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VolMapCreate Class Reference

Virtual class for dealing with the computation of VolMaps, based on atomic selections and atomic data and coordinates. It provides utilities for computing such maps. Various algorithms and specific calculations are done by child classes. The end result is a VolMap object, which can be passed to VMD (N/A yet) or written to a file. More...

#include <VolMapCreate.h>

Inheritance diagram for VolMapCreate:

List of all members.

Public Types
enum	CombineType { COMBINE_AVG, COMBINE_MIN, COMBINE_MAX, COMBINE_STDEV, COMBINE_PMF }
Public Methods
	VolMapCreate (VMDApp app, AtomSel sel, float resolution)
virtual	~VolMapCreate ()
void	set_minmax (float minx, float miny, float minz, float maxx, float maxy, float maxz)
void	set_checkpoint (int checkpointfreq, char *checkpointname)
int	compute_all (bool allframes, CombineType method, void *params)
	computes volmap for all (selected) frames and takes the average, min or max depending on what was specified by "method", for most cases, params is unused (set to NULL) XXX the "allframes" param should be a FrameRange object, but for now its a boolean. More...
virtual void	write_map (const char *filename)
	For now this will call write_dx_file, but this is going to change to using molfileplugin instead. In VolMapCreate*Energy this method is overridden by one that adds temperature and weight information to the data set name string. More...
int	write_dx_file (const char *filename)
Public Attributes
VolumetricData *	volmap
Protected Methods
virtual int	compute_frame (int frame, float *voldata)=0
int	compute_init (float padding)
virtual int	compute_init ()
	called before computing individual frames. More...
int	calculate_minmax (float min_coord, float max_coord)
	calculates minmax (into preallocated float[3] arrays) using volmapcreate's selection. More...
int	calculate_max_radius (float &radius)
	calculates max_radius (into a provided float) using volmapcreate's selection. More...
void	combo_begin (CombineType method, void *customptr, void params)
	for checkpointing. More...
void	combo_addframe (CombineType method, float voldata, void customptr, float *framedata)
void	combo_export (CombineType method, float voldata, void customptr)
	Output a copy of the combination buffer, to which a final transform appropriate for the combination type has been applied to. Frames can still be appended to the original combo buffer. This procedure should be used to create the final map as well as each checkpoint map. More...
void	combo_end (CombineType method, void *customptr)
	Do some cleaning up of the combination buffer. More...
Protected Attributes
VMDApp *	app
AtomSel *	sel
float	delta
int	computed_frames
int	checkpoint_freq
char *	checkpoint_name
bool	user_minmax
float	min_coord [3]
float	max_coord [3]

Detailed Description

Definition at line 34 of file VolMapCreate.h.

Member Enumeration Documentation

enum VolMapCreate::CombineType

Enumeration values:

COMBINE_AVG

COMBINE_MIN

COMBINE_MAX

COMBINE_STDEV

COMBINE_PMF

Definition at line 36 of file VolMapCreate.h.
Referenced by vmd_volmap_new_fromtype.

Constructor & Destructor Documentation

VolMapCreate::VolMapCreate ( VMDApp * app,

AtomSel * sel,

float resolution

)

Definition at line 76 of file VolMapCreate.C.
References app, checkpoint_freq, checkpoint_name, computed_frames, delta, NULL, sel, user_minmax, and volmap.

VolMapCreate::~VolMapCreate ( ) [virtual]

Definition at line 95 of file VolMapCreate.C.
References checkpoint_name, and volmap.

Member Function Documentation

int VolMapCreate::calculate_max_radius ( float & radius ) [protected]

calculates max_radius (into a provided float) using volmapcreate's selection.

Definition at line 160 of file VolMapCreate.C.
References app, NameList< float * >::data, BaseMolecule::extraflt, AtomSel::firstsel, AtomSel::lastsel, MEASURE_ERR_NORADII, MoleculeList::mol_from_id, VMDApp::moleculeList, AtomSel::molid, AtomSel::on, and sel.
Referenced by VolMapCreateDistance::compute_frame, VolMapCreateCoulombPotentialMSM::compute_init, VolMapCreateCoulombPotential::compute_init, VolMapCreateDistance::compute_init, VolMapCreateOccupancy::compute_init, and VolMapCreateDensity::compute_init.

int VolMapCreate::calculate_minmax ( float * min_coord,

float * max_coord

) [protected]

calculates minmax (into preallocated float[3] arrays) using volmapcreate's selection.

