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VolMapCreateILS Class Reference

Implicit Ligand Sampling (ILS) algorithm. It finds the energy of placing a monoatomic or diatomic ligand at many points in the protein. More...

#include <VolMapCreate.h>

List of all members.

Public Methods

VolMapCreateILS (VMDApp *_app, int molid, int firstframe, int lastframe, float T, float res, int subr, float cut, int maskonly)

~VolMapCreateILS ()

VolumetricData * get_volmap ()

int compute ()

int add_map_to_molecule ()

Add volumetric data to the molecule. More...

int write_map (const char *filename)

Include temperature and weight information to the data set name string and write the map into a dx file. More...

void set_probe (int num_probe_atoms, int num_conf, const float *probe_coords, const float *vdwrmin, const float *vdweps, const float *charge)

void set_probe_symmetry (int order1, const float *axis1, int order2, const float *axis2, int tetrahedral)

void set_minmax (float minx, float miny, float minz, float maxx, float maxy, float maxz)

void set_pbc (float center[3], int bbox)

void set_maxenergy (float maxenergy)

void set_alignsel (AtomSel *asel)

void set_transform (const Matrix4 *mat)

int get_conformers (float *&conform) const

void get_statistics (int &numconf, int &numorient, int &numrot)

Detailed Description

Implicit Ligand Sampling (ILS) algorithm. It finds the energy of placing a monoatomic or diatomic ligand at many points in the protein.

Definition at line 195 of file VolMapCreate.h.

Constructor & Destructor Documentation

VolMapCreateILS::VolMapCreateILS ( VMDApp * _app,

int molid,

int firstframe,

int lastframe,

float T,

float res,

int subr,

float cut,

int maskonly

)

Definition at line 217 of file VolMapCreateILS.C.

References DEFAULT_EXCL_ENERGY, mask, and NULL.

VolMapCreateILS::~VolMapCreateILS ( )

Definition at line 268 of file VolMapCreateILS.C.

Member Function Documentation

int VolMapCreateILS::add_map_to_molecule ( )

Add volumetric data to the molecule.

Definition at line 321 of file VolMapCreateILS.C.

References VolumetricData::data, MoleculeList::mol_from_id, VMDApp::molecule_add_volumetric, VMDApp::moleculeList, VolumetricData::name, NULL, BaseMolecule::num_volume_data, VolumetricData::origin, VolumetricData::xaxis, VolumetricData::xsize, VolumetricData::yaxis, VolumetricData::ysize, VolumetricData::zaxis, and VolumetricData::zsize.

Referenced by vmd_volmap_ils, and write_map.

int VolMapCreateILS::compute ( )

Definition at line 1999 of file VolMapCreateILS.C.

References VolumetricData::data, VolumetricData::gridsize, VMDApp::molecule_numframes, n, wkf_timer_create, wkf_timer_destroy, wkf_timer_start, wkf_timer_timenow, wkf_timerhandle, VolumetricData::xsize, and VolumetricData::ysize.

Referenced by vmd_volmap_ils.

int VolMapCreateILS::get_conformers ( float *& conform ) const [inline]

Definition at line 406 of file VolMapCreate.h.

Referenced by vmd_volmap_ils.

void VolMapCreateILS::get_statistics ( int & numconf,

int & numorient,

int & numrot

) [inline]

Definition at line 411 of file VolMapCreate.h.

Referenced by vmd_volmap_ils.

VolumetricData* VolMapCreateILS::get_volmap ( ) [inline]

Definition at line 365 of file VolMapCreate.h.

void VolMapCreateILS::set_alignsel ( AtomSel * asel )

Definition at line 487 of file VolMapCreateILS.C.

Referenced by vmd_volmap_ils.

void VolMapCreateILS::set_maxenergy ( float maxenergy )

Definition at line 478 of file VolMapCreateILS.C.

References DEFAULT_EXCL_ENERGY.

Referenced by vmd_volmap_ils.

void VolMapCreateILS::set_minmax ( float minx,

float miny,

float minz,

float maxx,

float maxy,

float maxz

)

Definition at line 453 of file VolMapCreateILS.C.

Referenced by vmd_volmap_ils.

void VolMapCreateILS::set_pbc ( float center[3],

int bbox

)

Definition at line 470 of file VolMapCreateILS.C.

References vec_copy.

Referenced by vmd_volmap_ils.

void VolMapCreateILS::set_probe ( int num_probe_atoms,

int num_conf,

const float * probe_coords,

const float * vdwrmin,

const float * vdweps,

const float * charge

)

Definition at line 358 of file VolMapCreateILS.C.

References vec_add, vec_scale, vec_sub, and vec_zero.

Referenced by vmd_volmap_ils.

void VolMapCreateILS::set_probe_symmetry ( int order1,

const float * axis1,

int order2,

const float * axis2,

int tetrahedral

)

Definition at line 425 of file VolMapCreateILS.C.

References dot_prod, vec_copy, and vec_normalize.

Referenced by vmd_volmap_ils.

void VolMapCreateILS::set_transform ( const Matrix4 * mat )

Definition at line 494 of file VolMapCreateILS.C.

References mat.

Referenced by vmd_volmap_ils.

int VolMapCreateILS::write_map ( const char * filename )

Include temperature and weight information to the data set name string and write the map into a dx file.

Definition at line 285 of file VolMapCreateILS.C.

References add_map_to_molecule, MoleculeList::mol_from_id, VMDApp::molecule_savetrajectory, VMDApp::moleculeList, BaseMolecule::num_volume_data, FileSpec::nvolsets, VolumetricData::set_name, and FileSpec::setids.

Referenced by vmd_volmap_ils.

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