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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:
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