#include <UHBDgrd.hpp>

Collaboration diagram for UHBD< T1 >:

Classes
struct	dimensions
struct	origin
	dimensions of the grid (number of grid points) More...

Public Member Functions
	UHBD (char , char , bool, float)
	UHBD constructor - 2.
	UHBD (char *, float, bool, float)
	UHBD constructor - 1.
	UHBD (char *)
	UHBD constructor - 3.
	~UHBD ()
	UHBD destructor.
void	Generate_Skin (float, int)
	Calculate the molecule skin (molecular interaction field).
void	print_slice_grid (int)
	Print a 2D slice of an excluded volume grid.

Public Attributes
std::ifstream	file
float	scale
int	grdflag
	scaling for every value
int	one
	flag for the type of grid: UHBD, DT-Grid, etc.
float	spacing
char *	Title
	grid spacing/resolution
float	dummy1
	Text header kept in the UHBD file.
float	dummy2
float	dummy3
float	dummy4
float	dummy5
float	dummy6
float	dummy7
int	idummy1
int	idummy2
int	idummy3
int	idummy4
int	idummy5
struct UHBD::dimensions	dim
struct UHBD::origin	o
T1 ***	Grid
	grid origin coordinates
bool ***	Skin
	Store the grid data in a 3d array.
float	probes
	Boolean for Skin! expanded for other types, though.

Private Member Functions
void	write_uhbd_grid ()
	Exclusion : 1, Non-exclusion : 0.
void	Test_Format_Grid (char *)
	Determine the type of grid: binary or ascii?
void	Read_Header (char *)
	Read the header of an input UHBD file.
void	Read_Data ()
	Read the body of the input UHBD file.
int	excluded_volume (bool ***, double, double, double, double)
	Calculate the excluded volume.
void	make_exclusion_grid ()
	construct the excluded volume grid
template<typename type>
type ***	Allocate ()
	create a 3d array and allocate memory for it.
template<typename type>
void	Deallocate (type ***)
	deallocate the memory for a 3D array
template<typename type>
void	Initialize (type ***)
	initialize values of a given 3D array to zero

Private Attributes
PDB *	structure
	probe size
int	iform
	structure object for the input molecule
int	exclusion_flag
	Binary : 0, ASCII : 1.

Constructor & Destructor Documentation

◆ UHBD() [1/3]

template<typename T1>

UHBD< T1 >::UHBD	(	char *	pdbfilename,
		char *	Input,
		bool	pqr_fl,
		float	probe_size )

UHBD constructor - 2.

Parameters

pdbfilename	name of the input pdb(or pqr) file
Input	UHBD file name.
pqr_fl	flag for pqr file (otherwise pdb)
probe_size	size of the probe for molecular surface

Note: Overloaded constructor! For UHBD object with an input UHBD file.

Warning: gcc/4.9.2 error. it seems to be not allowed to assign a default value anymore.

: UHBD<T1>::UHBD(char * pdbfilename, char * Input, bool pqr_fl, float probe_size = 1.7)

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◆ UHBD() [2/3]

template<typename T1>

UHBD< T1 >::UHBD	(	char *	pdbfilename,
		float	probe_size,
		bool	pqr_fl,
		float	spcng )

UHBD constructor - 1.

Parameters

pdbfilename	name of the input pdb(or pqr) file
probe_size	size of the probe for molecular surface
pqr_fl	flag for pqr file (otherwise pdb)
spcng	spacing for the constructed grid

Note: Overloaded constructor! For UHBD object without an input UHBD file.

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◆ UHBD() [3/3]

template<typename T1>

UHBD< T1 >::UHBD ( char * Input )

UHBD constructor - 3.

Parameters

Input UHBD file name.

Note: Overloaded constructor! When no molecule needs to be associated with the data grid.

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◆ ~UHBD()

template<typename T1>

UHBD< T1 >::~UHBD ( )

UHBD destructor.

Member Function Documentation

◆ Allocate()

template<typename T1>

template<typename type>

type *** UHBD< T1 >::Allocate ( )

private

create a 3d array and allocate memory for it.

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◆ Deallocate()

template<typename T1>

template<typename type>

void UHBD< T1 >::Deallocate ( type *** grd )

private

deallocate the memory for a 3D array

Parameters

grd	pointer for the 3D array to be deallocated

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◆ excluded_volume()

template<typename T1>

int UHBD< T1 >::excluded_volume	(	bool ***	IEV,
		double	oex,
		double	oey,
		double	oez,
		double	probep )

private

Calculate the excluded volume.

called from function make_exclusion_grid, this function calculates the grid points overlap with the actual excluded volume and store it in a 3d array.

Note: this function should be similar to that in the SDA7 and PIPSA codes!

Parameters

IEV	array that the excluded volume data is stored
oex	origin coordinate x
oey	origin coordinate y
oez	origin coordinate z
probep	probe size

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◆ Generate_Skin()

template<typename T1>

void UHBD< T1 >::Generate_Skin	(	float	skin,
		int	iterate_inside_skin )

Calculate the molecule skin (molecular interaction field).

Parameters

skin	'thickness' of the skin zone
iterate_inside_skin	grid points to be included towards the interior of the molecule. This is to avoid any missing points at the boundary. default is 5, can be changed, though.

Note: gcc/4.9.2 error when: void UHBD<T1>::Generate_Skin(float skin, int iterate_inside_skin = 5); this function should be similar to that in the PIPSA code!

