蛋白质PDB文件读取C++代码

柔情只为你懂 2022-10-01 00:47 165阅读 0赞

在生物信息学中，PDB数据库是非常重要的蛋白质结构数据库。PDB数据文件的读取是进行蛋白质结构相关预测的重要步骤！下面给出了简单的PDB文件读取的C++代码，以供参考：

#include <stdio.h>
    #include <stdlib.h>
    #include <math.h>
    #include <string.h>
    #include <sstream>
    #include <iostream>
    #include <fstream>
    #include <vector>
    using namespace std;
    
    class Residue {
    public:
    	vector<double*> atomxyzs;
    	vector<string> atominfos;	// each element for example : "ATOM      1  N   GLU    98    "
    	int caind;
    	int cbind;
    	int res_pos;
    	int orig_res_pos;
    
    	Residue(vector<double*> _atomxyzs, vector<string> _atominfos, int _caind, int _cbind, int _res_pos, int _orig_res_pos){
    		atomxyzs = _atomxyzs;
    		atominfos = _atominfos;
    		caind = _caind;
    		cbind = _cbind;
    		res_pos = _res_pos;
    		orig_res_pos = _orig_res_pos;
    	}
    };
    
    class Protein{
    private:
    	string pdbpath;				// in
    	vector<Residue> residues;	// out
    
    public:
    	Protein(string _pdbpath){
    		pdbpath = _pdbpath;
    
    		readPDB();
    	}
    
    	int size(){
    		return residues.size();
    	}
    
    	Residue getIthResidue(int i){
    		return residues[i];
    	}
    
    	int getIthResidueOriginalIndexInProt(int i){
    		return residues[i].orig_res_pos;
    	}
    
    	double* getIthResidueCAXYZ(int i){
    		return residues[i].atomxyzs[residues[i].caind];
    	}
    
    	double* getIthResidueCBXYZ(int i){
    		return residues[i].atomxyzs[residues[i].cbind];
    	}
    
    	vector<Residue> getResidues(){
    		return residues;
    	}
    
    	void save(vector<Residue> _residues, string savepath){
    		ofstream fout(savepath);
    		for (int i = 0; i < _residues.size(); i++){
    			Residue res = _residues[i];
    			for (int j = 0 ; j < res.atominfos.size(); j++){
    				char temp[1000];
    
    				string atominfo = res.atominfos[j];	// "ATOM      1  N   GLU    98    "
    				double* xyz = res.atomxyzs[j];	//"  66.677"
    				char xstr[9];
    				char ystr[9];
    				char zstr[9];
    				sprintf(xstr, "%8.3f", xyz[0]);
    				sprintf(ystr, "%8.3f", xyz[1]);
    				sprintf(zstr, "%8.3f", xyz[2]);
    				string useless = "  1.00  0.00";
    				fout << atominfo << xstr << ystr << zstr << useless << endl;
    			}
    		}
    
    		fout.close();
    	}
    	
    	/*char* formatDouble(double v, int ch_num){
    		char tmp[64];
    		sprintf(tmp, "%8.3f %8.3f %8.3f\n", x[i][0], x[i][1], x[i][2]);
    	}*/
    
    private:
    	void readPDB(){
    		vector<int> atomindex;
    		vector<string> atominfos;
    		vector<double*> points;
    		int ca_pos_in_res = 0;
    		int cb_pos_in_res = 0;
    
    		int pre_index = -9999999;
    		ifstream fin(pdbpath);
    		string line;
    		getline(fin, line);
    		string lastline(line);
    		bool isFirstATOM = true;
    		bool isContainCA = false;
    		int tmp_pos = 0;
    		int res_pos = 1;
    		int atom_pos = 1;
    		while (fin.good()){
    			if (line.compare(0, 3, "TER")==0)
    				break;
    			if (line.compare(0, 4, "ATOM")==0){
    				char cstr[50];
    				double x = 0.0;
    				strcpy(cstr, (line.substr(30, 8)).c_str());
    				sscanf(cstr, "%lf", &x);
    
    				double y = 0.0;
    				strcpy(cstr, (line.substr(38, 8)).c_str());
    				sscanf(cstr, "%lf", &y);
    
    				double z = 0.0;
    				strcpy(cstr, (line.substr(46, 8)).c_str());
    				sscanf(cstr, "%lf", &z);
    
    				double* xyz = new double[3];
    				xyz[0] = x;
    				xyz[1] = y;
    				xyz[2] = z;
    
    				string atominfo = line.substr(0, 30);	
    				
    				int now_index = -999999;
    				strcpy(cstr, (line.substr(22, 4)).c_str());
    				sscanf(cstr, "%d", &now_index);
    
    				if (line.compare(13, 3, "CA ")==0){
    					isContainCA = true;
    					ca_pos_in_res = tmp_pos;
    
    					if (isFirstATOM){
    						pre_index = now_index;
    					}
    				}
    
    				if (line.compare(13, 3, "CB ")==0){
    					cb_pos_in_res = tmp_pos;
    				}
    
    				if (now_index != pre_index){
    					if (isContainCA){
    						if (pre_index != -9999999){
    							Residue tmpResidue(points, atominfos, ca_pos_in_res, cb_pos_in_res, res_pos, pre_index);
    							residues.push_back(tmpResidue);
    							res_pos++;
    						}
    						points.clear();
    						points.push_back(xyz);
    						atominfos.clear();
    						atominfos.push_back(atominfo);
    
    						tmp_pos = 0;
    						isContainCA = false;
    						if (line.compare(13, 3, "CA ")==0){
    							isContainCA = true;
    						}
    					}else{
    						if (isFirstATOM){
    							points.push_back(xyz);
    							atominfos.push_back(atominfo);
    						}
    					}
    					pre_index = now_index;
    				}else{
    					points.push_back(xyz);
    					atominfos.push_back(atominfo);
    				}
    
    				isFirstATOM = false;
    
    				tmp_pos++;
    			}
    
    			lastline = line;
    			getline(fin, line);
    		}
    
    		if (isContainCA || lastline.length() >= 16 || lastline.compare(13, 3, "CA ")==0){
    			Residue tmpResidue(points, atominfos, ca_pos_in_res, cb_pos_in_res, res_pos, pre_index);
    			residues.push_back(tmpResidue);
    		}
    		
    		fin.close();
    	}
    };