

References boundX, boundY, boundZ, initialize(), RECEPTOR, and type.

00011                                                         {
00012         boundX = sizeX;
00013         boundY = sizeY;
00014         boundZ = sizeZ;
00015         type = RECEPTOR;
00016         initialize();
00017 }

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Member Function Documentation

Atom * VoxelSeries::getAtomID (  int  posX,
int  posY,
int  posZ
) 
 

Definition at line 105 of file VoxelSeries.cpp.

References Voxel::getAtomID(), and voxelSrs.

Referenced by Filter::createAtomSiteFile(), Filter::createMSSiteFile(), and discretise_structure().

00105                                                           {
00106         return voxelSrs[posX][posY][posZ].getAtomID();
00107 }

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int VoxelSeries::getBlockedDirectionSize (  int  x,
int  y,
int  z
) 
 

Definition at line 81 of file VoxelSeries.cpp.

References Voxel::getBlockedDirectionSize(), and voxelSrs.

00081                                                             {
00082         return voxelSrs[x][y][z].getBlockedDirectionSize();
00083 }

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int VoxelSeries::getBoundX (   ) 
 

Definition at line 35 of file VoxelSeries.cpp.

References boundX.

Referenced by Mask::checkVoxelVisibility(), createFile(), Filter::getNeighbours(), Filter::groupInternalCavity(), identify_surface_voxels(), Filter::identifyActiveSite(), invertVoxels(), Filter::marchNeighbours(), readFile(), and Filter::setRelatedNeighbouringVoxels().

00035                            {
00036         return boundX;
00037 }

int VoxelSeries::getBoundY (   ) 
 

Definition at line 39 of file VoxelSeries.cpp.

References boundY.

Referenced by Mask::checkVoxelVisibility(), createFile(), Filter::getNeighbours(), Filter::marchNeighbours(), and readFile().

00039                            {
00040         return boundY;
00041 }

int VoxelSeries::getBoundZ (   ) 
 

Definition at line 43 of file VoxelSeries.cpp.

References boundZ.

Referenced by Mask::checkVoxelVisibility(), createFile(), Filter::getNeighbours(), Filter::marchNeighbours(), and readFile().

00043                            {
00044         return boundZ;
00045 }

int VoxelSeries::getCtr (  int  posX,
int  posY,
int  posZ
) 
 

int VoxelSeries::getDirectionalVisibility (  int  posX,
int  posY,
int  posZ,
int  dirX,
int  dirY,
int  dirZ
) 
 

Definition at line 89 of file VoxelSeries.cpp.

References Voxel::getDirectionalVisibility(), and voxelSrs.

00089                                                                                                     {
00090         return voxelSrs[posX][posY][posZ].getDirectionalVisibility(dirX, dirY, dirZ);
00091 }

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int VoxelSeries::getGID (  int  posX,
int  posY,
int  posZ
) 
 

Definition at line 97 of file VoxelSeries.cpp.

References Voxel::getGID(), and voxelSrs.

Referenced by Filter::convertOtherGroups(), Filter::createAtomSiteFile(), createFile(), Filter::createMSSiteFile(), Filter::createResidueSiteFile(), Filter::groupInternalCavity(), Filter::identifyActiveSite(), Filter::marchNeighbours(), Filter::resetGIDs(), and Filter::setRelatedNeighbouringVoxels().

00097                                                     {
00098         return voxelSrs[posX][posY][posZ].getGID();
00099 }

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Amino_Acid * VoxelSeries::getResidueID (  int  posX,
int  posY,
int  posZ
) 
 

Definition at line 109 of file VoxelSeries.cpp.

References Voxel::getResidueID(), and voxelSrs.

Referenced by Filter::createResidueSiteFile(), and Filter::setRelatedNeighbouringVoxels().

00109                                                                    {
00110         return voxelSrs[posX][posY][posZ].getResidueID();
00111 }

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bool VoxelSeries::getType (   ) 
 

Definition at line 130 of file VoxelSeries.cpp.

References type.

Referenced by main().

00130                           {
00131         return type;
00132 }

Voxel VoxelSeries::getVoxel (  int  x,
int  y,
int  z
) 
 

Definition at line 23 of file VoxelSeries.cpp.

References voxelSrs.

00023                                                {
00024         return voxelSrs[x][y][z];
00025 }

void VoxelSeries::initialize (   ) 
 

Definition at line 113 of file VoxelSeries.cpp.

