#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) |
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Definition at line 182 of file MeasureCluster.C. Referenced by normalize3d. |
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Definition at line 829 of file MeasureCluster.C. |
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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. |
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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. |
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Definition at line 381 of file MeasureCluster.C. References distance2, AtomSel::firstsel, AtomSel::lastsel, measure_center, and AtomSel::on. Referenced by find_cluster_thr. |
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Definition at line 371 of file MeasureCluster.C. References measure_rmsd, and AtomSel::num_atoms. Referenced by find_cluster_thr. |
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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. |
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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. |
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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. |
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Definition at line 199 of file MeasureCluster.C. References cc, n, normalize3d, and wt. Referenced by cluster_get_fitrmsd. |
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Definition at line 184 of file MeasureCluster.C. References R_SMALL. Referenced by MatrixFitRMS, and MyMatrixFitRMS. |