///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
void
sasio::Files::
read_pdb(const std::string &filename)
{
std::string line, word ;
std::string element_string ;
std::ifstream infile(filename) ;
int count = 0 ;
int frame = 0 ;
//string s(line, index, number_characters) ;
std::vector<float> vector_x;
std::vector<float> vector_y;
std::vector<float> vector_z;
while(getline(infile,line))
{
std::istringstream record(line) ;
record >> word ;
std::string temp1(word,0,5) ;
if(temp1 != "ATOM" && temp1 != "HETAT")
{
std::cout << "excluding: " << word << std::endl ;
}
else
{
std::string tmp(line,0,6) ;
_atom_record().push_back(tmp) ;
std::string tmp2(line,6,5) ;
_atom_index().push_back(stoi(tmp2)) ;
std::string tmp3(line,12,4) ;
_atom_name().push_back(tmp3) ;
std::string tmp4(line,16,1) ;
_atom_altloc().push_back(tmp4) ;
std::string tmp5(line,17,3) ;
_atom_resname().push_back(tmp5) ;
std::string tmp6(line,21,1) ;
_atom_chain().push_back(tmp6) ;
std::string tmp7(line,22,4) ;
_atom_resid().push_back(stoi(tmp7)) ;
std::string tmp8(line,26,1) ;
_atom_icode().push_back(tmp8) ;
std::string tmp9(line,30,8) ;
vector_x.push_back(stof(tmp9)) ;
std::string tmp10(line,38,8) ;
vector_y.push_back(stof(tmp10)) ;
std::string tmp11(line,46,8) ;
vector_z.push_back(stof(tmp11)) ;
try
{
std::string tmp12(line,54,6) ;
if(util::has_only_spaces(tmp12))
{
_atom_occupancy().push_back("0.00") ;
}
else
{
_atom_occupancy().push_back(tmp12) ;
}
}
catch(const std::out_of_range& oor)
{
_atom_occupancy().push_back("0.00") ;
std::cerr<<"Occupancy: Out of range error: "<< oor.what() <<std::endl ;
}
try
{
std::string tmp13(line,60,6) ;
if(util::has_only_spaces(tmp13))
{
_atom_beta().push_back("0.00") ;
}
else
{
_atom_beta().push_back(tmp13) ;
}
}
catch(const std::out_of_range& oor)
{
_atom_beta().push_back("0.00") ;
std::cerr<<"Beta: Out of range error: "<< oor.what() <<std::endl ;
}
try
{
std::string tmp14(line,72,4) ;
if(util::has_only_spaces(tmp14))
{
_atom_segname().push_back("SEGN") ;
}
else
{
_atom_segname().push_back(tmp14) ;
}
}
catch(const std::out_of_range& oor)
{
_atom_segname().push_back("SEGN") ;
std::cerr<<"Segname: Out of range error: "<< oor.what() <<std::endl ;
}
try
{
std::string tmp15(line,76,2) ;
if(util::has_only_spaces(tmp15))
{
std::cout << "Element not found" << std::endl;
element_string = element_from_name(tmp3) ;
_atom_element().push_back(element_string) ;
}
else
{
_atom_element().push_back(tmp15) ;
}
}
catch(const std::out_of_range& oor)
{
element_string = element_from_name(tmp3) ;
_atom_element().push_back(element_string) ;
std::cerr<<"Element: Out of range error: "<< oor.what() <<std::endl ;
}
try
{
std::string tmp16(line,78,2) ;
if(util::has_only_spaces(tmp16))
{
_atom_charge().push_back(" ") ;
}
else
{
_atom_charge().push_back(tmp16) ;
}
}
catch(const std::out_of_range& oor)
{
_atom_charge().push_back(" ") ;
std::cerr<<"Charge: Out of range error: "<< oor.what() <<std::endl ;
}
count++ ;
}
}
_natoms() = count ;
infile.close() ;
int nf = _number_of_frames() ;
if(_number_of_frames() == 0)
{
_x().setZero(_natoms(), 1);
_y().setZero(_natoms(), 1);
_z().setZero(_natoms(), 1);
}
else
{
resize_array() ;
}
for(int i = 0 ; i < _natoms() ; ++i)
{
_x()(i,_number_of_frames()) = vector_x[i] ;
_y()(i,_number_of_frames()) = vector_y[i] ;
