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VolMapCreateILS.C File Reference

#include <math.h>
#include <stdio.h>
#include "VolMapCreate.h"
#include "MoleculeList.h"
#include "VolumetricData.h"
#include "utilities.h"
#include "WKFUtils.h"
#include "VMDApp.h"
#include "Measure.h"
#include "Inform.h"

Go to the source code of this file.

Compounds

struct  AtomPosType
struct  BinOfAtoms
struct  ComputeOccupancyMap_t
union  flint_t

Defines

#define TIMING
#define BIN_DEPTH   8
#define BIN_SLOTSIZE   4
#define BIN_SIZE   (BIN_DEPTH * BIN_SLOTSIZE)
#define BIN_DEPTH   8
#define DEFAULT_EXCL_DIST   1.f
#define DEFAULT_EXCL_ENERGY   87.f
#define DEFAULT_BIN_LENGTH   3.f
#define MAX_BIN_VOLUME   27.f
#define MIN_BIN_VOLUME   8.f
#define MAX_UNIQUE_TYPES   200
#define MAX_EXTRA_ATOMS   50

Typedefs

typedef flint_t flint
typedef ComputeOccupancyMap_t ComputeOccupancyMap

Functions

int ComputeOccupancyMap_setup (ComputeOccupancyMap *)
int ComputeOccupancyMap_calculate_slab (ComputeOccupancyMap *)
void ComputeOccupancyMap_cleanup (ComputeOccupancyMap *)
void write_bin_histogram_map (const ComputeOccupancyMap *, const char *filename)
void atom_bin_stats (const ComputeOccupancyMap *)
void compute_allatoms (float *map, int mx, int my, int mz, float lx, float ly, float lz, const float origin[3], const float axes[9], const float alignmat[16], int num_coords, const float *coords, const int *vdw_type, const float *vdw_params, float cutoff, const float *probe_vdw_params, int num_probe_atoms, int num_conformers, const float *conformers, float excl_energy)
bool collinear (const float *axis1, const float *axis2, float tol)
int triangulate (const float *pole, const float *eq1, const float *eq2, int freq, float *v)
void octahedron (float *vertices, int C2symm)
void hexahedron (float *vertices, int C2symm)
void dodecahedron (float *faces, float *vertices, int C2symm)
int icosahedron_geodesic (float *(&orientations), int C2symm, int freq)
float signed_angle (const float *axis, const float *v1, const float *v2)
int fill_atom_bins (ComputeOccupancyMap *p)
void tighten_bin_neighborhood (ComputeOccupancyMap *p)
void find_distance_exclusions (ComputeOccupancyMap *p)
void find_energy_exclusions (ComputeOccupancyMap *p)
void compute_occupancy_monoatom (ComputeOccupancyMap *p)
void compute_occupancy_multiatom (ComputeOccupancyMap *p)

Define Documentation

#define BIN_DEPTH   8
 

Definition at line 54 of file VolMapCreateILS.C.

#define BIN_DEPTH   8
 

Definition at line 54 of file VolMapCreateILS.C.

Referenced by compute_occupancy_monoatom, compute_occupancy_multiatom, fill_atom_bins, find_distance_exclusions, and find_energy_exclusions.

#define BIN_SIZE   (BIN_DEPTH * BIN_SLOTSIZE)
 

Definition at line 51 of file VolMapCreateILS.C.

#define BIN_SLOTSIZE   4
 

Definition at line 50 of file VolMapCreateILS.C.

#define DEFAULT_BIN_LENGTH   3.f
 

Definition at line 140 of file VolMapCreateILS.C.

Referenced by ComputeOccupancyMap_setup.

#define DEFAULT_EXCL_DIST   1.f
 

Definition at line 137 of file VolMapCreateILS.C.

#define DEFAULT_EXCL_ENERGY   87.f
 

Definition at line 138 of file VolMapCreateILS.C.

Referenced by VolMapCreateILS::set_maxenergy, and VolMapCreateILS::VolMapCreateILS.

#define MAX_BIN_VOLUME   27.f
 

Definition at line 141 of file VolMapCreateILS.C.

Referenced by ComputeOccupancyMap_setup.

#define MAX_EXTRA_ATOMS   50
 

Definition at line 2734 of file VolMapCreateILS.C.

Referenced by fill_atom_bins.

#define MAX_UNIQUE_TYPES   200
 

#define MIN_BIN_VOLUME   8.f
 

Definition at line 142 of file VolMapCreateILS.C.

Referenced by ComputeOccupancyMap_setup.

#define TIMING
 

Definition at line 41 of file VolMapCreateILS.C.

Typedef Documentation

typedef struct ComputeOccupancyMap_t ComputeOccupancyMap
 

typedef union flint_t flint
 

Function Documentation

void atom_bin_stats (  const ComputeOccupancyMap *    )  [static]
 

Definition at line 3389 of file VolMapCreateILS.C.

References ComputeOccupancyMap_t::bincnt, ComputeOccupancyMap_t::bx, ComputeOccupancyMap_t::bx_1, ComputeOccupancyMap_t::by, ComputeOccupancyMap_t::by_1, ComputeOccupancyMap_t::bz, ComputeOccupancyMap_t::bz_1, ComputeOccupancyMap_t::cutoff, ComputeOccupancyMap_t::extcutoff, ComputeOccupancyMap_t::lx, ComputeOccupancyMap_t::ly, ComputeOccupancyMap_t::lz, ComputeOccupancyMap_t::nbx, ComputeOccupancyMap_t::nby, ComputeOccupancyMap_t::nbz, ComputeOccupancyMap_t::num_bin_offsets, ComputeOccupancyMap_t::num_extras, ComputeOccupancyMap_t::padx, ComputeOccupancyMap_t::pady, ComputeOccupancyMap_t::padz, write_bin_histogram_map, ComputeOccupancyMap_t::x0, ComputeOccupancyMap_t::y0, and ComputeOccupancyMap_t::z0.

bool collinear (  const float *    axis1,
const float *    axis2,
float    tol
)  [static]
 

Definition at line 883 of file VolMapCreateILS.C.

References DEGTORAD, and dot_prod.

void compute_allatoms (  float *    map,
int    mx,
int    my,
int    mz,
float    lx,
float    ly,
float    lz,
const float    origin[3],
const float    axes[9],
const float    alignmat[16],
int    num_coords,
const float *    coords,
const int *    vdw_type,
const float *    vdw_params,
float    cutoff,
const float *    probe_vdw_params,
int    num_probe_atoms,
int    num_conformers,
const float *    conformers,
float    excl_energy
)  [static]
 

Definition at line 3432 of file VolMapCreateILS.C.

References n, and z.

void compute_occupancy_monoatom (  ComputeOccupancyMap *    p )  [static]
 

Definition at line 3093 of file VolMapCreateILS.C.

References BinOfAtoms::atom, BIN_DEPTH, ComputeOccupancyMap_t::bin_offsets, ComputeOccupancyMap_t::bin_zero, ComputeOccupancyMap_t::bx_1, ComputeOccupancyMap_t::by_1, ComputeOccupancyMap_t::bz_1, ComputeOccupancyMap_t::cutoff, ComputeOccupancyMap_t::excl_energy, ComputeOccupancyMap_t::exclusions, ComputeOccupancyMap_t::extra, ComputeOccupancyMap_t::hx, ComputeOccupancyMap_t::hy, ComputeOccupancyMap_t::hz, ComputeOccupancyMap_t::kstart, ComputeOccupancyMap_t::kstop, ComputeOccupancyMap_t::map, ComputeOccupancyMap_t::mx, ComputeOccupancyMap_t::my, n, ComputeOccupancyMap_t::nbx, ComputeOccupancyMap_t::nby, ComputeOccupancyMap_t::num_bin_offsets, ComputeOccupancyMap_t::num_extras, ComputeOccupancyMap_t::probe_vdw_params, ComputeOccupancyMap_t::vdw_params, ComputeOccupancyMap_t::x0, ComputeOccupancyMap_t::y0, and ComputeOccupancyMap_t::z0.

Referenced by ComputeOccupancyMap_calculate_slab.

void compute_occupancy_multiatom (  ComputeOccupancyMap *    p )  [static]
 

Definition at line 3211 of file VolMapCreateILS.C.

References BinOfAtoms::atom, BIN_DEPTH, ComputeOccupancyMap_t::bin_offsets, ComputeOccupancyMap_t::bin_zero, ComputeOccupancyMap_t::bx_1, ComputeOccupancyMap_t::by_1, ComputeOccupancyMap_t::bz_1, ComputeOccupancyMap_t::conformers, ComputeOccupancyMap_t::cutoff, ComputeOccupancyMap_t::excl_energy, ComputeOccupancyMap_t::exclusions, ComputeOccupancyMap_t::extra, ComputeOccupancyMap_t::hx, ComputeOccupancyMap_t::hy, ComputeOccupancyMap_t::hz, ComputeOccupancyMap_t::kstart, ComputeOccupancyMap_t::kstop, ComputeOccupancyMap_t::map, ComputeOccupancyMap_t::mx, ComputeOccupancyMap_t::my, n, ComputeOccupancyMap_t::nbx, ComputeOccupancyMap_t::nby, ComputeOccupancyMap_t::num_bin_offsets, ComputeOccupancyMap_t::num_conformers, ComputeOccupancyMap_t::num_extras, ComputeOccupancyMap_t::num_probes, ComputeOccupancyMap_t::probe_vdw_params, ComputeOccupancyMap_t::vdw_params, ComputeOccupancyMap_t::x0, ComputeOccupancyMap_t::y0, z, and ComputeOccupancyMap_t::z0.

Referenced by ComputeOccupancyMap_calculate_slab.

int ComputeOccupancyMap_calculate_slab (  ComputeOccupancyMap *    )  [static]
 

Definition at line 2646 of file VolMapCreateILS.C.

References compute_occupancy_monoatom, compute_occupancy_multiatom, ComputeOccupancyMap_t::exclusions, find_distance_exclusions, find_energy_exclusions, ComputeOccupancyMap_t::mx, ComputeOccupancyMap_t::my, ComputeOccupancyMap_t::mz, ComputeOccupancyMap_t::num_probes, wkf_timer_create, wkf_timer_destroy, wkf_timer_start, wkf_timer_timenow, and wkf_timerhandle.

void ComputeOccupancyMap_cleanup (  ComputeOccupancyMap *    )  [static]
 

Definition at line 2723 of file VolMapCreateILS.C.

References ComputeOccupancyMap_t::bin, ComputeOccupancyMap_t::bin_offsets, ComputeOccupancyMap_t::bincnt, ComputeOccupancyMap_t::exclusions, and ComputeOccupancyMap_t::extra.

int ComputeOccupancyMap_setup (  ComputeOccupancyMap *    )  [static]
 

Definition at line 2564 of file VolMapCreateILS.C.

References ComputeOccupancyMap_t::bin, ComputeOccupancyMap_t::bin_offsets, ComputeOccupancyMap_t::bin_zero, ComputeOccupancyMap_t::bincnt, ComputeOccupancyMap_t::bincnt_zero, ComputeOccupancyMap_t::bx, ComputeOccupancyMap_t::bx_1, ComputeOccupancyMap_t::by, ComputeOccupancyMap_t::by_1, ComputeOccupancyMap_t::bz, ComputeOccupancyMap_t::bz_1, ComputeOccupancyMap_t::cpu_only, DEFAULT_BIN_LENGTH, ComputeOccupancyMap_t::exclusions, ComputeOccupancyMap_t::extra, fill_atom_bins, ComputeOccupancyMap_t::hx, ComputeOccupancyMap_t::hy, ComputeOccupancyMap_t::hz, ComputeOccupancyMap_t::lx, ComputeOccupancyMap_t::ly, ComputeOccupancyMap_t::lz, ComputeOccupancyMap_t::map, MAX_BIN_VOLUME, MIN_BIN_VOLUME, ComputeOccupancyMap_t::mpblx, ComputeOccupancyMap_t::mpbly, ComputeOccupancyMap_t::mpblz, ComputeOccupancyMap_t::mx, ComputeOccupancyMap_t::my, ComputeOccupancyMap_t::mz, NULL, and tighten_bin_neighborhood.

void dodecahedron (  float *    faces,
float *    vertices,
int    C2symm
)  [static]
 

Definition at line 989 of file VolMapCreateILS.C.

References angle, cross_prod, DEGTORAD, Matrix4::identity, Matrix4::multpoint3d, RADTODEG, Matrix4::rot, Matrix4::rotate_axis, vec_add, vec_copy, vec_negate, vec_normalize, and vec_zero.

Referenced by icosahedron_geodesic.

int fill_atom_bins (  ComputeOccupancyMap *    p )  [static]
 

Definition at line 2736 of file VolMapCreateILS.C.

References BinOfAtoms::atom, ComputeOccupancyMap_t::bin, bin, BIN_DEPTH, ComputeOccupancyMap_t::bin_zero, ComputeOccupancyMap_t::bincnt, ComputeOccupancyMap_t::bincnt_zero, ComputeOccupancyMap_t::bx_1, ComputeOccupancyMap_t::by_1, ComputeOccupancyMap_t::bz_1, ComputeOccupancyMap_t::coords, ComputeOccupancyMap_t::extcutoff, ComputeOccupancyMap_t::extra, ComputeOccupancyMap_t::lx, ComputeOccupancyMap_t::ly, ComputeOccupancyMap_t::lz, MAX_EXTRA_ATOMS, n, ComputeOccupancyMap_t::nbx, ComputeOccupancyMap_t::nby, ComputeOccupancyMap_t::nbz, ComputeOccupancyMap_t::num_coords, ComputeOccupancyMap_t::num_extras, ComputeOccupancyMap_t::padx, ComputeOccupancyMap_t::pady, ComputeOccupancyMap_t::padz, ComputeOccupancyMap_t::vdw_type, AtomPosType::vdwtype, AtomPosType::x, ComputeOccupancyMap_t::x0, AtomPosType::y, ComputeOccupancyMap_t::y0, AtomPosType::z, z, and ComputeOccupancyMap_t::z0.

Referenced by ComputeOccupancyMap_setup.

void find_distance_exclusions (  ComputeOccupancyMap *    p )  [static]
 

Definition at line 2883 of file VolMapCreateILS.C.

References BinOfAtoms::atom, BIN_DEPTH, ComputeOccupancyMap_t::bin_zero, ComputeOccupancyMap_t::bx_1, ComputeOccupancyMap_t::by_1, ComputeOccupancyMap_t::bz_1, ComputeOccupancyMap_t::excl_dist, ComputeOccupancyMap_t::exclusions, ComputeOccupancyMap_t::extra, ComputeOccupancyMap_t::hx, ComputeOccupancyMap_t::hy, ComputeOccupancyMap_t::hz, ComputeOccupancyMap_t::kstart, ComputeOccupancyMap_t::kstop, ComputeOccupancyMap_t::mx, ComputeOccupancyMap_t::my, n, ComputeOccupancyMap_t::nbx, ComputeOccupancyMap_t::nby, ComputeOccupancyMap_t::num_extras, ComputeOccupancyMap_t::x0, ComputeOccupancyMap_t::y0, and ComputeOccupancyMap_t::z0.

Referenced by ComputeOccupancyMap_calculate_slab.

void find_energy_exclusions (  ComputeOccupancyMap *    p )  [static]
 

Definition at line 2982 of file VolMapCreateILS.C.

