#include <UHBDgrd.hpp>
◆ UHBD() [1/3]
template<typename T1 >
UHBD< T1 >::UHBD |
( |
char * |
pdbfilename, |
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char * |
Input, |
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bool |
pqr_fl, |
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float |
probe_size |
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) |
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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)
◆ UHBD() [2/3]
template<typename T1 >
UHBD< T1 >::UHBD |
( |
char * |
pdbfilename, |
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|
float |
probe_size, |
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bool |
pqr_fl, |
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float |
spcng |
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) |
| |
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.
◆ UHBD() [3/3]
UHBD constructor - 3.
- Parameters
-
- Note
- Overloaded constructor! When no molecule needs to be associated with the data grid.
◆ ~UHBD()
◆ Allocate()
template<typename T1 >
template<typename type >
type *** UHBD< T1 >::Allocate |
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private |
create a 3d array and allocate memory for it.
◆ Deallocate()
template<typename T1 >
template<typename type >
void UHBD< T1 >::Deallocate |
( |
type *** |
grd | ) |
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private |
deallocate the memory for a 3D array
- Parameters
-
grd | pointer for the 3D array to be deallocated |
◆ excluded_volume()
template<typename T1 >
int UHBD< T1 >::excluded_volume |
( |
bool *** |
IEV, |
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double |
oex, |
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double |
oey, |
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double |
oez, |
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double |
probep |
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) |
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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 |
◆ Generate_Skin()
template<typename T1 >
void UHBD< T1 >::Generate_Skin |
( |
float |
skin, |
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int |
iterate_inside_skin |
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) |
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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!
◆ Initialize()
template<typename T1 >
template<typename type >
void UHBD< T1 >::Initialize |
( |
type *** |
grd | ) |
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private |
initialize values of a given 3D array to zero
- Parameters
-
grd | pointer for the 3D array. |
◆ make_exclusion_grid()
template<typename T1 >
void UHBD< T1 >::make_exclusion_grid |
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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!
◆ print_slice_grid()
template<typename T1 >
void UHBD< T1 >::print_slice_grid |
( |
int |
k | ) |
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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
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k | index z for the xy plane to be written to a txt file. |
◆ Read_Data()
template<typename T1 >
void UHBD< T1 >::Read_Data |
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private |
Read the body of the input UHBD file.
This function reads the body of the UHBD file where actual grid data is stored.
◆ Read_Header()
template<typename T1 >
void UHBD< T1 >::Read_Header |
( |
char * |
Input | ) |
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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 |
◆ Test_Format_Grid()
template<typename T1 >
void UHBD< T1 >::Test_Format_Grid |
( |
char * |
Input | ) |
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private |
Determine the type of grid: binary or ascii?
- Parameters
-
Input | name of the grid file |
◆ write_uhbd_grid()
template<typename T1 >
void UHBD< T1 >::write_uhbd_grid |
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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!
◆ dim
◆ dummy1
Text header kept in the UHBD file.
Default dummy variables in UHBD file- start
◆ dummy2
◆ dummy3
◆ dummy4
◆ dummy5
◆ dummy6
◆ dummy7
◆ exclusion_flag
template<typename T1 >
int UHBD< T1 >::exclusion_flag |
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private |
◆ file
template<typename T1 >
std::ifstream UHBD< T1 >::file |
◆ grdflag
◆ Grid
◆ idummy1
◆ idummy2
◆ idummy3
◆ idummy4
◆ idummy5
◆ iform
structure object for the input molecule
◆ one
flag for the type of grid: UHBD, DT-Grid, etc.
◆ probes
Boolean for Skin! expanded for other types, though.
◆ scale
◆ Skin
Store the grid data in a 3d array.
◆ spacing
template<typename T1 >
float UHBD< T1 >::spacing |
◆ structure
◆ Title
The documentation for this class was generated from the following file: