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AtomSel.C File Reference

#include <math.h>
#include <stdlib.h>
#include <stdio.h>
#include <ctype.h>
#include <string.h>
#include "Atom.h"
#include "AtomSel.h"
#include "DrawMolecule.h"
#include "MoleculeList.h"
#include "VMDApp.h"
#include "Inform.h"
#include "SymbolTable.h"
#include "ParseTree.h"
#include "JRegex.h"
#include "VolumetricData.h"
#include "PeriodicTable.h"
#include "DrawRingsUtils.h"

Go to the source code of this file.

Defines

#define generic_atom_data(fctnname, datatype, field)
#define generic_set_atom_data(fctnname, datatype, fieldtype, field)
#define generic_atom_boolean(fctnname, comparison)
#define generic_sstruct_boolean(fctnname, comparison)
#define generic_set_sstruct_boolean(fctnname, newval)
#define fragment_data(fctn, fragtype)
#define atomsel_get_vel(name, offset)
#define set_position_data(fctn, offset)
#define set_force_data(fctn, offset)
#define set_vel_data(fctn, offset)

Functions

int atomsel_all (void *,int, int *)
int atomsel_none (void *, int num, int *flgs)
int atomsel_name (void *v, int num, const char **data, int *flgs)
int atomsel_type (void *v, int num, const char **data, int *flgs)
int atomsel_backbonetype (void *v, int num, const char **data, int *flgs)
int atomsel_residuetype (void *v, int num, const char **data, int *flgs)
 generic_atom_data (atomsel_atomicnumber, int, atomicnumber) static int atomsel_set_atomicnumber(void *v
int atomsel_volume_array (void *v, int num, double *data, int *flgs, int array_index)
int atomsel_interp_volume_array (void *v, int num, double *data, int *flgs, int array_index)
int atomsel_gridindex_array (void *v, int num, double *data, int *flgs, int array_index)
int atomsel_gridindex0 (void *v, int num, double *data, int *flgs)
int atomsel_gridindex1 (void *v, int num, double *data, int *flgs)
int atomsel_gridindex2 (void *v, int num, double *data, int *flgs)
int atomsel_gridindex3 (void *v, int num, double *data, int *flgs)
int atomsel_gridindex4 (void *v, int num, double *data, int *flgs)
int atomsel_gridindex5 (void *v, int num, double *data, int *flgs)
int atomsel_gridindex6 (void *v, int num, double *data, int *flgs)
int atomsel_gridindex7 (void *v, int num, double *data, int *flgs)
int atomsel_volume0 (void *v, int num, double *data, int *flgs)
int atomsel_volume1 (void *v, int num, double *data, int *flgs)
int atomsel_volume2 (void *v, int num, double *data, int *flgs)
int atomsel_volume3 (void *v, int num, double *data, int *flgs)
int atomsel_volume4 (void *v, int num, double *data, int *flgs)
int atomsel_volume5 (void *v, int num, double *data, int *flgs)
int atomsel_volume6 (void *v, int num, double *data, int *flgs)
int atomsel_volume7 (void *v, int num, double *data, int *flgs)
int atomsel_interp_volume0 (void *v, int num, double *data, int *flgs)
int atomsel_interp_volume1 (void *v, int num, double *data, int *flgs)
int atomsel_interp_volume2 (void *v, int num, double *data, int *flgs)
int atomsel_interp_volume3 (void *v, int num, double *data, int *flgs)
int atomsel_interp_volume4 (void *v, int num, double *data, int *flgs)
int atomsel_interp_volume5 (void *v, int num, double *data, int *flgs)
int atomsel_interp_volume6 (void *v, int num, double *data, int *flgs)
int atomsel_interp_volume7 (void *v, int num, double *data, int *flgs)
void atomSelParser_init (SymbolTable *atomSelParser)

Variables

int num
int int * data

Define Documentation

#define atomsel_get_vel (  name,
offset    ) 
 

Value:

static int atomsel_##name(void *v, int num, double *data, int *flgs) {  \
  DrawMolecule *atom_sel_mol = ((atomsel_ctxt *)v)->atom_sel_mol;       \
  int which_frame = ((atomsel_ctxt *)v)->which_frame;  \
  Timestep *ts = selframe(atom_sel_mol, which_frame);  \
  int i;                                               \
  if (!ts || !ts->vel) {                               \
    for (i=0; i<num; i++)                              \
      if (flgs[i]) data[i] = 0.0;                      \
    return 0;                                          \
  }                                                    \
  for (i=0; i<num; i++) {                              \
    if (flgs[i]) {                                     \
      data[i] = ts->vel[3L*i + (offset)];              \
    }                                                  \
  }                                                    \
  return 1;                                            \
}

#define fragment_data (  fctn,
fragtype    ) 
 

Value:

static int fctn(void *v, int num, int *data, int *)                           \
{                                                                             \
  DrawMolecule *atom_sel_mol = ((atomsel_ctxt *)v)->atom_sel_mol;                     \
   int *tmp = new int[num];                                                   \
   int i;                                                                     \
   for (i=num-1; i>=0; i--) {                         \
      tmp[i] = 0;                                                             \
      data[i] = -1;                   \
   }                                                                          \
                                                      \
   for ( i=atom_sel_mol->fragtype.num()-1; i>=0; i--) {                       \
                                      \
      int j;                                                                  \
      for (j=atom_sel_mol->fragtype[i]->num()-1; j>=0; j--) {                 \
                                              \
         mark_atoms_given_residue(atom_sel_mol,(*atom_sel_mol->fragtype[i])[j], tmp);      \
      }                                                                       \
                              \
      for (j=num-1; j>=0; j--) {                                              \
         if (tmp[j]) {                                                        \
            data[j] = i;                                                      \
            tmp[j] = 0;                                                       \
         }                                                                    \
      }                                                                       \
   }                                                                          \
   delete [] tmp;                                                             \
   return 1;                                                                  \
}

#define generic_atom_boolean (  fctnname,
comparison    ) 
 

Value:

static int fctnname(void *v, int num, int *flgs) {                    \
  DrawMolecule *atom_sel_mol = ((atomsel_ctxt *)v)->atom_sel_mol;     \
  for (int i=0; i<num; i++) {                                         \
    if (flgs[i]) {                                                    \
      flgs[i] = atom_sel_mol->atom(i)->comparison;                    \
    }                                                                 \
  }                                                                   \
  return 1;                                                           \
}

#define generic_atom_data (  fctnname,
datatype,
field    ) 
 

Value:

static int fctnname(void *v, int num, datatype *data, int *flgs) {     \
  DrawMolecule *atom_sel_mol = ((atomsel_ctxt *)v)->atom_sel_mol;      \
  for (int i=0; i<num; i++) {                                          \
    if (flgs[i]) {                                                     \
      data[i] = atom_sel_mol->atom(i)->field;                          \
    }                                                                  \
  }                                                                    \
  return 1;                                                            \
}

Definition at line 59 of file AtomSel.C.

#define generic_set_atom_data (  fctnname,
datatype,
fieldtype,
field    ) 
 

Value:

static int fctnname(void *v, int num, datatype *data, int *flgs) {     \
  DrawMolecule *atom_sel_mol = ((atomsel_ctxt *)v)->atom_sel_mol;      \
  int i;                                                               \
  for (i=0; i<num; i++) {                                              \
    if (flgs[i]) {                                                     \
      atom_sel_mol->atom(i)->field = (fieldtype) data[i];              \
    }                                                                  \
  }                                                                    \
  return 1;                                                            \
}

Definition at line 71 of file AtomSel.C.

#define generic_set_sstruct_boolean (  fctnname,
newval    ) 
 

Value:

static int fctnname(void *v, int num, int *data, int *flgs) {            \
  DrawMolecule *atom_sel_mol = ((atomsel_ctxt *)v)->atom_sel_mol;        \
  atom_sel_mol->need_secondary_structure(0);                             \
  for (int i=0; i<num; i++) {                                            \
    if (flgs[i] && data[i]) {                                            \
        atom_sel_mol->residue(atom_sel_mol->atom(i)->uniq_resid)         \
          ->sstruct = newval;                                            \
    }                                                                    \
  }                                                                      \
  return 1;                                                              \
}

#define generic_sstruct_boolean (  fctnname,
comparison    ) 
 

Value:

static int fctnname(void *v, int num, int *flgs) {                       \
  DrawMolecule *atom_sel_mol = ((atomsel_ctxt *)v)->atom_sel_mol;        \
  atom_sel_mol->need_secondary_structure(1);                             \
  for (int i=0; i<num; i++) {                                            \
    int s;                                                               \
    if (flgs[i]) {                                                       \
      s = atom_sel_mol->residue(                                         \
                                  atom_sel_mol->atom(i)->uniq_resid      \
                                  )->sstruct;                            \
      if (!comparison) {                                                 \
        flgs[i] = 0;                                                     \
      }                                                                  \
    }                                                                    \
  }                                                                      \
  return 1;                                                              \
}

#define set_force_data (  fctn,
offset    ) 
 

Value:

static int fctn(void *v, int num, double *data, int *flgs)                    \
{                                                                             \
  DrawMolecule *atom_sel_mol = ((atomsel_ctxt *)v)->atom_sel_mol;                     \
  int which_frame = ((atomsel_ctxt *)v)->which_frame;                                 \
  Timestep *ts = selframe(atom_sel_mol, which_frame);                         \
  if (!ts) return 0;                                                          \
  if (!ts->force) {                                                           \
    ts->force = new float[3L*num];                                            \
    memset(ts->force, 0, 3L*num*sizeof(float));                               \
  }                                                                           \
  for (int i=num-1; i>=0; i--) {                                              \
    if (flgs[i]) {                                                            \
      ts->force[3L*i + offset] = (float) data[i];                             \
    }                                                                         \
  }                                                                           \
  return 1;                                                                   \
}

#define set_position_data (  fctn,
offset    ) 
 

Value:

static int fctn(void *v, int num, double *data, int *flgs)                    \
{                                                                             \
  DrawMolecule *atom_sel_mol = ((atomsel_ctxt *)v)->atom_sel_mol;                     \
  int which_frame = ((atomsel_ctxt *)v)->which_frame;                                 \
  Timestep *ts = selframe(atom_sel_mol, which_frame);                         \
  if (!ts) return 0;                                                          \
  for (int i=num-1; i>=0; i--) {                                              \
    if (flgs[i]) {                                                            \
      ts->pos[3L*i + offset] = (float) data[i];                               \
    }                                                                         \
  }                                                                           \
  return 1;                                                                   \
}

#define set_vel_data (  fctn,
offset    ) 
 

Value:

static int fctn(void *v, int num, double *data, int *flgs)                    \
{                                                                             \
  DrawMolecule *atom_sel_mol = ((atomsel_ctxt *)v)->atom_sel_mol;                     \
  int which_frame = ((atomsel_ctxt *)v)->which_frame;                                 \
  Timestep *ts = selframe(atom_sel_mol, which_frame);                         \
  if (!ts) return 0;                                                          \
  if (!ts->vel) {                                                             \
    ts->vel= new float[3L*num];                                               \
    memset(ts->vel, 0, 3L*num*sizeof(float));                                 \
  }                                                                           \
  for (int i=num-1; i>=0; i--) {                                              \
    if (flgs[i]) {                                                            \
      ts->vel[3L*i + offset] = (float) data[i];                               \
    }                                                                         \
  }                                                                           \
  return 1;                                                                   \
}

Function Documentation

int atomsel_all (  void *   ,
int   ,
int *   
)  [static]
 

Definition at line 47 of file AtomSel.C.

Referenced by atomSelParser_init.

int atomsel_backbonetype (  void *    v,
int    num,
const char **    data,
int *    flgs
)  [static]
 

Definition at line 109 of file AtomSel.C.

References BaseMolecule::atom, ATOMHYDROGEN, ATOMNORMAL, ATOMNUCLEICBACK, ATOMPROTEINBACK, MolAtom::atomType, data, and num.

Referenced by atomSelParser_init.

int atomsel_gridindex0 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2100 of file AtomSel.C.

References atomsel_gridindex_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_gridindex1 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2103 of file AtomSel.C.

References atomsel_gridindex_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_gridindex2 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2106 of file AtomSel.C.

References atomsel_gridindex_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_gridindex3 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2109 of file AtomSel.C.

References atomsel_gridindex_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_gridindex4 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2112 of file AtomSel.C.

References atomsel_gridindex_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_gridindex5 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2115 of file AtomSel.C.

References atomsel_gridindex_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_gridindex6 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2118 of file AtomSel.C.

References atomsel_gridindex_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_gridindex7 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2121 of file AtomSel.C.

References atomsel_gridindex_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_gridindex_array (  void *    v,
int    num,
double *    data,
int *    flgs,
int    array_index
)  [static]
 

Definition at line 2080 of file AtomSel.C.

References data, BaseMolecule::get_volume_data, NAN, num, Timestep::pos, selframe, and VolumetricData::voxel_index_from_coord.

Referenced by atomsel_gridindex0, atomsel_gridindex1, atomsel_gridindex2, atomsel_gridindex3, atomsel_gridindex4, atomsel_gridindex5, atomsel_gridindex6, and atomsel_gridindex7.

int atomsel_interp_volume0 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2154 of file AtomSel.C.

References atomsel_interp_volume_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_interp_volume1 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2157 of file AtomSel.C.

References atomsel_interp_volume_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_interp_volume2 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2160 of file AtomSel.C.

References atomsel_interp_volume_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_interp_volume3 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2163 of file AtomSel.C.

References atomsel_interp_volume_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_interp_volume4 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2166 of file AtomSel.C.

References atomsel_interp_volume_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_interp_volume5 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2169 of file AtomSel.C.

References atomsel_interp_volume_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_interp_volume6 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2172 of file AtomSel.C.

References atomsel_interp_volume_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_interp_volume7 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2175 of file AtomSel.C.

References atomsel_interp_volume_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_interp_volume_array (  void *    v,
int    num,
double *    data,
int *    flgs,
int    array_index
)  [static]
 

Definition at line 2060 of file AtomSel.C.

References data, BaseMolecule::get_volume_data, NAN, num, Timestep::pos, selframe, and VolumetricData::voxel_value_interpolate_from_coord.

Referenced by atomsel_interp_volume0, atomsel_interp_volume1, atomsel_interp_volume2, atomsel_interp_volume3, atomsel_interp_volume4, atomsel_interp_volume5, atomsel_interp_volume6, and atomsel_interp_volume7.

int atomsel_name (  void *    v,
int    num,
const char **    data,
int *    flgs
)  [static]
 

Definition at line 85 of file AtomSel.C.

References BaseMolecule::atom, BaseMolecule::atomNames, data, MolAtom::nameindex, and num.

Referenced by atomSelParser_init.

int atomsel_none (  void *   ,
int    num,
int *    flgs
)  [static]
 

Definition at line 52 of file AtomSel.C.

References num.

Referenced by atomSelParser_init.

int atomsel_residuetype (  void *    v,
int    num,
const char **    data,
int *    flgs
)  [static]
 

Definition at line 142 of file AtomSel.C.

References BaseMolecule::atom, data, num, MolAtom::residueType, RESNOTHING, RESNUCLEIC, RESPROTEIN, and RESWATERS.

Referenced by atomSelParser_init.

int atomsel_type (  void *    v,
int    num,
const char **    data,
int *    flgs
)  [static]
 

Definition at line 97 of file AtomSel.C.

References BaseMolecule::atom, BaseMolecule::atomTypes, data, num, and MolAtom::typeindex.

Referenced by atomSelParser_init.

int atomsel_volume0 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2127 of file AtomSel.C.

References atomsel_volume_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_volume1 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2130 of file AtomSel.C.

References atomsel_volume_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_volume2 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2133 of file AtomSel.C.

References atomsel_volume_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_volume3 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2136 of file AtomSel.C.

References atomsel_volume_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_volume4 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2139 of file AtomSel.C.

References atomsel_volume_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_volume5 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2142 of file AtomSel.C.

References atomsel_volume_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_volume6 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2145 of file AtomSel.C.

References atomsel_volume_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_volume7 (  void *    v,
int    num,
double *    data,
int *    flgs
)  [static]
 

Definition at line 2148 of file AtomSel.C.

References atomsel_volume_array, data, and num.

Referenced by atomSelParser_init.

int atomsel_volume_array (  void *    v,
int    num,
double *    data,
int *    flgs,
int    array_index
)  [static]
 

Definition at line 2040 of file AtomSel.C.

References data, BaseMolecule::get_volume_data, NAN, num, Timestep::pos, selframe, and VolumetricData::voxel_value_from_coord.

Referenced by atomsel_volume0, atomsel_volume1, atomsel_volume2, atomsel_volume3, atomsel_volume4, atomsel_volume5, atomsel_volume6, and atomsel_volume7.

void atomSelParser_init (  SymbolTable *    atomSelParser ) 
 

Definition at line 2182 of file AtomSel.C.

