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Measure.h File Reference

#include "ResizeArray.h"
#include "Molecule.h"

Go to the source code of this file.

Defines

#define MEASURE_NOERR   0
#define MEASURE_ERR_NOSEL   -1
#define MEASURE_ERR_NOATOMS   -2
#define MEASURE_ERR_BADWEIGHTNUM   -3
#define MEASURE_ERR_NOWEIGHT   -4
#define MEASURE_ERR_NOCOM   -4
#define MEASURE_ERR_NOMINMAXCOORDS   -4
#define MEASURE_ERR_NORGYR   -4
#define MEASURE_ERR_BADWEIGHTSUM   -5
#define MEASURE_ERR_NOMOLECULE   -6
#define MEASURE_ERR_BADWEIGHTPARM   -7
#define MEASURE_ERR_NONNUMBERPARM   -8
#define MEASURE_ERR_MISMATCHEDCNT   -9
#define MEASURE_ERR_RGYRMISMATCH   -10
#define MEASURE_ERR_NOFRAMEPOS   -11
#define MEASURE_ERR_NONZEROJACOBI   -12
#define MEASURE_ERR_GENERAL   -13
#define MEASURE_ERR_NORADII   -14
#define MEASURE_ERR_BADORDERINDEX   -15
#define MEASURE_ERR_NOTSUP   -16
#define MEASURE_ERR_BADFRAMERANGE   -17
#define MEASURE_ERR_MISMATCHEDMOLS   -18
#define MEASURE_ERR_REPEATEDATOM   -19
#define MEASURE_ERR_NOFRAMES   -20
#define MEASURE_ERR_BADATOMID   -21
#define MEASURE_ERR_BADCUTOFF   -22
#define MEASURE_ERR_ZEROGRIDSIZE   -23
#define MEASURE_BOND   2
#define MEASURE_ANGLE   3
#define MEASURE_DIHED   4
#define MEASURE_IMPRP   5
#define MEASURE_VDW   6
#define MEASURE_ELECT   7

Enumerations

enum  {
  MEASURE_DIST_RMSD = 0, MEASURE_DIST_FITRMSD, MEASURE_DIST_RGYRD, MEASURE_DIST_CUSTOM,
  MEASURE_NUM_DIST
}

Functions

const char * measure_error (int errnum)
int measure_move (const AtomSel *sel, float *framepos, const Matrix4 &mat)
int measure_avpos (const AtomSel *sel, MoleculeList *mlist, int start, int end, int step, float *avpos)
int measure_center (const AtomSel *sel, const float *framepos, const float *weight, float *com)
int measure_center_perresidue (MoleculeList *mlist, const AtomSel *sel, const float *framepos, const float *weight, float *com)
int measure_dipole (const AtomSel *sel, MoleculeList *mlist, float *dipole, int unitsdebye, int usecenter)
int measure_hbonds (Molecule *mol, AtomSel *sel1, AtomSel *sel2, double cut, double maxangle, int *donlist, int *hydlist, int *acclist, int maxsize)
int measure_fit (const AtomSel *sel1, const AtomSel *sel2, const float *x, const float *y, const float *weight, const int *order, Matrix4 *mat)
int measure_minmax (int num, const int *on, const float *framepos, const float *radii, float *min_coord, float *max_coord)
int measure_rgyr (const AtomSel *sel, MoleculeList *mlist, const float *weight, float *rgyr)
 measure the radius of gyration, including the given weights. More...

int measure_rmsd (const AtomSel *sel1, const AtomSel *sel2, int num, const float *f1, const float *f2, float *weight, float *rmsd)
 measure the rmsd given a selection and weight term. More...

int measure_rmsd_perresidue (const AtomSel *sel1, const AtomSel *sel2, MoleculeList *mlist, int num, float *weight, float *rmsd)
int measure_rmsd_qcp (VMDApp *app, const AtomSel *sel1, const AtomSel *sel2, int num, const float *f1, const float *f2, float *weight, float *rmsd)
int measure_rmsdmat_qcp (VMDApp *app, const AtomSel *sel, MoleculeList *mlist, int num, float *weight, int start, int end, int step, float *rmsd)
int measure_rmsdmat_qcp_ooc (VMDApp *app, const AtomSel *sel, MoleculeList *mlist, int nfiles, const char **trjfileset, int num, float *weight, int start, int end, int step, int &framecount, float *&rmsd)
int FastCalcRMSDAndRotation (double *rot, double *A, float *rmsd, double E0, int len, double minScore)
int measure_rmsf (const AtomSel *sel, MoleculeList *mlist, int start, int end, int step, float *rmsf)
int measure_rmsf_perresidue (const AtomSel *sel, MoleculeList *mlist, int start, int end, int step, float *rmsf)
int measure_sumweights (const AtomSel *sel, int numweights, const float *weights, float *weightsum)
int measure_sasa (const AtomSel *sel, const float *framepos, const float *radius, float srad, float *sasa, ResizeArray< float > *pts, const AtomSel *restrictsel, const int *nsamples)
int measure_sasalist (MoleculeList *mlist, const AtomSel **sellist, int numsels, float srad, float *sasalist, const int *nsamples)
int measure_cluster (AtomSel *sel, MoleculeList *mlist, const int numcluster, const int algorithm, const int likeness, const double cutoff, int *clustersize, int **clusterlist, int first, int last, int step, int selupdate, float *weights)
int measure_clustsize (const AtomSel *sel, MoleculeList *mlist, const double cutoff, int *clustersize, int *clusternum, int *clusteridx, int minsize, int numshared, int usepbc)
int measure_gofr (AtomSel *sel1, AtomSel *sel2, MoleculeList *mlist, const int count_h, double *gofr, double *numint, double *histog, const float delta, int first, int last, int step, int *framecntr, int usepbc, int selupdate)
int measure_rdf (VMDApp *app, AtomSel *sel1, AtomSel *sel2, MoleculeList *mlist, const int count_h, double *gofr, double *numint, double *histog, const float delta, int first, int last, int step, int *framecntr, int usepbc, int selupdate)
int measure_geom (MoleculeList *mlist, int *molid, int *atmid, ResizeArray< float > *gValues, int frame, int first, int last, int defmolid, int geomtype)
int calculate_bond (MoleculeList *mlist, int *molid, int *atmid, float *value)
int calculate_angle (MoleculeList *mlist, int *molid, int *atmid, float *value)
int calculate_dihed (MoleculeList *mlist, int *molid, int *atmid, float *value)
int check_mol (Molecule *mol, int a)
int normal_atom_coord (Molecule *m, int a, float *pos)
int measure_energy (MoleculeList *mlist, int *molid, int *atmid, int natoms, ResizeArray< float > *gValues, int frame, int first, int last, int defmolid, double *params, int geomtype)
int compute_bond_energy (MoleculeList *mlist, int *molid, int *atmid, float *energy, float k, float x0)
int compute_angle_energy (MoleculeList *mlist, int *molid, int *atmid, float *energy, float k, float x0, float kub, float s0)
int compute_dihed_energy (MoleculeList *mlist, int *molid, int *atmid, float *energy, float k, int n, float delta)
int compute_imprp_energy (MoleculeList *mlist, int *molid, int *atmid, float *energy, float k, float x0)
int compute_vdw_energy (MoleculeList *mlist, int *molid, int *atmid, float *energy, float rmin1, float eps1, float rmin2, float eps2, float cutoff, float switchdist)
int compute_elect_energy (MoleculeList *mlist, int *molid, int *atmid, float *energy, float q1, float q2, bool flag1, bool flag2, float cutoff)
int measure_pbc2onc (MoleculeList *mlist, int molid, int frame, const float *center, Matrix4 &transform)
void get_transform_to_orthonormal_cell (const float *cell, const float center[3], Matrix4 &transform)
int measure_pbc_neighbors (MoleculeList *mlist, AtomSel *sel, int molid, int frame, const Matrix4 *alignment, const float *center, const float *cutoff, const float *box, ResizeArray< float > *extcoord_array, ResizeArray< int > *indexmap_array)
int compute_pbcminmax (MoleculeList *mlist, int molid, int frame, const float *center, const Matrix4 *transform, float *min, float *max)
int measure_surface (AtomSel *sel, MoleculeList *mlist, const float *framepos, const double gridsz, const double radius, const double sel_dist, int **surface, int *n_surf)
int measure_inertia (AtomSel *sel, MoleculeList *mlist, const float *coor, float rcom[3], float priaxes[3][3], float itensor[4][4], float evalue[3])


Define Documentation

#define MEASURE_ANGLE   3
 

Definition at line 57 of file Measure.h.

Referenced by measure_energy, measure_geom, py_measure_angle, vmd_measure_angle, and vmd_measure_energy.

#define MEASURE_BOND   2
 

Definition at line 56 of file Measure.h.

Referenced by measure_energy, measure_geom, py_measure_bond, vmd_measure_bond, and vmd_measure_energy.

#define MEASURE_DIHED   4
 

Definition at line 58 of file Measure.h.

Referenced by measure_energy, measure_geom, py_measure_dihed, vmd_measure_dihed, and vmd_measure_energy.

#define MEASURE_ELECT   7
 

Definition at line 61 of file Measure.h.

Referenced by measure_energy, and vmd_measure_energy.

#define MEASURE_ERR_BADATOMID   -21
 

Definition at line 52 of file Measure.h.

Referenced by check_mol.

#define MEASURE_ERR_BADCUTOFF   -22
 

Definition at line 53 of file Measure.h.

Referenced by measure_pbc_neighbors.

#define MEASURE_ERR_BADFRAMERANGE   -17
 

Definition at line 48 of file Measure.h.

Referenced by measure_avpos, measure_cluster, measure_gofr, measure_rdf, measure_rmsdmat_qcp, measure_rmsdmat_qcp_ooc, measure_rmsf, and measure_rmsf_perresidue.

#define MEASURE_ERR_BADORDERINDEX   -15
 

Definition at line 46 of file Measure.h.

Referenced by tcl_get_orders.

#define MEASURE_ERR_BADWEIGHTNUM   -3
 

Definition at line 31 of file Measure.h.

Referenced by get_weights_from_tcl_list, and tcl_get_weights.

#define MEASURE_ERR_BADWEIGHTPARM   -7
 

Definition at line 38 of file Measure.h.

Referenced by get_weights_from_attribute, get_weights_from_tcl_list, measure_sumweights, tcl_get_weights, vmd_measure_cluster, and vmd_volmap_new_fromtype.

#define MEASURE_ERR_BADWEIGHTSUM   -5
 

Definition at line 36 of file Measure.h.

Referenced by measure_center, measure_rgyr, measure_rmsd, and measure_rmsd_perresidue.

#define MEASURE_ERR_GENERAL   -13
 

Definition at line 44 of file Measure.h.

Referenced by measure_fit, measure_gofr, measure_rdf, measure_rgyr, and measure_sumweights.

#define MEASURE_ERR_MISMATCHEDCNT   -9
 

Definition at line 40 of file Measure.h.

Referenced by measure_fit, measure_rmsd, measure_rmsd_perresidue, measure_rmsd_qcp, and measure_sasa.

#define MEASURE_ERR_MISMATCHEDMOLS   -18
 

Definition at line 49 of file Measure.h.

Referenced by measure_gofr, and measure_rdf.

#define MEASURE_ERR_NOATOMS   -2
 

Definition at line 30 of file Measure.h.

Referenced by VolMapCreate::compute_init, Symmetry::guess, measure_avpos, measure_dipole, measure_inertia, measure_minmax, measure_rmsf, measure_rmsf_perresidue, measure_surface, and measure_trans_overlap.

#define MEASURE_ERR_NOCOM   -4
 

Definition at line 33 of file Measure.h.

Referenced by measure_center, and measure_center_perresidue.

#define MEASURE_ERR_NOFRAMEPOS   -11
 

Definition at line 42 of file Measure.h.

Referenced by measure_center, measure_center_perresidue, measure_move, and measure_sasa.

#define MEASURE_ERR_NOFRAMES   -20
 

Definition at line 51 of file Measure.h.

Referenced by compute_pbcminmax, measure_energy, measure_geom, measure_pbc2onc, measure_pbc_neighbors, and normal_atom_coord.

#define MEASURE_ERR_NOMINMAXCOORDS   -4
 

Definition at line 34 of file Measure.h.

Referenced by measure_minmax.

#define MEASURE_ERR_NOMOLECULE   -6
 

Definition at line 37 of file Measure.h.

Referenced by check_mol, compute_pbcminmax, measure_energy, measure_geom, measure_pbc2onc, measure_pbc_neighbors, tcl_get_weights, vmd_measure_cluster, vmd_measure_clustsize, vmd_measure_fit, vmd_measure_inertia, vmd_measure_pbc_neighbors, vmd_measure_symmetry, vmd_measure_trans_overlap, vmd_volmap_ils, and vmd_volmap_new_fromtype.

