#include <DTgrd.hpp>

Collaboration diagram for DT_FILE< T1 >:

Public Member Functions
	DT_FILE (int)
	DT_FILE constructor - 1. More...

	DT_FILE (int, bool)
	DT_FILE constructor - 2. More...

	DT_FILE (int, int, int, int)
	DT_FILE constructor - 3. More...

	~DT_FILE ()

void	UHBD_upload (char , char , float, float)
	Create a UHBD object using the uhbd-file input. More...

void	exclusion (char *, float, float)
	Create a UHBD object for excluded volume type interactions. More...

void	exclusion (char *)
	Create a UHBD object for excluded volume type interactions. More...

int	Generate_DTGrid (bool *, T1 *)
	Generate the DT-Grid structure! More...

int	print_layer (bool ***, int, int)
	Print a 2D slice for an exterior grid. More...

int	write_dtgrdfile_ascii (FILE *)
	Write the DT-Grid structure into the DT-Grid file in ASCII format. More...

int	write_dtgrdfile_binary (FILE *)
	Write the DT-Grid structure into the DT-Grid file in binary format. More...

int	write_dtgrdfile_ascii_nouhbd (FILE *)
	Write dt-grid file for test cases. More...

int	write_dtgrdfile_binary_nouhbd (FILE *)
	Write dt-grid file for test cases. More...

Private Member Functions
int	check_neighbours (bool *, bool *, int, int, int)
	projection array to bridge 2D and 3D DT-Grids More...

bool ***	exterior_grid (bool ***)
	Create the exterior grid. More...

int	write_dtgrdfilebody_ascii (FILE *)
	Write the DT-Grid body into the DT-Grid file in ASCII format. More...

int	write_dtgrdfilebody_binary (FILE *)
	Write the DT-Grid body into the DT-Grid file in Binary format. More...

Private Attributes
int	grid_type_flag

bool	pqr_flag
	0 for excluded volume, 1 for data grid More...

int	LengthX
	input pqr or pdb? More...

int	LengthY
	number of points along x axis (in uhbd grid) More...

int	LengthZ
	number of points along y axis (in uhbd grid) More...

UHBD< T1 > *	uhbd
	number of points along z axis (in uhbd grid) More...

int	uhbd_alloc
	a uhbd object for the input UHBD file More...

std::vector< T1 >	Value

std::vector< int >	xcoord
	'value' array of the DT-Grid More...

std::vector< int >	ycoord
	icoord array (min and max indices of connected components in x direction) More...

std::vector< int >	zcoord
	icoord array (min and max indices of connected components in y direction) More...

std::vector< int >	acc
	icoord array (min and max indices of connected components in z direction) More...

std::vector< int >	acc2D
	acc pointer array for one dimensional DT-Grid More...

std::vector< int >	acc3D
	acc pointer array for two dimensional DT-Grid More...

std::vector< int >	proj1D
	acc pointer array for three dimensional DT-Grid More...

std::vector< int >	proj2D
	projection array to bridge 1D and 2D DT-Grids More...

Detailed Description

template<typename T1>
class DT_FILE< T1 >

the parameters and data for a DT-Grid file.

Author: Musa Ozboyaci

Copyright: Heidelberg Institute for Theoretical Studies (HITS) 2016

Constructor & Destructor Documentation

◆ DT_FILE() [1/3]

template<typename T1 >

DT_FILE< T1 >::DT_FILE ( int flag )

DT_FILE constructor - 1.

Parameters

flag	input parameter for grid type: excluded, data, etc.

Note: Overloaded constructor!

◆ DT_FILE() [2/3]

template<typename T1 >

DT_FILE< T1 >::DT_FILE	(	int	flag,
		bool	pqr_fl
	)

DT_FILE constructor - 2.

Parameters

flag	input parameter for grid type: excluded, data, etc.
pqr_fl	flag for pqr file. when pqr file required (or considered?)

Note: Overloaded constructor!

◆ DT_FILE() [3/3]

template<typename T1 >

DT_FILE< T1 >::DT_FILE	(	int	flag,
		int	i,
		int	j,
		int	k
	)

DT_FILE constructor - 3.

Parameters

flag	input parameter for grid type: excluded, data, etc.
i	number of points along x axis
j	number of points along y axis
k	number of points along z axis

Note: Overloaded constructor!

◆ ~DT_FILE()

template<typename T1 >

DT_FILE< T1 >::~DT_FILE ( )

Member Function Documentation

◆ check_neighbours()

template<typename T1 >

int DT_FILE< T1 >::check_neighbours	(	bool ***	Exterior,
		bool ***	Skin_Grid,
		int	x,
		int	y,
		int	z
	)

private

projection array to bridge 2D and 3D DT-Grids

Iterate over adjacent grid points for connectivity information.

This function is used by exterior_grid to check whether the neighbors of a grid point is also lie in exterior or not!

Parameters

Exterior	the 3d array that stores the exterior grid.
Skin_Grid	the 3D array that stores the skin grid.
x	grid coordinate x
y	grid coordinate y
z	grid coordinate z

See also: exterior_grid

◆ exclusion() [1/2]

template<typename T1 >

void DT_FILE< T1 >::exclusion ( char * UHBDFILE )

Create a UHBD object for excluded volume type interactions.

This function creates a UHBD object with a uhbd-file. Similar to UHBD_upload, this is then combined with the molecular interaction grid to generate the DT-Grid data structure.

Parameters

UHBDFILE uhbd-file name

Note: overloaded function!

◆ exclusion() [2/2]

template<typename T1 >

void DT_FILE< T1 >::exclusion	(	char *	PDBFILE,
		float	probe_size,
		float	spacing
	)

Create a UHBD object for excluded volume type interactions.

This function creates a UHBD object without a uhbd-file. Similar to UHBD_upload, this is then combined with the molecular interaction grid to generate the DT-Grid data structure.

Parameters

PDBFILE	pdb-file name
probe_size	size of the molecular surface probe
spacing	the resolution for the excluded volume desired by the user.

Note: overloaded function!

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◆ exterior_grid()

template<typename T1 >

bool *** DT_FILE< T1 >::exterior_grid ( bool *** Skin_Grid )

private

Create the exterior grid.

The exterior_grid can be used to determine the points that lie outside the molecular surface and do not have direct grid point neighbors to those that are isolated inside the excluded volumes. Therefore, reducing the complexity and size of the data to be stored.

The function starts checking the outermost grid points (points on grid walls) and their direct neighbors until surface of the molecule is reached. The negative of this grid will represent an excluded volume structure with unaccessible cavities buried inside the structure included in the excluded volume definition.

Note: Not tested, completely! Please use with caution!

Parameters

Skin_Grid the 3D array that stores the skin grid.

◆ Generate_DTGrid()

template<typename T1 >

int DT_FILE< T1 >::Generate_DTGrid	(	bool ***	Skin_Grid,
		T1 ***	UHBD_Grid
	)

Generate the DT-Grid structure!

This is the main function that computes the individual data components and generates the DT-Grid structure The values to be stored at arrays: Value, xcoord, ycoord, zcoord, acc, acc2D, acc3D, proj1D, proj2D are computed here and then stored within.

Parameters

Skin_Grid	to define the molecular interaction field
UHBD_Grid	to extract the data that lie at the molecular interaction field.

◆ print_layer()

template<typename T1 >

int DT_FILE< T1 >::print_layer	(	bool ***	Exterior,
		int	dimension,
		int	layer
	)

Print a 2D slice for an exterior grid.

Similar to UHBD::print_slice_grid, this function is used to print the shape of the volume for a slice given by the input index for x, y and z dimensions. Exterior volume points are shown with 'X' sign.

Parameters

Exterior	exterior grid
dimension	for an XY plane=0, for a YZ plane=1 and for an XZ plane=2
layer	index of the plane

◆ UHBD_upload()

template<typename T1 >

void DT_FILE< T1 >::UHBD_upload	(	char *	PDBFILE,
		char *	UHBDFILE,
		float	probe_size,
		float	skin_size
	)

Create a UHBD object using the uhbd-file input.

This function uploads the uhbd grid file and creates a UHBD object from that. This is then combined with the molecular interaction grid to generate the DT-Grid data structure.

Parameters

PDBFILE	pdb-file name
UHBDFILE	uhbd-file name
probe_size	size of the molecular surface probe
skin_size	thickness of the molecule skin that defines the molecular interaction field.

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◆ write_dtgrdfile_ascii()

template<typename T1 >

int DT_FILE< T1 >::write_dtgrdfile_ascii ( FILE * output_file )

Write the DT-Grid structure into the DT-Grid file in ASCII format.

This function writes the header of the DT-Grid file and calls write_dtgrdfilebody_ascii to write the body of the grid data.