Definition at line 124 of file VolMapCreate.C.
References app, AtomSel::change, AtomSel::coordinates, measure_minmax, MEASURE_NOERR, MoleculeList::mol_from_id, VMDApp::molecule_numframes, VMDApp::moleculeList, AtomSel::molid, NULL, AtomSel::num_atoms, AtomSel::on, sel, and AtomSel::which_frame.
Referenced by compute_init.

void VolMapCreate::combo_addframe ( CombineType method,

float * voldata,

void * customptr,

float * framedata

) [protected]

Definition at line 194 of file VolMapCreate.C.
References COMBINE_AVG, COMBINE_MAX, COMBINE_MIN, COMBINE_PMF, COMBINE_STDEV, computed_frames, MAX, MIN, n, volmap, VolumetricData::xsize, VolumetricData::ysize, and VolumetricData::zsize.
Referenced by compute_all.

void VolMapCreate::combo_begin ( CombineType method,

void ** customptr,

void * params

) [protected]

for checkpointing.

Definition at line 178 of file VolMapCreate.C.
References COMBINE_STDEV, computed_frames, VolumetricData::data, NULL, volmap, VolumetricData::xsize, VolumetricData::ysize, and VolumetricData::zsize.
Referenced by compute_all.

void VolMapCreate::combo_end ( CombineType method,

void * customptr

) [protected]

Do some cleaning up of the combination buffer.

Definition at line 278 of file VolMapCreate.C.
References COMBINE_STDEV.
Referenced by compute_all.

void VolMapCreate::combo_export ( CombineType method,

float * voldata,

void * customptr

) [protected]

Output a copy of the combination buffer, to which a final transform appropriate for the combination type has been applied to. Frames can still be appended to the original combo buffer. This procedure should be used to create the final map as well as each checkpoint map.

Definition at line 246 of file VolMapCreate.C.
References COMBINE_AVG, COMBINE_MAX, COMBINE_MIN, COMBINE_PMF, COMBINE_STDEV, computed_frames, VolumetricData::data, MAX_ENERGY, n, volmap, VolumetricData::xsize, VolumetricData::ysize, and VolumetricData::zsize.
Referenced by compute_all.

int VolMapCreate::compute_all ( bool allframes,

CombineType method,

void * params

)

computes volmap for all (selected) frames and takes the average, min or max depending on what was specified by "method", for most cases, params is unused (set to NULL) XXX the "allframes" param should be a FrameRange object, but for now its a boolean.

Definition at line 290 of file VolMapCreate.C.
References app, checkpoint_freq, checkpoint_name, combo_addframe, combo_begin, combo_end, combo_export, compute_frame, compute_init, computed_frames, VolumetricData::data, VMDApp::molecule_numframes, AtomSel::molid, NULL, sel, volmap, AtomSel::which_frame, wkf_timer_create, wkf_timer_destroy, wkf_timer_start, wkf_timer_stop, wkf_timer_time, wkf_timerhandle, write_map, VolumetricData::xsize, VolumetricData::ysize, and VolumetricData::zsize.
Referenced by mask, and vmd_volmap_new_fromtype.

virtual int VolMapCreate::compute_frame ( int frame,

float * voldata

) [protected, pure virtual]

Implemented in VolMapCreateMask.
Referenced by compute_all.

virtual int VolMapCreate::compute_init ( ) [inline, protected, virtual]

called before computing individual frames.

Reimplemented in VolMapCreateMask.
Definition at line 53 of file VolMapCreate.h.
Referenced by compute_all, VolMapCreateCoulombPotentialMSM::compute_init, VolMapCreateCoulombPotential::compute_init, VolMapCreateDistance::compute_init, VolMapCreateOccupancy::compute_init, VolMapCreateInterp::compute_init, VolMapCreateDensity::compute_init, and VolMapCreateMask::compute_init.

int VolMapCreate::compute_init ( float padding ) [protected]

