操作pdb文件的类C++版

Nov 25	操作pdb文件的类C++版
	Categories: BIO, C/C++ \| Tags: C/C++ \| Views: 816

有时候总需要对一些pdb文件进行操作，特别是读数据，所以就写了这个库文件但是这个只是个比较粗略的，一时也不能补得很全，只是仅仅对ATOM的行进行了操作并进行了归类，其他的行暂时还没有进行操作，这些等到实际用到时，再进行补充吧另外，关于atom_id和chain_id发现有些不是整型，因为在x-ray或者mnr测结构时无法确定而加的abcd之类的也没有考虑在内，如果要考虑这个的话，我想是否可以用map将id与整个原子的信息对应起来。代码

#ifndef _PDB_H_  
#define _PDB_H_ 
 
#include<iostream> 
#include<fstream> 
#include<cstdio> 
#include<string>  
#include<vector>  
 
#define atoms vector<atom>  
#define chains vector<chain>  
#define aint vector<atom>::size_type  
#define cint vector<chain>::size_type   
 
using namespace std;   
 
class atom{   
private:   
    short atom_id;   
    string atom_nick;   
    string atom_res;   
    char atom_chain;   
    short atom_res_id;   
    float atom_x, atom_y, atom_z, atom_w, atom_bfactor;   
    char atom_name;   
 
public:   
    atom(short, string, string, char, short, float, float, float, float, float, char);   
    atom(string);   
    string line();   
};   
 
atom::atom( short a_id,   
            string a_nick,   
            string r,   
            char c,   
            short r_id,   
            float a_x,   
            float a_y,   
            float a_z,   
            float a_w,   
            float b,   
            char a_name){   
    atom_id = a_id;   
    atom_nick = a_nick;   
    atom_res = r;   
    atom_chain = c;   
    atom_res_id = r_id;   
    atom_x = a_x;   
    atom_y = a_y;   
    atom_z = a_z;   
    atom_w = a_w;   
    atom_bfactor = b;   
    atom_name = a_name;   
}   
 
atom::atom(string l){   
    atom_id = atoi(l.substr(6,5).c_str());   
    atom_nick = l.substr(13,3);   
    atom_res = l.substr(17,3);   
    atom_chain = l[21];   
    atom_res_id = atoi(l.substr(22,4).c_str());   
    atom_x = atof(l.substr(30,8).c_str());   
    atom_y = atof(l.substr(38,8).c_str());   
    atom_z = atof(l.substr(46,8).c_str());   
    atom_w = atof(l.substr(54,6).c_str());   
    atom_bfactor = atof(l.substr(60,6).c_str());   
    atom_name = l.size()>77 ? l[77] : ' ';   
}   
 
string atom::line(){   
    char line[255];   
    (void)sprintf(  line,   
                    "ATOM  %5u  %-3s %-3s %c%4u    %8.3f%8.3f%8.3f%6.2f%6.2f           %c",   
                    atom_id,   
                    atom_nick.c_str(),   
                    atom_res.c_str(),   
                    atom_chain,   
                    atom_res_id,   
                    atom_x,   
                    atom_y,   
                    atom_z,   
                    atom_w,   
                    atom_bfactor,   
                    atom_name);   
    return string(line);   
}   
 
//===============================================   
class chain{   
private:   
    atoms chain_atms;   
    char chain_label;   
public:   
    chain(char);   
    void addAtom(atom);   
    void saveToFile(string);   
    aint size();   
    char label();   
    atom operator[](aint);   
};   
 
chain::chain(char l){ chain_label = l; }   
 
aint chain::size(){   
    return chain_atms.size();   
}   
 
atom chain::operator[](aint i){   
    if(i>=0 and i<chain_atms.size())   
        return chain_atms[i];   
}   
 
char chain::label(){   
    return chain_label;   
}   
 
void chain::addAtom(atom a){   
    chain_atms.push_back(a);   
    return;   
}   
 
void chain::saveToFile(string f){   
    ofstream in(f.c_str());   
    for(cint i=0; i<chain_atms.size(); i++){   
        in << chain_atms[i].line() << endl;   
    }   
    in << "TER" << endl;   
    in.close();   
    return;   
}   
 
//===============================================   
class pdb{   
private:   
    chains pdb_chns;   
 
public:   
    pdb(string);   
    cint size();   
    chain operator[](cint);   
};   
 
cint pdb::size(){   
    return pdb_chns.size();   
}   
 
chain pdb::operator[](cint i){   
    if(i>=0 and i<pdb_chns.size()) return pdb_chns[i];   
}   
 
pdb::pdb(string pdbfile){   
    string l;   
    char flag, chain_label;   
    ifstream out1(pdbfile.c_str());   
    while(getline(out1, l)){    //get the chain labels first   
        if(l.substr(0,4) == "ATOM"){   
            chain_label = l[21];   
            if(flag != chain_label){   
                chain chn(chain_label);   
                pdb_chns.push_back(chn);   
                flag = chain_label;   
            }   
        }   
    }   
    out1.close();   
    ifstream out2(pdbfile.c_str());   
    while(getline(out2, l)){   
        if(l.substr(0,4) == "ATOM"){   
            atom atm(l);   
            chain_label = l[21];   
            for(cint i=0; i<pdb_chns.size(); i++){   
                if(chain_label == pdb_chns[i].label())   
                    pdb_chns[i].addAtom(atm);   
            }   
        }   
    }   
    out2.close();   
}  
#endif