#define MEASURE_ERR_NONNUMBERPARM   -8
 

Definition at line 39 of file Measure.h.

Referenced by tcl_get_orders, and tcl_get_weights.

#define MEASURE_ERR_NONZEROJACOBI   -12
 

Definition at line 43 of file Measure.h.

Referenced by measure_fit, and measure_inertia.

#define MEASURE_ERR_NORADII   -14
 

Definition at line 45 of file Measure.h.

Referenced by VolMapCreate::calculate_max_radius, VolMapCreateCoulombPotentialMSM::compute_frame, VolMapCreateCoulombPotential::compute_frame, VolMapCreateDistance::compute_frame, VolMapCreateOccupancy::compute_frame, VolMapCreateDensity::compute_frame, and measure_sasa.

#define MEASURE_ERR_NORGYR   -4
 

Definition at line 35 of file Measure.h.

Referenced by measure_rgyr.

#define MEASURE_ERR_NOSEL   -1
 

Definition at line 29 of file Measure.h.

Referenced by VolMapCreate::compute_init, Symmetry::guess, measure_avpos, measure_center, measure_center_perresidue, measure_dipole, measure_gofr, measure_inertia, measure_minmax, measure_move, measure_rdf, measure_rgyr, measure_rmsd, measure_rmsd_perresidue, measure_rmsd_qcp, measure_rmsdmat_qcp, measure_rmsdmat_qcp_ooc, measure_rmsf, measure_rmsf_perresidue, measure_sasa, measure_sasalist, measure_sumweights, measure_surface, measure_trans_overlap, tcl_get_orders, and tcl_get_weights.

#define MEASURE_ERR_NOTSUP   -16
 

Definition at line 47 of file Measure.h.

Referenced by measure_fit.

#define MEASURE_ERR_NOWEIGHT   -4
 

Definition at line 32 of file Measure.h.

Referenced by VolMapCreateInterp::compute_frame, VolMapCreateDensity::compute_frame, measure_center, measure_center_perresidue, measure_rmsd, measure_rmsd_perresidue, measure_rmsd_qcp, and measure_sumweights.

#define MEASURE_ERR_REPEATEDATOM   -19
 

Definition at line 50 of file Measure.h.

Referenced by measure_energy, and measure_geom.

#define MEASURE_ERR_RGYRMISMATCH   -10
 

Definition at line 41 of file Measure.h.

#define MEASURE_ERR_ZEROGRIDSIZE   -23
 

Definition at line 54 of file Measure.h.

Referenced by VolMapCreate::compute_init.

#define MEASURE_IMPRP   5
 

Definition at line 59 of file Measure.h.

Referenced by measure_energy, and vmd_measure_energy.

#define MEASURE_NOERR   0
 

Definition at line 28 of file Measure.h.

Referenced by atomselect_move, calculate_angle, calculate_bond, calculate_dihed, VolMapCreate::calculate_minmax, check_mol, compute_angle_energy, compute_bond_energy, compute_dihed_energy, compute_elect_energy, VolMapCreateDistance::compute_frame, compute_imprp_energy, compute_pbcminmax, compute_vdw_energy, find_cluster_thr, Symmetry::guess, measure_avpos, measure_avpos_perresidue, measure_center, measure_cluster, measure_clustsize, measure_dipole, measure_energy, measure_fit, measure_geom, measure_gofr, measure_gofr_orth, measure_inertia, measure_minmax, measure_move, measure_pbc2onc, measure_pbc_neighbors, measure_pointset_overlap, measure_rdf, measure_rgyr, measure_rmsd, measure_rmsd_qcp, measure_rmsdmat_qcp, measure_rmsdmat_qcp_ooc, measure_rmsf, measure_sasa, measure_sumweights, measure_surface, measure_trans_overlap, normal_atom_coord, tcl_get_orders, tcl_get_weights, vmd_measure_cluster, vmd_measure_clustsize, vmd_measure_gofr, and vmd_measure_rdf.

#define MEASURE_VDW   6
 

Definition at line 60 of file Measure.h.

Referenced by measure_energy, and vmd_measure_energy.


Enumeration Type Documentation

anonymous enum
 

Enumeration values:
MEASURE_DIST_RMSD 
MEASURE_DIST_FITRMSD 
MEASURE_DIST_RGYRD 
MEASURE_DIST_CUSTOM 
MEASURE_NUM_DIST 

Definition at line 64 of file Measure.h.


