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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_sasa_perresidue (const AtomSel *sel, const float *framepos, const float *radius, float srad, float *sasa, ResizeArray< float > *sasapts, const AtomSel *restrictsel, const int *nsamples, int *rescount, MoleculeList *mlist)

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, measure_sasa, and measure_sasa_perresidue.

#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, measure_sasa, and measure_sasa_perresidue.

#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, measure_sasa, and measure_sasa_perresidue.

#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_sasa_perresidue, 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_sasa_perresidue, 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 2583 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 2566 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 2603 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 2654 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 2757 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 2743 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 2783 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 2845 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 2797 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 2815 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 2665 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, sasa_perresidue, 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_sasaperresidue, 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 2502 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 2146 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 2916 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 1556 of file Measure.C.
Referenced by sasa, and vmd_measure_sasa.

int measure_sasa_perresidue ( const AtomSel * sel,

const float * framepos,

const float * radius,

float srad,

float * sasa,

ResizeArray< float > * sasapts,

const AtomSel * restrictsel,

const int * nsamples,

int * rescount,

MoleculeList * mlist

)

Definition at line 1416 of file Measure.C.
Referenced by sasa_perresidue, and vmd_measure_sasaperresidue.

int measure_sasalist ( MoleculeList * mlist,

const AtomSel ** sellist,

int numsels,

float srad,

float * sasalist,

const int * nsamples

)

Definition at line 1828 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 2625 of file Measure.C.
Referenced by calculate_angle, calculate_bond, and calculate_dihed.

Generated on Mon Feb 10 02:45:30 2025 for VMD (current) by

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_sasa_perresidue (const AtomSel sel, const float framepos, const float radius, float srad, float sasa, ResizeArray< float > sasapts, const AtomSel restrictsel, const int nsamples, int rescount, MoleculeList *mlist)
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])