References BinOfAtoms::atom, BIN_DEPTH, ComputeOccupancyMap_t::bin_offsets, ComputeOccupancyMap_t::bin_zero, ComputeOccupancyMap_t::bx_1, ComputeOccupancyMap_t::by_1, ComputeOccupancyMap_t::bz_1, ComputeOccupancyMap_t::cutoff, ComputeOccupancyMap_t::excl_energy, ComputeOccupancyMap_t::exclusions, ComputeOccupancyMap_t::extra, ComputeOccupancyMap_t::hx, ComputeOccupancyMap_t::hy, ComputeOccupancyMap_t::hz, ComputeOccupancyMap_t::kstart, ComputeOccupancyMap_t::kstop, ComputeOccupancyMap_t::mx, ComputeOccupancyMap_t::my, n, ComputeOccupancyMap_t::nbx, ComputeOccupancyMap_t::nby, ComputeOccupancyMap_t::num_bin_offsets, ComputeOccupancyMap_t::num_extras, ComputeOccupancyMap_t::probe_vdw_params, ComputeOccupancyMap_t::vdw_params, ComputeOccupancyMap_t::x0, ComputeOccupancyMap_t::y0, and ComputeOccupancyMap_t::z0.

Referenced by ComputeOccupancyMap_calculate_slab.

void hexahedron (  float *    vertices,
int    C2symm
)  [static]
 

Definition at line 968 of file VolMapCreateILS.C.

References vec_negate.

int icosahedron_geodesic (  float *&    orientations,
int    C2symm,
int    freq
)  [static]
 

Definition at line 1054 of file VolMapCreateILS.C.

References dodecahedron, norm, triangulate, vec_copy, vec_negate, vec_normalize, vec_scaled_add, and vec_sub.

void octahedron (  float *    vertices,
int    C2symm
)  [static]
 

Definition at line 953 of file VolMapCreateILS.C.

References vec_negate.

float signed_angle (  const float *    axis,
const float *    v1,
const float *    v2
)  [static]
 

Definition at line 1292 of file VolMapCreateILS.C.

References angle, cross_prod, dot_prod, vec_copy, and vec_normalize.

void tighten_bin_neighborhood (  ComputeOccupancyMap *    p )  [static]
 

Definition at line 2851 of file VolMapCreateILS.C.

References ComputeOccupancyMap_t::bin_offsets, ComputeOccupancyMap_t::bx, ComputeOccupancyMap_t::by, ComputeOccupancyMap_t::bz, ComputeOccupancyMap_t::extcutoff, n, ComputeOccupancyMap_t::num_bin_offsets, ComputeOccupancyMap_t::padx, ComputeOccupancyMap_t::pady, and ComputeOccupancyMap_t::padz.

Referenced by ComputeOccupancyMap_setup.

int triangulate (  const float *    pole,
const float *    eq1,
const float *    eq2,
int    freq,
float *    v
)  [static]
 

Definition at line 918 of file VolMapCreateILS.C.

References norm, vec_copy, vec_normalize, vec_scaled_add, and vec_sub.

Referenced by icosahedron_geodesic.

void write_bin_histogram_map (  const ComputeOccupancyMap *   ,
const char *    filename
)  [static]
 

Definition at line 3351 of file VolMapCreateILS.C.

References ComputeOccupancyMap_t::bincnt, ComputeOccupancyMap_t::bx, ComputeOccupancyMap_t::by, ComputeOccupancyMap_t::bz, data, ComputeOccupancyMap_t::nbx, ComputeOccupancyMap_t::nby, ComputeOccupancyMap_t::nbz, ComputeOccupancyMap_t::padx, ComputeOccupancyMap_t::pady, ComputeOccupancyMap_t::padz, volmap_write_dx_file, ComputeOccupancyMap_t::x0, ComputeOccupancyMap_t::y0, and ComputeOccupancyMap_t::z0.

Referenced by atom_bin_stats.

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