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◆ Initialize()

template<typename T1>

template<typename type>

void UHBD< T1 >::Initialize ( type *** grd )

private

initialize values of a given 3D array to zero

Parameters

grd	pointer for the 3D array.

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◆ make_exclusion_grid()

template<typename T1>

void UHBD< T1 >::make_exclusion_grid ( )

private

construct the excluded volume grid

This function constructs and stores the excluded volume grid.

Note: this function should be similar to that in the SDA7 and PIPSA codes!

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◆ print_slice_grid()

template<typename T1>

void UHBD< T1 >::print_slice_grid ( int k )

Print a 2D slice of an excluded volume grid.

This function is used to check the shape of the volume for a slice given by the input index z. Excluded volume points are shown with '*' sign.

Parameters

k	index z for the xy plane to be written to a txt file.

◆ Read_Data()

template<typename T1>

void UHBD< T1 >::Read_Data ( )

private

Read the body of the input UHBD file.

This function reads the body of the UHBD file where actual grid data is stored.

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◆ Read_Header()

template<typename T1>

void UHBD< T1 >::Read_Header ( char * Input )

private

Read the header of an input UHBD file.

This function reads the header of the UHBD file and extract grid parameters from it.

Parameters

Input name of the grid file

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◆ Test_Format_Grid()

template<typename T1>

void UHBD< T1 >::Test_Format_Grid ( char * Input )

private

Determine the type of grid: binary or ascii?

Parameters

Input name of the grid file

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◆ write_uhbd_grid()

template<typename T1>

void UHBD< T1 >::write_uhbd_grid ( )

private

Exclusion : 1, Non-exclusion : 0.

Write the excluded volume grid to a file.

This function writes the excluded volume grid into UHBD format file.

Note: To be able to visualize the excluded volume grid with a UHBD file format. Only binary format at the moment!

Member Data Documentation

◆ dim

template<typename T1>

struct UHBD::dimensions UHBD< T1 >::dim

◆ dummy1

template<typename T1>

float UHBD< T1 >::dummy1

Text header kept in the UHBD file.

Default dummy variables in UHBD file- start

◆ dummy2

template<typename T1>

float UHBD< T1 >::dummy2

◆ dummy3

template<typename T1>

float UHBD< T1 >::dummy3

◆ dummy4

template<typename T1>

float UHBD< T1 >::dummy4

◆ dummy5

template<typename T1>

float UHBD< T1 >::dummy5

◆ dummy6

template<typename T1>

float UHBD< T1 >::dummy6

◆ dummy7

template<typename T1>

float UHBD< T1 >::dummy7

◆ exclusion_flag

template<typename T1>

int UHBD< T1 >::exclusion_flag

private

Binary : 0, ASCII : 1.

◆ file

template<typename T1>

std::ifstream UHBD< T1 >::file

◆ grdflag

template<typename T1>

int UHBD< T1 >::grdflag

scaling for every value

◆ Grid

template<typename T1>

T1*** UHBD< T1 >::Grid

grid origin coordinates

◆ idummy1

template<typename T1>

int UHBD< T1 >::idummy1

◆ idummy2

template<typename T1>

int UHBD< T1 >::idummy2

◆ idummy3

template<typename T1>

int UHBD< T1 >::idummy3

◆ idummy4

template<typename T1>

int UHBD< T1 >::idummy4

◆ idummy5

template<typename T1>

int UHBD< T1 >::idummy5

◆ iform

template<typename T1>

int UHBD< T1 >::iform

private

structure object for the input molecule

◆ o

template<typename T1>

struct UHBD::origin UHBD< T1 >::o

◆ one

template<typename T1>

int UHBD< T1 >::one

flag for the type of grid: UHBD, DT-Grid, etc.

◆ probes

template<typename T1>

float UHBD< T1 >::probes

Boolean for Skin! expanded for other types, though.

◆ scale

template<typename T1>

float UHBD< T1 >::scale

◆ Skin

template<typename T1>

bool*** UHBD< T1 >::Skin

Store the grid data in a 3d array.

◆ spacing

template<typename T1>

float UHBD< T1 >::spacing

◆ structure

template<typename T1>

PDB* UHBD< T1 >::structure

private

probe size

◆ Title

template<typename T1>

char* UHBD< T1 >::Title

grid spacing/resolution

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

tools/DT-Grid/tools/UHBDgrd.hpp

Classes

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ UHBD() [1/3]

◆ UHBD() [2/3]

◆ UHBD() [3/3]

◆ ~UHBD()

Member Function Documentation

◆ Allocate()

◆ Deallocate()

◆ excluded_volume()

◆ Generate_Skin()

◆ Initialize()

◆ make_exclusion_grid()

◆ print_slice_grid()

◆ Read_Data()

◆ Read_Header()

◆ Test_Format_Grid()

◆ write_uhbd_grid()

Member Data Documentation

◆ dim

◆ dummy1

◆ dummy2

◆ dummy3

◆ dummy4

◆ dummy5

◆ dummy6

◆ dummy7

◆ exclusion_flag

◆ file

◆ grdflag

◆ Grid

◆ idummy1

◆ idummy2

◆ idummy3

◆ idummy4

◆ idummy5

◆ iform

◆ o

◆ one

◆ probes

◆ scale

◆ Skin

◆ spacing

◆ structure

◆ Title