Function Documentation

int calculate_angle MoleculeList   mlist,
int *    molid,
int *    atmid,
float *    value
 

Definition at line 2442 of file Measure.C.

Referenced by compute_angle_energy, and measure_geom.

int calculate_bond MoleculeList   mlist,
int *    molid,
int *    atmid,
float *    value
 

Definition at line 2425 of file Measure.C.

Referenced by compute_angle_energy, compute_bond_energy, compute_elect_energy, compute_vdw_energy, and measure_geom.

int calculate_dihed MoleculeList   mlist,
int *    molid,
int *    atmid,
float *    value
 

Definition at line 2462 of file Measure.C.

Referenced by compute_dihed_energy, compute_imprp_energy, and measure_geom.

int check_mol Molecule   mol,
int    a
 

Definition at line 2513 of file Measure.C.

Referenced by normal_atom_coord.

int compute_angle_energy MoleculeList   mlist,
int *    molid,
int *    atmid,
float *    energy,
float    k,
float    x0,
float    kub,
float    s0
 

Definition at line 2616 of file Measure.C.

Referenced by measure_energy.

int compute_bond_energy MoleculeList   mlist,
int *    molid,
int *    atmid,
float *    energy,
float    k,
float    x0
 

Definition at line 2602 of file Measure.C.

Referenced by measure_energy.

int compute_dihed_energy MoleculeList   mlist,
int *    molid,
int *    atmid,
float *    energy,
float    k,
int    n,
float    delta
 

Definition at line 2642 of file Measure.C.

Referenced by measure_energy.

int compute_elect_energy MoleculeList   mlist,
int *    molid,
int *    atmid,
float *    energy,
float    q1,
float    q2,
bool    flag1,
bool    flag2,
float    cutoff
 

Definition at line 2704 of file Measure.C.

Referenced by measure_energy.

int compute_imprp_energy MoleculeList   mlist,
int *    molid,
int *    atmid,
float *    energy,
float    k,
float    x0
 

Definition at line 2656 of file Measure.C.

Referenced by measure_energy.

int compute_pbcminmax MoleculeList   mlist,
int    molid,
int    frame,
const float *    center,
const Matrix4   transform,
float *    min,
float *    max
 

Definition at line 652 of file MeasurePBC.C.

int compute_vdw_energy MoleculeList   mlist,
int *    molid,
int *    atmid,
float *    energy,
float    rmin1,
float    eps1,
float    rmin2,
float    eps2,
float    cutoff,
float    switchdist
 

Definition at line 2674 of file Measure.C.

Referenced by measure_energy.

int FastCalcRMSDAndRotation double *    rot,
double *    A,
float *    rmsd,
double    E0,
int    len,
double    minScore
 

Definition at line 1432 of file MeasureQCP.C.

void get_transform_to_orthonormal_cell const float *    cell,
const float    center[3],
Matrix4   transform
 

int measure_avpos const AtomSel   sel,
MoleculeList   mlist,
int    start,
int    end,
int    step,
float *    avpos
 

Definition at line 419 of file Measure.C.

Referenced by measure_avpos_perresidue, measure_rmsf, and vmd_measure_avpos.

int measure_center const AtomSel   sel,
const float *    framepos,
const float *    weight,
float *    com
 

Definition at line 196 of file Measure.C.

Referenced by center, cluster_get_rgyrd, fit, fpbc_exec_wrapatomic_cpu, fpbc_exec_wrapcompound_cpu, measure_fit, measure_rgyr, and vmd_measure_center.

int measure_center_perresidue MoleculeList   mlist,
const AtomSel   sel,
const float *    framepos,
const float *    weight,
float *    com
 

Definition at line 154 of file Measure.C.

References num.

Referenced by centerperresidue, measure_rmsf_perresidue, and vmd_measure_centerperresidue.

int measure_cluster AtomSel   sel,
MoleculeList   mlist,
const int    numcluster,
const int    algorithm,
const int    likeness,
const double    cutoff,
int *    clustersize,
int **    clusterlist,
int    first,
int    last,
int    step,
int    selupdate,
float *    weights
 

Definition at line 738 of file MeasureCluster.C.

int measure_clustsize const AtomSel   sel,
MoleculeList   mlist,
const double    cutoff,
int *    clustersize,
int *    clusternum,
int *    clusteridx,
int    minsize,
int    numshared,
int    usepbc
 

Definition at line 919 of file MeasureCluster.C.

int measure_dipole const AtomSel   sel,
MoleculeList   mlist,
float *    dipole,
int    unitsdebye,
int    usecenter
 

Definition at line 462 of file Measure.C.