Parameters

output_file name of the output dt-grid file

Warning: The header must be the same both in DT-Grid and uhbd files

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◆ write_dtgrdfile_ascii_nouhbd()

template<typename T1 >

int DT_FILE< T1 >::write_dtgrdfile_ascii_nouhbd ( FILE * output_file )

Write dt-grid file for test cases.

This function writes the header of a DT-Grid file without requiring a uhbd-file and used only for testing purposes!

Parameters

output_file name of the output dt-grid file

◆ write_dtgrdfile_binary()

template<typename T1 >

int DT_FILE< T1 >::write_dtgrdfile_binary ( FILE * output_file )

Write the DT-Grid structure into the DT-Grid file in binary format.

This function writes the header of the DT-Grid file and calls write_dtgrdfilebody_binary to write the body of the grid data.

Parameters

output_file name of the output dt-grid file

Warning: The header must be the same both in DT-Grid and uhbd files

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◆ write_dtgrdfile_binary_nouhbd()

template<typename T1 >

int DT_FILE< T1 >::write_dtgrdfile_binary_nouhbd ( FILE * output_file )

Write dt-grid file for test cases.

Similar to write_dtgrdfile_ascii_nouhbd. Used only for testing purposes!

Parameters

output_file name of the output dt-grid file

See also: write_dtgrdfile_ascii_nouhbd

◆ write_dtgrdfilebody_ascii()

template<typename T1 >

int DT_FILE< T1 >::write_dtgrdfilebody_ascii ( FILE * output_file )

private

Write the DT-Grid body into the DT-Grid file in ASCII format.

This function writes the DT-Grid body including the header information specific to DT-Grid into the file.

Parameters

output_file name of the output dt-grid file

◆ write_dtgrdfilebody_binary()

template<typename T1 >

int DT_FILE< T1 >::write_dtgrdfilebody_binary ( FILE * output_file )

private

Write the DT-Grid body into the DT-Grid file in Binary format.

This function writes the DT-Grid body including the header information specific to DT-Grid into the file.

Parameters

output_file name of the output dt-grid file

Member Data Documentation

◆ acc

template<typename T1 >

std::vector<int> DT_FILE< T1 >::acc

private

icoord array (min and max indices of connected components in z direction)

◆ acc2D

template<typename T1 >

std::vector<int> DT_FILE< T1 >::acc2D

private

acc pointer array for one dimensional DT-Grid

See also: DTGrid1D

◆ acc3D

template<typename T1 >

std::vector<int> DT_FILE< T1 >::acc3D

private

acc pointer array for two dimensional DT-Grid

See also: DTGrid2D

template<typename T1 >

std::vector<int> DT_FILE< T1 >::proj1D

private

acc pointer array for three dimensional DT-Grid

See also: DTGrid3D

◆ proj2D

template<typename T1 >

std::vector<int> DT_FILE< T1 >::proj2D

private

projection array to bridge 1D and 2D DT-Grids

◆ uhbd

template<typename T1 >

UHBD<T1>* DT_FILE< T1 >::uhbd

private

number of points along z axis (in uhbd grid)

◆ uhbd_alloc

template<typename T1 >

int DT_FILE< T1 >::uhbd_alloc

private

a uhbd object for the input UHBD file

template<typename T1 >

std::vector<int> DT_FILE< T1 >::zcoord

private

icoord array (min and max indices of connected components in y direction)

The documentation for this class was generated from the following file:

tools/DT-Grid/tools/DTgrd.hpp

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

template<typename T1> class DT_FILE< T1 >

Constructor & Destructor Documentation

◆ DT_FILE() [1/3]

◆ DT_FILE() [2/3]

◆ DT_FILE() [3/3]

◆ ~DT_FILE()

Member Function Documentation

◆ check_neighbours()

◆ exclusion() [1/2]

◆ exclusion() [2/2]

◆ exterior_grid()

◆ Generate_DTGrid()

◆ print_layer()

◆ UHBD_upload()

◆ write_dtgrdfile_ascii()

◆ write_dtgrdfile_ascii_nouhbd()

◆ write_dtgrdfile_binary()

◆ write_dtgrdfile_binary_nouhbd()

◆ write_dtgrdfilebody_ascii()

◆ write_dtgrdfilebody_binary()

Member Data Documentation

◆ acc

◆ acc2D

◆ acc3D

◆ grid_type_flag

◆ LengthX

◆ LengthY

◆ LengthZ

◆ pqr_flag

◆ proj1D

◆ proj2D

◆ uhbd

◆ uhbd_alloc

◆ Value

◆ xcoord

◆ ycoord

◆ zcoord

template<typename T1>
class DT_FILE< T1 >