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MeasureCluster.C File Reference

#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include "Measure.h"
#include "AtomSel.h"
#include "utilities.h"
#include "ResizeArray.h"
#include "MoleculeList.h"
#include "Inform.h"
#include "Timestep.h"
#include "VMDApp.h"
#include "WKFThreads.h"
#include "WKFUtils.h"
#include "SpatialSearch.h"

Go to the source code of this file.

Compounds

class  AtomSelThr
struct  clusterparms_t

Defines

#define R_SMALL   0.000000001

Typedefs

typedef ResizeArray< int > intlist

Functions

void normalize3d (double *v)
float MyMatrixFitRMS (int n, float *v1, float *v2, const float *wt, const double tol)
float cluster_get_rmsd (const float *Frame1Pos, const float *Frame2Pos, AtomSel *sel, float *weights)
float cluster_get_rgyrd (const float *Frame1Pos, const float *Frame2Pos, AtomSel *sel, float *weights)
float cluster_get_fitrmsd (const float *Frame1Pos, const float *Frame2Pos, AtomSel *sel, float *weights, const double tol)
void * find_cluster_thr (void *voidparms)
int * find_next_cluster (Molecule *mymol, int *framesList, const int numframes, const int remframes, const int *skipList, int **newSkipList, const int likeness, AtomSel *sel, const int selupdate, const double cutoff, float *weights)
 find the next largest cluster for the selected range of time steps. More...

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)
void assemble_cluster (intlist &cluster_list, intlist &candidate_list, intlist **neighbor_grid, int atom, int numshared, int *idxmap)
int measure_clustsize (const AtomSel *sel, MoleculeList *mlist, const double cutoff, int *clustersize, int *clusternum, int *clusteridx, int minsize, int numshared, int usepbc)


Define Documentation

#define R_SMALL   0.000000001
 

Definition at line 182 of file MeasureCluster.C.

Referenced by normalize3d.


Typedef Documentation

typedef ResizeArray<int> intlist
 

Definition at line 829 of file MeasureCluster.C.


Function Documentation

void assemble_cluster intlist   cluster_list,
intlist   candidate_list,
intlist **    neighbor_grid,
int    atom,
int    numshared,
int *    idxmap
[static]
 

Definition at line 833 of file MeasureCluster.C.

References ResizeArray< int >::append, ResizeArray< int >::clear, ResizeArray< int >::find, and ResizeArray< int >::num.

Referenced by measure_clustsize.

float cluster_get_fitrmsd const float *    Frame1Pos,
const float *    Frame2Pos,
AtomSel   sel,
float *    weights,
const double    tol
[static]
 

Definition at line 425 of file MeasureCluster.C.

References AtomSel::firstsel, AtomSel::lastsel, MyMatrixFitRMS, num, AtomSel::on, AtomSel::selected, and wt.

Referenced by find_cluster_thr.

float cluster_get_rgyrd const float *    Frame1Pos,
const float *    Frame2Pos,
AtomSel   sel,
float *    weights
[static]
 

Definition at line 381 of file MeasureCluster.C.

References distance2, AtomSel::firstsel, AtomSel::lastsel, measure_center, and AtomSel::on.

Referenced by find_cluster_thr.

float cluster_get_rmsd const float *    Frame1Pos,
const float *    Frame2Pos,
AtomSel   sel,
float *    weights
[static]
 

Definition at line 371 of file MeasureCluster.C.

References measure_rmsd, and AtomSel::num_atoms.

Referenced by find_cluster_thr.

void* find_cluster_thr void *    voidparms
 

Definition at line 497 of file MeasureCluster.C.

References cluster_get_fitrmsd, cluster_get_rgyrd, cluster_get_rmsd, clusterparms_t::cutoff, clusterparms_t::frames_list, DrawMolecule::get_frame, clusterparms_t::iend, clusterparms_t::istart, clusterparms_t::likeness, clusterparms_t::max_cluster, clusterparms_t::max_cluster_size, MEASURE_DIST_FITRMSD, MEASURE_DIST_RGYRD, MEASURE_DIST_RMSD, MEASURE_NOERR, clusterparms_t::mol, clusterparms_t::new_skip_list, clusterparms_t::numframes, Timestep::pos, clusterparms_t::sel, clusterparms_t::selupdate, clusterparms_t::skip_list, AtomSelThr::update, and clusterparms_t::weights.

Referenced by find_next_cluster.

int* find_next_cluster Molecule   mymol,
int *    framesList,
const int    numframes,
const int    remframes,
const int *    skipList,
int **    newSkipList,
const int    likeness,
AtomSel   sel,
const int    selupdate,
const double    cutoff,
float *    weights
[static]
 

find the next largest cluster for the selected range of time steps.

Definition at line 612 of file MeasureCluster.C.

References DrawMolecule::app, clusterparms_t::cutoff, find_cluster_thr, clusterparms_t::frames_list, clusterparms_t::iend, clusterparms_t::istart, clusterparms_t::likeness, clusterparms_t::max_cluster, clusterparms_t::max_cluster_size, clusterparms_t::mol, clusterparms_t::new_skip_list, NULL, clusterparms_t::numframes, clusterparms_t::sel, clusterparms_t::selupdate, clusterparms_t::skip_list, clusterparms_t::threadcount, clusterparms_t::threadid, clusterparms_t::weights, wkf_mutex_destroy, wkf_mutex_init, wkf_mutex_t, wkf_thread_create, wkf_thread_join, wkf_thread_numprocessors, and wkf_thread_t.

Referenced by measure_cluster.

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.

References find_next_cluster, MEASURE_ERR_BADFRAMERANGE, MEASURE_NOERR, MoleculeList::mol_from_id, AtomSel::molid, n, DrawMolecule::numframes, wkf_msg_timer_create, wkf_msg_timer_destroy, and wkf_msg_timer_timeout.

Referenced by vmd_measure_cluster.

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.

References assemble_cluster, AtomSel::coordinates, AtomSel::firstsel, GridSearchPair::ind1, GridSearchPair::ind2, AtomSel::lastsel, MEASURE_NOERR, GridSearchPair::next, NULL, ResizeArray< int >::num, AtomSel::num_atoms, AtomSel::on, AtomSel::selected, and vmd_gridsearch1.

Referenced by vmd_measure_clustsize.

float MyMatrixFitRMS int    n,
float *    v1,
float *    v2,
const float *    wt,
const double    tol
[static]
 

Definition at line 199 of file MeasureCluster.C.

References cc, n, normalize3d, and wt.

Referenced by cluster_get_fitrmsd.

void normalize3d double *    v [static]
 

Definition at line 184 of file MeasureCluster.C.

References R_SMALL.

Referenced by MatrixFitRMS, and MyMatrixFitRMS.


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