Referenced by vmd_measure_dipole.

int measure_energy MoleculeList   mlist,
int *    molid,
int *    atmid,
int    natoms,
ResizeArray< float > *    gValues,
int    frame,
int    first,
int    last,
int    defmolid,
double *    params,
int    geomtype
 

Definition at line 2524 of file Measure.C.

Referenced by vmd_measure_energy.

const char* measure_error int    errnum
 

Definition at line 65 of file Measure.C.

References MEASURE_DIST_CUSTOM, MEASURE_DIST_FITRMSD, MEASURE_DIST_RGYRD, and MEASURE_NUM_DIST.

Referenced by atomselect_move, center, centerperresidue, fpbc_recenter, fpbc_wrap, minmax, py_fit, py_measure_angle, py_measure_bond, py_measure_dihed, py_move, py_rgyr, py_rmsd, py_rmsd_q, py_rmsdmat_q, py_rmsdperresidue, py_rmsf, py_rmsfperresidue, sasa, vmd_measure_angle, vmd_measure_avpos, vmd_measure_bond, vmd_measure_center, vmd_measure_centerperresidue, vmd_measure_dihed, vmd_measure_dipole, vmd_measure_energy, vmd_measure_fit, vmd_measure_inertia, vmd_measure_minmax, vmd_measure_pbc2onc_transform, vmd_measure_pbc_neighbors, vmd_measure_rgyr, vmd_measure_rmsd, vmd_measure_rmsd_qcp, vmd_measure_rmsdmat_qcp, vmd_measure_rmsdmat_qcp_ooc, vmd_measure_rmsdperresidue, vmd_measure_rmsf, vmd_measure_rmsfperresidue, vmd_measure_sasa, vmd_measure_sasalist, vmd_measure_sumweights, vmd_measure_surface, vmd_measure_symmetry, vmd_measure_trans_overlap, vmd_volmap_ils, and vmd_volmap_new_fromtype.

int measure_fit const AtomSel   sel1,
const AtomSel   sel2,
const float *    x,
const float *    y,
const float *    weight,
const int *    order,
Matrix4   mat
 

Definition at line 1128 of file Measure.C.

Referenced by py_fit, and vmd_measure_fit.

int measure_geom MoleculeList   mlist,
int *    molid,
int *    atmid,
ResizeArray< float > *    gValues,
int    frame,
int    first,
int    last,
int    defmolid,
int    geomtype
 

Definition at line 2361 of file Measure.C.

Referenced by py_measure_angle, py_measure_bond, py_measure_dihed, vmd_measure_angle, vmd_measure_bond, and vmd_measure_dihed.

int measure_gofr AtomSel   sel1,
AtomSel   sel2,
MoleculeList   mlist,
const int    count_h,
double *    gofr,
double *    numint,
double *    histog,
const float    delta,
int    first,
int    last,
int    step,
int *    framecntr,
int    usepbc,
int    selupdate
 

Definition at line 2005 of file Measure.C.

Referenced by vmd_measure_gofr.

int measure_hbonds Molecule   mol,
AtomSel   sel1,
AtomSel   sel2,
double    cut,
double    maxangle,
int *    donlist,
int *    hydlist,
int *    acclist,
int    maxsize
 

Definition at line 557 of file Measure.C.

Referenced by py_hbonds, and vmd_measure_hbonds.

int measure_inertia AtomSel   sel,
MoleculeList   mlist,
const float *    coor,
float    rcom[3],
float    priaxes[3][3],
float    itensor[4][4],
float    evalue[3]
 

Definition at line 2775 of file Measure.C.

Referenced by Symmetry::impose, and vmd_measure_inertia.

int measure_minmax int    num,
const int *    on,
const float *    framepos,
const float *    radii,
float *    min_coord,
float *    max_coord
 

Definition at line 281 of file Measure.C.

Referenced by VolMapCreate::calculate_minmax, measure_surface, minmax, and vmd_measure_minmax.

int measure_move const AtomSel   sel,
float *    framepos,
const Matrix4   mat
 

Definition at line 71 of file Measure.C.

References mat.