References boundX, CAVITY_VACANT, EXTERNAL_CAVITY, Voxel::setFilled(), Voxel::setInternalCavity(), and voxelSrs.

Referenced by VoxelSeries().

00113                              {
00114         // initialize voxel series internal properties
00115 
00116         for ( int k = 0; k<boundX; k++ ) {              
00117                 for ( int j = 0; j<boundX; j++ ) {              
00118                         for ( int i = 0; i<boundX; i++ ) {
00119                                 voxelSrs[i][j][k].setFilled(CAVITY_VACANT);
00120                                 voxelSrs[i][j][k].setInternalCavity(EXTERNAL_CAVITY);
00121                         }
00122                 }
00123         }
00124 }

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bool VoxelSeries::isActiveSite (  int  x,
int  y,
int  z
) 
 

Definition at line 68 of file VoxelSeries.cpp.

References Voxel::isActiveSite(), and voxelSrs.

Referenced by createFile(), Filter::identifyActiveSite(), and Filter::setRelatedNeighbouringVoxels().

00068                                                   {
00069         return voxelSrs[x][y][z].isActiveSite();
00070 }

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bool VoxelSeries::isCoreVoxel (  int  x,
int  y,
int  z
) 
 

Definition at line 73 of file VoxelSeries.cpp.

References Voxel::isFilled(), Voxel::isSurfaceVoxel(), and voxelSrs.

00073                                                  {
00074         return !voxelSrs[x][y][z].isSurfaceVoxel() && voxelSrs[x][y][z].isFilled();
00075 }

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bool VoxelSeries::isInternalCavity (  int  x,
int  y,
int  z
) 
 

Definition at line 52 of file VoxelSeries.cpp.

References Voxel::isInternalCavity(), and voxelSrs.

Referenced by createFile(), Filter::groupInternalCavity(), and Filter::marchNeighbours().

00052                                                       {
00053         return voxelSrs[x][y][z].isInternalCavity();
00054 }

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bool VoxelSeries::isSurfaceVoxel (  int  x,
int  y,
int  z
) 
 

Definition at line 60 of file VoxelSeries.cpp.

References Voxel::isSurfaceVoxel(), and voxelSrs.

Referenced by createFile(), invertVoxels(), and Filter::setRelatedNeighbouringVoxels().

00060                                                     {
00061         return voxelSrs[x][y][z].isSurfaceVoxel();
00062 }

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bool VoxelSeries::isVoxelFilled (  int  x,
int  y,
int  z
) 
 

Definition at line 31 of file VoxelSeries.cpp.

References Voxel::isFilled(), and voxelSrs.

Referenced by Mask::checkVoxelVisibility(), createFile(), identify_surface_voxels(), Filter::identifyActiveSite(), invertVoxels(), Filter::setInternalCavity(), and surface_grid().

00031                                                    {
00032         return voxelSrs[x][y][z].isFilled();
00033 }

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void VoxelSeries::setActiveSite (  int  x,
int  y,
int  z,
bool  activesite
) 
 

Definition at line 64 of file VoxelSeries.cpp.

References Voxel::setActiveSite(), and voxelSrs.

Referenced by Filter::identifyActiveSite(), Filter::resetGIDs(), and Filter::setRelatedNeighbouringVoxels().

00064                                                                     {
00065         voxelSrs[x][y][z].setActiveSite(activesite);
00066 }

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void VoxelSeries::setAtomID (  int  posX,
int  posY,
int  posZ,
Atom *  atom
) 
 

Definition at line 101 of file VoxelSeries.cpp.

References Voxel::setAtomID(), and voxelSrs.

Referenced by discretise_structure().

00101                                                                      {
00102         voxelSrs[posX][posY][posZ].setAtomID(atom);
00103 }

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void VoxelSeries::setBlockedDirectionSize (  int  x,
int  y,
int  z,
int  blockNumber
) 
 

Definition at line 77 of file VoxelSeries.cpp.

References Voxel::setBlockedDirectionSize(), and voxelSrs.

00077                                                                               {
00078         voxelSrs[x][y][z].setBlockedDirectionSize(blockNumber);
00079 }

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void VoxelSeries::setCtr (  int  posX,
int  posY,
int  posZ,
int  cnt
) 
 

void VoxelSeries::setDirectionalVisibility (  int  posX,
int  posY,
int  posZ,
int  dirX,
int  dirY,
int  dirZ,
int  visibility
) 
 

Definition at line 85 of file VoxelSeries.cpp.

References Voxel::setDirectionalVisibility(), and voxelSrs.

Referenced by Mask::checkVoxelVisibility().

00085                                                                                                                      {
00086         voxelSrs[posX][posY][posZ].setDirectionalVisibility(dirX, dirY, dirZ, visibility);
00087 }

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void VoxelSeries::setGID (  int  posX,
int  posY,
int  posZ,
int  id
) 
 

Definition at line 93 of file VoxelSeries.cpp.

References Voxel::setGID(), and voxelSrs.

Referenced by Filter::convertOtherGroups(), Filter::groupInternalCavity(), Filter::identifyActiveSite(), Filter::marchNeighbours(), Filter::resetGIDs(), and Filter::setRelatedNeighbouringVoxels().

00093                                                              {
00094         voxelSrs[posX][posY][posZ].setGID(id);
00095 }

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void VoxelSeries::setInternalCavity (  int  x,
int  y,
int  z,
bool  internalCv
) 
 

Definition at line 48 of file VoxelSeries.cpp.

References Voxel::setInternalCavity(), and voxelSrs.

Referenced by Filter::convertOtherGroups(), Filter::setInternalCavity(), and Mask::testInternalCavityEligibility().

00048                                                                         {
00049         voxelSrs[x][y][z].setInternalCavity(internalCv);
00050 }

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void VoxelSeries::setSurfaceVoxel (  int  x,
int  y,
int  z,
bool  surface
) 
 

Definition at line 56 of file VoxelSeries.cpp.

References Voxel::setSurfaceVoxel(), and voxelSrs.

Referenced by identify_surface_voxels(), and surface_grid().

00056                                                                    {
00057         voxelSrs[x][y][z].setSurfaceVoxel(surface);
00058 }

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void VoxelSeries::setType (  bool  t  ) 
 

Definition at line 126 of file VoxelSeries.cpp.

References type.

Referenced by voxelize_protein().

00126                                 {
00127         type = t;
00128 }

void VoxelSeries::setVoxel (  int  x,
int  y,
int  z,
bool  fill
) 
 

Definition at line 19 of file VoxelSeries.cpp.

References Voxel::setFilled(), and voxelSrs.

00019                                                          {
00020         voxelSrs[x][y][z].setFilled(fill);
00021 }

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void VoxelSeries::setVoxelFilled (  int  x,
int  y,
int  z,
bool  fill
) 
 

Definition at line 27 of file VoxelSeries.cpp.

References Voxel::setFilled(), and voxelSrs.

Referenced by Filter::convertOtherGroups(), discretise_structure(), invertVoxels(), and readFile().

00027                                                                {
00028         voxelSrs[x][y][z].setFilled(fill);
00029 }

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Member Data Documentation

int VoxelSeries::boundX [private]
 

Definition at line 44 of file VoxelSeries.h.

Referenced by getBoundX(), initialize(), and VoxelSeries().

int VoxelSeries::boundY [private]
 

Definition at line 45 of file VoxelSeries.h.

Referenced by getBoundY(), and VoxelSeries().

int VoxelSeries::boundZ [private]
 

Definition at line 46 of file VoxelSeries.h.

Referenced by getBoundZ(), and VoxelSeries().

float VoxelSeries::grid_span
 

Definition at line 11 of file VoxelSeries.h.

Referenced by Filter::getNeighbours(), and voxelize_protein().

bool VoxelSeries::type [private]
 

Definition at line 47 of file VoxelSeries.h.

Referenced by getType(), setType(), and VoxelSeries().

Voxel VoxelSeries::voxelSrs[VOXELSERIES_X_MAX][VOXELSERIES_Y_MAX][VOXELSERIES_Z_MAX] [private]
 

Definition at line 43 of file VoxelSeries.h.

Referenced by getAtomID(), getBlockedDirectionSize(), getDirectionalVisibility(), getGID(), getResidueID(), getVoxel(), initialize(), isActiveSite(), isCoreVoxel(), isInternalCavity(), isSurfaceVoxel(), isVoxelFilled(), setActiveSite(), setAtomID(), setBlockedDirectionSize(), setDirectionalVisibility(), setGID(), setInternalCavity(), setSurfaceVoxel(), setVoxel(), and setVoxelFilled().

The documentation for this class was generated from the following files:
Generated on Fri Oct 21 00:21:54 2005 for Cavity by  doxygen 1.4.4