References SymbolTable::add_cfunction, SymbolTable::add_keyword, SymbolTable::add_singleword, SymbolTable::add_stringfctn, atomsel_all, atomsel_backbonetype, atomsel_gridindex0, atomsel_gridindex1, atomsel_gridindex2, atomsel_gridindex3, atomsel_gridindex4, atomsel_gridindex5, atomsel_gridindex6, atomsel_gridindex7, atomsel_interp_volume0, atomsel_interp_volume1, atomsel_interp_volume2, atomsel_interp_volume3, atomsel_interp_volume4, atomsel_interp_volume5, atomsel_interp_volume6, atomsel_interp_volume7, atomsel_name, atomsel_none, atomsel_residuetype, atomsel_type, atomsel_volume0, atomsel_volume1, atomsel_volume2, atomsel_volume3, atomsel_volume4, atomsel_volume5, atomsel_volume6, atomsel_volume7, and NULL.

generic_atom_data (  atomsel_atomicnumber   ,
int   ,
atomicnumber   
) 
 

Variable Documentation

int int* data
 

Definition at line 176 of file AtomSel.C.

Referenced by colvarparse::_get_keyval_scalar_, colvarparse::_get_keyval_scalar_value_, colvarparse::_get_keyval_vector_, MoleculeGraphics::add_cone, Molecule::add_coor_file, MoleculeGraphics::add_cylinder, MoleculeGraphics::add_line, MoleculeGraphics::add_pickpoint, MoleculeGraphics::add_point, MoleculeGraphics::add_sphere, MoleculeGraphics::add_spheretube, MoleculeGraphics::add_text, MoleculeGraphics::add_triangle, MoleculeGraphics::add_tricolor, MoleculeGraphics::add_trinorm, addData, atomsel_backbonetype, atomsel_gridindex0, atomsel_gridindex1, atomsel_gridindex2, atomsel_gridindex3, atomsel_gridindex4, atomsel_gridindex5, atomsel_gridindex6, atomsel_gridindex7, atomsel_gridindex_array, atomsel_interp_volume0, atomsel_interp_volume1, atomsel_interp_volume2, atomsel_interp_volume3, atomsel_interp_volume4, atomsel_interp_volume5, atomsel_interp_volume6, atomsel_interp_volume7, atomsel_interp_volume_array, atomsel_name, atomsel_residuetype, atomsel_set, atomsel_type, atomsel_volume0, atomsel_volume1, atomsel_volume2, atomsel_volume3, atomsel_volume4, atomsel_volume5, atomsel_volume6, atomsel_volume7, atomsel_volume_array, colvarmodule::vector1d::c_array, cc_threaded, colvarmodule::matrix2d::clear, colvarmodule::vector1d::clear, Molecule::close_coor_file, IsoSurface::compute, IsoContour::compute, DrawMolecule::cov, colvarmodule::matrix2d::data_array, colvarmodule::vector1d::data_array, AtomColor::find, find_ellipse_coords, find_within, find_within_routine, free_to_CAVE_memory, free_to_FreeVR_memory, colvarmodule::matrix2d::from_simple_string, colvarmodule::vector1d::from_simple_string, VolumeTexture::generateColorScaleTexture, colvarparse::get_key_string_multi_value, handle_vrpn_tracker, hash_delete, hash_insert, colvarbias_restraint_histogram::init, BaseMolecule::init_atoms, init_new_volume, inthash_delete, inthash_insert, colvarparse::key_lookup, layout_fr, malloc_from_FreeVR_memory, match, colvarmodule::matrix2d::matrix2d, VMDApp::molecule_load, VMDApp::molecule_savetrajectory, molecule_tcl, molinfo_set, obj_getdoublearray, obj_transabout, obj_transvec, obj_transvecinv, obj_vecadd, obj_veclength, colvarmodule::matrix2d::operator *=, colvarmodule::matrix2d::row::operator vector1d, colvarmodule::matrix2d::operator+=, colvarmodule::matrix2d::operator-=, colvarmodule::matrix2d::operator/=, colvarmodule::matrix2d::operator=, colvarmodule::matrix2d::row::operator[], colvarmodule::vector1d::operator[], parse_minmax_args, py_mol_add_volumetric, py_mol_get_volumetric, colvarparse::read_block::read_block, colvarbias_meta::read_hill, MolFilePlugin::read_rawgraphics, MolData::readData, MolData::readFile, OSPRayRenderer::render_compile_and_validate, colvarmodule::matrix2d::reset, colvarmodule::vector1d::reset, colvarmodule::matrix2d::resize, colvarmodule::vector1d::resize, colvarmodule::matrix2d::row::row, sampleColors, sampleVolume, DrawMolecule::scale_factor, Segmentation::Segmentation, colvarmodule::matrix2d::row::set, myFl_Chart::set_data, colvarmodule::matrix2d::size, colvarmodule::vector1d::size, colvarparse::split_string, swap4, IMDSim::swap4_aligned, swap4_aligned, tcl_get_orders, tcl_get_weights, text_cmd_mol, colvarmodule::matrix2d::to_simple_string, GraphicsFltkMenu::update_molchooser, MoleculeGraphics::use_color, MoleculeGraphics::use_material, MoleculeGraphics::use_materials, colvarmodule::vector1d::vector1d, vmd_cave_is_initialized, vmd_measure_angle, vmd_measure_bond, vmd_measure_dihed, vmd_measure_energy, GraphicsFltkMenu::volindex_update, write_bin_histogram_map, and colvarmodule::vector1d::~vector1d.