Definition at line 379 of file VolMapCreate.C.
References calculate_minmax, delta, MAX, max_coord, MEASURE_ERR_NOATOMS, MEASURE_ERR_NOSEL, MEASURE_ERR_ZEROGRIDSIZE, min_coord, AtomSel::num_atoms, VolumetricData::origin, sel, volmap, VolumetricData::xaxis, VolumetricData::xsize, VolumetricData::yaxis, VolumetricData::ysize, VolumetricData::zaxis, and VolumetricData::zsize.

void VolMapCreate::set_checkpoint ( int checkpointfreq,

char * checkpointname

)

Definition at line 112 of file VolMapCreate.C.
References checkpoint_freq, and checkpoint_name.
Referenced by vmd_volmap_new_fromtype.

void VolMapCreate::set_minmax ( float minx,

float miny,

float minz,

float maxx,

float maxy,

float maxz

)

Definition at line 101 of file VolMapCreate.C.
References max_coord, min_coord, and user_minmax.
Referenced by vmd_volmap_new_fromtype.

int VolMapCreate::write_dx_file ( const char * filename )

void VolMapCreate::write_map ( const char * filename ) [virtual]

For now this will call write_dx_file, but this is going to change to using molfileplugin instead. In VolMapCreate*Energy this method is overridden by one that adds temperature and weight information to the data set name string.

Definition at line 1236 of file VolMapCreate.C.
References volmap, and volmap_write_dx_file.
Referenced by compute_all, and vmd_volmap_new_fromtype.

Member Data Documentation

VMDApp* VolMapCreate::app [protected]

Definition at line 39 of file VolMapCreate.h.
Referenced by calculate_max_radius, calculate_minmax, compute_all, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateInterp::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, VolMapCreate, VolMapCreateCoulombPotential::VolMapCreateCoulombPotential, VolMapCreateCoulombPotentialMSM::VolMapCreateCoulombPotentialMSM, VolMapCreateDensity::VolMapCreateDensity, VolMapCreateDistance::VolMapCreateDistance, VolMapCreateInterp::VolMapCreateInterp, VolMapCreateMask::VolMapCreateMask, and VolMapCreateOccupancy::VolMapCreateOccupancy.

int VolMapCreate::checkpoint_freq [protected]

Definition at line 43 of file VolMapCreate.h.
Referenced by compute_all, set_checkpoint, and VolMapCreate.

char* VolMapCreate::checkpoint_name [protected]

Definition at line 44 of file VolMapCreate.h.
Referenced by compute_all, set_checkpoint, VolMapCreate, and ~VolMapCreate.

int VolMapCreate::computed_frames [protected]

Definition at line 42 of file VolMapCreate.h.
Referenced by combo_addframe, combo_begin, combo_export, compute_all, and VolMapCreate.

float VolMapCreate::delta [protected]

Definition at line 41 of file VolMapCreate.h.
Referenced by VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateInterp::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, VolMapCreateInterp::compute_init, compute_init, and VolMapCreate.

float VolMapCreate::max_coord[3] [protected]

Definition at line 46 of file VolMapCreate.h.
Referenced by compute_init, and set_minmax.

float VolMapCreate::min_coord[3] [protected]

Definition at line 46 of file VolMapCreate.h.
Referenced by compute_init, and set_minmax.

bool VolMapCreate::user_minmax [protected]

Definition at line 45 of file VolMapCreate.h.
Referenced by set_minmax, and VolMapCreate.

VolumetricData* VolMapCreate::volmap

Definition at line 69 of file VolMapCreate.h.
Referenced by combo_addframe, combo_begin, combo_export, compute_all, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateInterp::compute_frame, VolMapCreateDensity::compute_frame, VolMapCreateMask::compute_frame, VolMapCreateCoulombPotentialMSM::compute_init, VolMapCreateCoulombPotential::compute_init, VolMapCreateDistance::compute_init, VolMapCreateOccupancy::compute_init, VolMapCreateInterp::compute_init, VolMapCreateDensity::compute_init, VolMapCreateMask::compute_init, compute_init, mask, vmd_volmap_new_fromtype, VolMapCreate, write_map, and ~VolMapCreate.

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

Generated on Thu Apr 18 02:47:32 2024 for VMD (current) by

VolMapCreate Class Reference

Public Types

Public Methods

Public Attributes

Protected Methods

Protected Attributes

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation