SSAGES::ReadBackbone Class Reference

Utility class to read protein backbone atoms from a reference file. More...

#include <ReadBackbone.h>

Static Public Member Functions
static std::vector< std::vector< std::string > >	GetPdbBackbone (std::string refpdb, std::vector< int > resids)
	Read protein backbone atoms from reference PDB file. More...

Detailed Description

Utility class to read protein backbone atoms from a reference file.

This utility class allows for the backbone atoms along a protein segment to be extracted from a reference file (most likely in a .pdb).

Supported filetypes:

• PDB

Definition at line 42 of file ReadBackbone.h.

Member Function Documentation

GetPdbBackbone()

static std::vector< std::vector< std::string> > SSAGES::ReadBackbone::GetPdbBackbone ( std::string  refpdb, std::vector< int >  resids  )

inlinestatic

Read protein backbone atoms from reference PDB file.

Parameters

refpdb	Name of reference PDB file.
resids	Vector of residue numbers for which to find backbone atoms.

Returns

atomids Vector of atom numbers corresponding to specified residues.

Extract backbone atom from a reference PDB file, corresponding to a sequence of protein residues of interest. Five backbone atoms are extracted for each residue in the order: N CA CB C O. For Glycine residues, HA1 is located in place of CB.

Definition at line 57 of file ReadBackbone.h.

        {
            //std::vector<int> atomids;
            std::vector< std::vector< std::string > > atomids(2, std::vector<std::string> (0));
            //std::vector<int> atomnums;
            std::vector<std::string> atomnums;
            std::vector<std::string> atomtypes;
            std::vector<std::string> resnames;
            std::vector<std::string> chains;
            std::vector<int> resnums;
            //std::vector<int> tempatoms(5);
            std::vector<std::string> tempatoms(5);
            std::vector<std::string> backboneAtoms = {"N", "CA", "CB", "C", "O", "OT1"};
            std::vector<std::string> glycineAtoms = {"N", "CA", "HA1", "C", "O", "OT1"};
            std::string atomnum, resnum;
            std::string record, atomtype, resname, chain;
            std::ifstream pdbfile;
            pdbfile.open(refpdb, std::ios::in);
            std::string line;
 
            while(std::getline(pdbfile, line)){
                if(line.length() < 26) line.append(26 - line.length(), ' ');
                record = line.substr(0, 6);
                atomnum = line.substr(6, 5);
                atomtype = line.substr(12, 4);
                resname = line.substr(17, 3);
                chain = line.substr(21, 1);
                resnum = line.substr(22, 4);
                record.erase( std::remove( record.begin(), record.end(), ' '), record.end());
                if((record == "ATOM") && ((std::stoi(resnum) - resids[0]) <= (resids.back() - resids[0]))){
                    atomtype.erase( std::remove( atomtype.begin(), atomtype.end(), ' '), atomtype.end());
                    resname.erase( std::remove( resname.begin(), resname.end(), ' '), resname.end());
                    if(resname == "GLY" && std::find(glycineAtoms.begin(), glycineAtoms.end(), atomtype) != glycineAtoms.end()){
                        //atomnums.push_back(std::stoi(atomnum));
                        atomnums.push_back(atomnum);
                        atomtypes.push_back(atomtype);
                        resnames.push_back(resname);
                        chains.push_back(chain);
                        resnums.push_back(std::stoi(resnum));
                    } else if(std::find(backboneAtoms.begin(), backboneAtoms.end(), atomtype) != backboneAtoms.end()){
                        //atomnums.push_back(std::stoi(atomnum));
                        atomnums.push_back(atomnum);
                        atomtypes.push_back(atomtype);
                        resnames.push_back(resname);
                        chains.push_back(chain);
                        resnums.push_back(std::stoi(resnum));
                    }
                }
            }
 
            // atoms in PDB not necessarily in N CA CB C O order, fix that:
            for(size_t i = 0; i < resids.size(); i++){
                for(size_t j = 5 * i; j < (5 * i + 5); j++){
                    if(atomtypes[j] == "N"){
                        tempatoms[0] = atomnums[j]; 
                        std::cout << "N  - Atom " << tempatoms[0] << " - Chain " << chains[j] << std::endl;
                    } else if(atomtypes[j] == "CA"){
                        tempatoms[1] = atomnums[j]; 
                        std::cout << "CA - Atom " << tempatoms[1] << " - Chain " << chains[j] << std::endl;
                    } else if(atomtypes[j] == "C"){
                        tempatoms[3] = atomnums[j]; 
                        std::cout << "C  - Atom " << tempatoms[3] << " - Chain " << chains[j] << std::endl;
                    } else if(atomtypes[j] == "O"){
                        tempatoms[4] = atomnums[j]; 
                        std::cout << "O  - Atom " << tempatoms[4] << " - Chain " << chains[j] << std::endl;
                    } else if(atomtypes[j] == "OT1"){
                        tempatoms[4] = atomnums[j];
                        std::cout << "OT1- Atom " << tempatoms[4] << " - Chain " << chains[j] << std::endl;
                    } else{
                        tempatoms[2] = atomnums[j]; 
                        std::cout << atomtypes[j] << " - Atom " << tempatoms[2] << " - Chain " << chains[j] << std::endl;
                    }
                    atomids[1].push_back(chains[j]);
                }
                //atomids.insert(atomids.end(), tempatoms.begin(), tempatoms.end());
                atomids[0].insert(atomids[0].end(), tempatoms.begin(), tempatoms.end());
            }
 
            return atomids;
        }

Referenced by SSAGES::AlphaRMSDCV::Initialize(), SSAGES::AntiBetaRMSDCV::Initialize(), and SSAGES::ParallelBetaRMSDCV::Initialize().

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The documentation for this class was generated from the following file:

• /home/michael/development/SSAGES/src/Utility/ReadBackbone.h