pdbreader.h

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/*
 * Author: Muthu Alagappan, 07/14/2009, (m.alagappan901@gmail.com)
 * 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_pdbreader_h_
#define eman_pdbreader_h_
 
#include "emdata.h"
#include "transform.h"
#include "pointarray.h"
 
#if defined USE_NFFT || USE_NFFT2
extern "C"
{
        #include "nfft.h"
        #include "utils.h"
}
#endif
 
#include <sys/stat.h>
#include <vector>
 
 
namespace EMAN
{
        class PDBReader
        {
                public:
                enum Density2PointsArrayAlgorithm
                {
                        PEAKS_SUB, PEAKS_DIV, KMEANS
                };
 
                public:
                PDBReader();
                explicit PDBReader(int nn);
                ~PDBReader();
                void zero();
                PDBReader *copy();
                PDBReader & operator=(PDBReader & pa);
                size_t get_number_points() const;
                void set_number_points(size_t nn);
 
                bool read_from_pdb(const char *file);
 
                void save_to_pdb(const char *file) const;
 
                double *get_points_array();
 
                void set_points_array(double *p);
 
                vector<float> get_points();
 
                void right_transform(const Transform& transform);
                PointArray* makePointArray (const PDBReader& p);
 
                vector<float> get_x();
                vector<float> get_y();
                vector<float> get_z();
                vector<string> get_atomName();
                vector<string> get_resName();
                vector<int> get_resNum();
                
 
                private:
                double *points;
                vector<int> pointInfo;
                vector<string> pWords;
                vector<string> atomName;
                vector<string> residueName;
                vector<string> chainId;
                vector<string> elementSym;
                vector<string> tail;
                vector<string> head;
                vector<string> lines;
                size_t n;
                int ter_stop;
                int count_stop;
 
                vector<float> x;
                vector<float> y;
                vector<float> z;
                vector<int> resNum;
        };
}
 
#endif