Referenced by atomselect_move, move, and py_move.

int measure_pbc2onc MoleculeList   mlist,
int    molid,
int    frame,
const float *    center,
Matrix4   transform
 

int measure_pbc_neighbors MoleculeList   mlist,
AtomSel   sel,
int    molid,
int    frame,
const Matrix4   alignment,
const float *    center,
const float *    cutoff,
const float *    box,
ResizeArray< float > *    extcoord_array,
ResizeArray< int > *    indexmap_array
 

Definition at line 228 of file MeasurePBC.C.

References n.

int measure_rdf VMDApp   app,
AtomSel   sel1,
AtomSel   sel2,
MoleculeList   mlist,
const int    count_h,
double *    gofr,
double *    numint,
double *    histog,
const float    delta,
int    first,
int    last,
int    step,
int *    framecntr,
int    usepbc,
int    selupdate
 

Definition at line 131 of file MeasureRDF.C.

References num.

int measure_rgyr const AtomSel   sel,
MoleculeList   mlist,
const float *    weight,
float *    rgyr
 

measure the radius of gyration, including the given weights.

Definition at line 737 of file Measure.C.

Referenced by py_rgyr, and vmd_measure_rgyr.

int measure_rmsd const AtomSel   sel1,
const AtomSel   sel2,
int    num,
const float *    f1,
const float *    f2,
float *    weight,
float *    rmsd
 

measure the rmsd given a selection and weight term.

Definition at line 866 of file Measure.C.

Referenced by cluster_get_rmsd, py_rmsd, and vmd_measure_rmsd.

int measure_rmsd_perresidue const AtomSel   sel1,
const AtomSel   sel2,
MoleculeList   mlist,
int    num,
float *    weight,
float *    rmsd
 

Definition at line 780 of file Measure.C.

Referenced by py_rmsdperresidue, and vmd_measure_rmsdperresidue.

int measure_rmsd_qcp VMDApp   app,
const AtomSel   sel1,
const AtomSel   sel2,
int    num,
const float *    f1,
const float *    f2,
float *    weight,
float *    rmsd
 

Definition at line 846 of file MeasureQCP.C.

int measure_rmsdmat_qcp VMDApp   app,
const AtomSel   sel,
MoleculeList   mlist,
int    num,
float *    weight,
int    start,
int    end,
int    step,
float *    rmsd
 

Definition at line 1068 of file MeasureQCP.C.

int measure_rmsdmat_qcp_ooc VMDApp   app,
const AtomSel   sel,
MoleculeList   mlist,
int    nfiles,
const char **    trjfileset,
int    num,
float *    weight,
int    start,
int    end,
int    step,
int &    framecount,
float *&    rmsd
 

Definition at line 1249 of file MeasureQCP.C.

int measure_rmsf const AtomSel   sel,
MoleculeList   mlist,
int    start,
int    end,
int    step,
float *    rmsf
 

Definition at line 682 of file Measure.C.

Referenced by py_rmsf, and vmd_measure_rmsf.

int measure_rmsf_perresidue const AtomSel   sel,
MoleculeList   mlist,
int    start,
int    end,
int    step,
float *    rmsf
 

Definition at line 626 of file Measure.C.

Referenced by py_rmsfperresidue, and vmd_measure_rmsfperresidue.

int measure_sasa const AtomSel   sel,
const float *    framepos,
const float *    radius,
float    srad,
float *    sasa,
ResizeArray< float > *    pts,
const AtomSel   restrictsel,
const int *    nsamples
 

Definition at line 1415 of file Measure.C.

Referenced by sasa, and vmd_measure_sasa.

int measure_sasalist MoleculeList   mlist,
const AtomSel **    sellist,
int    numsels,
float    srad,
float *    sasalist,
const int *    nsamples
 

Definition at line 1687 of file Measure.C.

Referenced by vmd_measure_sasalist.

int measure_sumweights const AtomSel   sel,
int    numweights,
const float *    weights,
float *    weightsum
 

Definition at line 123 of file Measure.C.

References num.

Referenced by vmd_measure_sumweights.

int measure_surface AtomSel   sel,
MoleculeList   mlist,
const float *    framepos,
const double    gridsz,
const double    radius,
const double    sel_dist,
int **    surface,
int *    n_surf
 

Definition at line 1481 of file MeasureSurface.C.

int normal_atom_coord Molecule   m,
int    a,
float *    pos
 

Definition at line 2484 of file Measure.C.

Referenced by calculate_angle, calculate_bond, and calculate_dihed.


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