int num
 

Definition at line 176 of file AtomSel.C.

Referenced by access_tcl_atomsel, UIVR::act_on_command, UIVR::add_tool_with_USL, atomsel_backbonetype, atomsel_gridindex0, atomsel_gridindex1, atomsel_gridindex2, atomsel_gridindex3, atomsel_gridindex4, atomsel_gridindex5, atomsel_gridindex6, atomsel_gridindex7, atomsel_gridindex_array, Atomsel_Init, atomsel_interp_volume0, atomsel_interp_volume1, atomsel_interp_volume2, atomsel_interp_volume3, atomsel_interp_volume4, atomsel_interp_volume5, atomsel_interp_volume6, atomsel_interp_volume7, atomsel_interp_volume_array, atomsel_name, atomsel_none, atomsel_residuetype, atomsel_type, atomsel_volume0, atomsel_volume1, atomsel_volume2, atomsel_volume3, atomsel_volume4, atomsel_volume5, atomsel_volume6, atomsel_volume7, atomsel_volume_array, center_convert_single_soa, center_convert_soa, cluster_get_fitrmsd, ANARIRender::commit_rep, Surf::compute, cylinder_full, density_rotate, CaveTracker::do_start, ParseTree::evaluate, BaseMolecule::find_atom_in_residue, find_minmax_selected, find_name_string_from_menuname, find_within, VolumeTexture::generateChargeTexture, VolumeTexture::generateColorScaleTexture, VolumeTexture::generateContourLineTexture, VolumeTexture::generateHSVTexture, VolumeTexture::generateIndexTexture, VolumeTexture::generatePosTexture, VMDApp::imd_sendforces, X3DOMDisplayDevice::line_array, X3DDisplayDevice::line_array, FileRenderer::line_array, make_tcl_atomsel, measure_center_perresidue, measure_fit, measure_minmax, measure_rdf, measure_rmsd, measure_rmsd_perresidue, measure_rmsd_qcp, measure_rmsdmat_qcp, measure_rmsdmat_qcp_ooc, measure_sumweights, molecule_tcl, obj_getdoublearray, obj_transabout, obj_transvec, obj_transvecinv, obj_vecadd, obj_veclength, obj_vecmean, obj_vecscale, obj_vecstddev, obj_vecsum, DrawMolecule::override_current_frame, parse_minmax_args, TclTextInterp::pick_selection_cb, X3DDisplayDevice::point_array, FileRenderer::point_array, FileRenderer::point_array_lit, X3DOMDisplayDevice::polyline_array, X3DDisplayDevice::polyline_array, FileRenderer::polyline_array, DispCmdPickPointArray::putdata, py_categories, py_mol_listall, py_scale_methods, py_set_rotation, py_stereomodes, Mobile::removeClient, OSPRayRenderer::render_compile_and_validate, OSPRay2Renderer::render_compile_and_validate, ANARIRender::render_compile_and_validate, same_double, same_int, same_string, IMDSimThread::send_forces, IMDSimBlocking::send_forces, GeometryMol::set_pick_selection, split_tcl_atomsel_info, VMDApp::stage_set_numpanels, Buttons::state, tcl_colorinfo_categories, tcl_get_array, tcl_get_intarray, tcl_get_vecarray, tcl_get_vector, tcl_get_weights, tcl_graphics, text_cmd_label, text_cmd_light, text_cmd_plugin, text_cmd_point_light, text_cmd_stage, text_cmd_user, TclTextInterp::update_completion_list, vmd_gridsearch1, vmd_gridsearch2, vmd_gridsearch3, vmd_gridsearch_bonds, vmd_measure_fit, vmd_volmap_compare, vmdsort_double, vmdsort_int, vmdsort_string, write_le_int16, write_le_int32, SymbolTable::~SymbolTable, and TclTextInterp::~TclTextInterp.

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