pointarray.h

Go to the documentation of this file.

/*
 * Author: Wen Jiang, 08/11/2004 (jiang12@purdue.edu)
 * Copyright (c) 2000-2006 Baylor College of Medicine
 *
 * This software is issued under a joint BSD/GNU license. You may use the
 * source code in this file under either license. However, note that the
 * complete EMAN2 and SPARX software packages have some GPL dependencies,
 * so you are responsible for compliance with the licenses of these packages
 * if you opt to use BSD licensing. The warranty disclaimer below holds
 * in either instance.
 *
 * This complete copyright notice must be included in any revised version of the
 * source code. Additional authorship citations may be added, but existing
 * author citations must be preserved.
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 *
 * */
 
#ifndef eman_pointarray_h_
#define eman_pointarray_h_
 
#include "emdata.h"
#include "transform.h"
 
#if defined USE_NFFT || USE_NFFT2
extern "C"
{
        #include "nfft.h"
        #include "utils.h"
}
#endif
 
#include <sys/stat.h>
 
namespace EMAN
{
        class PointArray
        {
                public:
                enum Density2PointsArrayAlgorithm
                {
                        PEAKS_SUB, PEAKS_DIV, KMEANS
                };
 
                public:
                PointArray();
                explicit PointArray(int nn);
                ~PointArray();
                void zero();
                PointArray *copy();
                PointArray & operator=(PointArray & pa);
                size_t get_number_points() const;
                void set_number_points(size_t nn);
                bool read_from_pdb(const char *file, const vector<int> &lines=vector<int>());
                void save_to_pdb(const char *file);
                FloatPoint get_center();
                void center_to_zero();  // shift center to zero
                Region get_bounding_box();
                double *get_points_array();
                Vec3f get_vector_at(int i);     // get the ith vector in the list
                double get_value_at(int i);  // get the amplitude of the ith vector
                void set_vector_at(int i,Vec3f vec,double value);
                void set_vector_at(int i,vector<double>);
                void set_points_array(double *p);
                vector<float> get_points();
 
                EMData *distmx(int sortrows=0); // computes a distance matrix
 
                vector<int> match_points(PointArray *to,float max_miss=-1.0);
 
 
                Transform *align_2d(PointArray *to,float max_dist);     // computes the optimal alignment between two (non-identical) sets of points
 
                void mask(double rmax, double rmin = 0.0);
                void mask_asymmetric_unit(const string & sym);
                void transform(const Transform& transform);
 
                void right_transform(const Transform& transform);
 
                void set_from(vector<float>);
                void set_from(PointArray * source, const string & sym = "", Transform *transform=0);
                void set_from(double *source, int num, const string & sym = "", Transform *transform=0);
                void set_from_density_map(EMData * map, int num, float thresh, float apix,
                                                                  Density2PointsArrayAlgorithm mode = PEAKS_DIV);
                void sort_by_axis(int axis = 1);        // x,y,z axes = 0, 1, 2
                EMData *pdb2mrc_by_nfft(int map_size, float apix, float res);   // return real space 3-D map
                EMData *pdb2mrc_by_summation(int map_size, float apix, float res, int addpdbbfactor);   // return real space 3-D map
                EMData *projection_by_nfft(int image_size, float apix, float res = 0);  // return 2-D Fourier Transform
                EMData *projection_by_summation(int image_size, float apix, float res); // return 2-D real space image
                void replace_by_summation(EMData *image, int i, Vec3f vec, float amp, float apix, float res); // changes a single Gaussian from the projection
 
                void opt_from_proj(const vector<EMData*> & proj,float pixres);
 
                inline double sim_pointpotential(double dist, double ang, double dihed) {
                        return pow(dist-dist0,2.0)*distc+ang*ang*angc+pow(dihed-dihed0,2.0)*dihedc;
                }
 
                double sim_potential();
                
                double sim_potentiald(int ind);
 
                double sim_potentialdxyz(int i,double dx, double dy, double dz);
                
                void sim_updategeom();
 
                Vec3f sim_descent(int i);
                
                void sim_minstep(double maxshift);
 
                void sim_minstep_seq(double meanshift);
 
                void sim_rescale();
                
                void sim_printstat();
                
                void sim_set_pot_parms(double pdist0,double pdistc,double pangc, double pdihed0, double pdihedc, double pmapc, EMData *pmap,double pmindistc,double pdistpenc);
                
                void sim_add_point_double();
                void sim_add_point_one();
                
                double calc_total_length();
                
                vector<double> fit_helix(EMData *pmap,int minlength,float mindensity,vector<int> edge,int twodir,size_t minl);
                
                vector<float> do_pca(int start, int end);
                
                vector<float> do_filter(vector<float> pts, float *ft, int num);
                
                vector<double> construct_helix(int start,int end,float phs, float &score,int &dir);
                
                void reverse_chain();
                
                void merge_to(PointArray &pa, float thr);
                
                float calc_helicity(vector<double> pts);
                
                void save_pdb_with_helix(const char *file, vector<float> hlxid);
                
                void delete_point(int id);
                
                void remove_helix_from_map(EMData *m, vector<float> hlxid);
                
                bool read_ca_from_pdb(const char *file);
                
                Transform calc_transform(PointArray *p);
                
                private:
                double *points;
                size_t n;
                double *bfactor;
                
                // These are used internally for the simple dynamics/minimization code, and are otherwise unallocated
                // Note that this is NOT for PDB MD, just for simplified point-chains, and mapping points into density
                double *adist;  // distance squared between the numbered point and the previous point with wrap-around
                double *aang;   // angle at the numbered point using the point before and the point after
                double *adihed; // dihedral using 2 points before and one point after
                
                double dist0, distc, angc, dihed0, dihedc, mapc, apix, mindistc, distpenc;
                bool map2d; // map is 2d
                EMData *map;
                EMData *gradx, *grady, *gradz;
                vector<Vec3f> oldshifts;
                int centx, centy, centz;
        };
}
 
#endif