_z()(i,_number_of_frames()) = vector_z[i] ;
}
std::vector<std::string> s_element ;
s_element = util::strip_white_space(_atom_element()) ;
_atom_selement() = s_element ;
dynamic_cast<sasmol::SasMol*>(this)->calc_mass() ;
_atom_com() = dynamic_cast<sasmol::SasMol*>(this)->calc_com(frame) ;
_number_of_frames() += 1 ;
_set_unique_attributes();
/*
1 2 3 4 5 6 7 8
012345678901234567890123456789012345678901234567890123456789012345678901234567890
1 2 3 4 5 6 7 8
12345678901234567890123456789012345678901234567890123456789012345678901234567890
0 6 1 2 7
ATOM 1 N GLY X 1 -21.525 -67.562 86.759 1.00 0.00 GAG N
ATOM 2 HT1 GLY X 1 -22.003 -68.460 86.892 1.00 0.00 GAG H
ATOM 3 HT2 GLY X 1 -21.905 -66.929 87.525 1.00 0.00 GAG H
*/
}
int runTests(Epetra_Map & map, Epetra_CrsMatrix & A, Epetra_Vector & x, Epetra_Vector & b, Epetra_Vector & xexact, bool verbose) {
int ierr = 0;
// Create MultiVectors and put x, b, xexact in both columns of X, B, and Xexact, respectively.
Epetra_MultiVector X( map, 2, false );
Epetra_MultiVector B( map, 2, false );
Epetra_MultiVector Xexact( map, 2, false );
for (int i=0; i<X.NumVectors(); ++i) {
*X(i) = x;
*B(i) = b;
*Xexact(i) = xexact;
}
double residual;
std::vector<double> residualmv(2);
residual = A.NormInf(); double rAInf = residual;
if (verbose) std::cout << "Inf Norm of A = " << residual << std::endl;
residual = A.NormOne(); double rAOne = residual;
if (verbose) std::cout << "One Norm of A = " << residual << std::endl;
xexact.Norm2(&residual); double rxx = residual;
Xexact.Norm2(&residualmv[0]); std::vector<double> rXX( residualmv );
if (verbose) std::cout << "Norm of xexact = " << residual << std::endl;
if (verbose) std::cout << "Norm of Xexact = (" << residualmv[0] << ", " <<residualmv[1] <<")"<< std::endl;
Epetra_Vector tmp1(map);
Epetra_MultiVector tmp1mv(map,2,false);
A.Multiply(false, xexact, tmp1);
A.Multiply(false, Xexact, tmp1mv);
tmp1.Norm2(&residual); double rAx = residual;
tmp1mv.Norm2(&residualmv[0]); std::vector<double> rAX( residualmv );
if (verbose) std::cout << "Norm of Ax = " << residual << std::endl;
if (verbose) std::cout << "Norm of AX = (" << residualmv[0] << ", " << residualmv[1] <<")"<< std::endl;
b.Norm2(&residual); double rb = residual;
B.Norm2(&residualmv[0]); std::vector<double> rB( residualmv );
if (verbose) std::cout << "Norm of b (should equal norm of Ax) = " << residual << std::endl;
if (verbose) std::cout << "Norm of B (should equal norm of AX) = (" << residualmv[0] << ", " << residualmv[1] <<")"<< std::endl;
tmp1.Update(1.0, b, -1.0);
tmp1mv.Update(1.0, B, -1.0);
tmp1.Norm2(&residual);
tmp1mv.Norm2(&residualmv[0]);
if (verbose) std::cout << "Norm of difference between compute Ax and Ax from file = " << residual << std::endl;
if (verbose) std::cout << "Norm of difference between compute AX and AX from file = (" << residualmv[0] << ", " << residualmv[1] <<")"<< std::endl;
map.Comm().Barrier();
EPETRA_CHK_ERR(EpetraExt::BlockMapToMatrixMarketFile("Test_map.mm", map, "Official EpetraExt test map",
"This is the official EpetraExt test map generated by the EpetraExt regression tests"));
EPETRA_CHK_ERR(EpetraExt::RowMatrixToMatrixMarketFile("Test_A.mm", A, "Official EpetraExt test matrix",
"This is the official EpetraExt test matrix generated by the EpetraExt regression tests"));
EPETRA_CHK_ERR(EpetraExt::VectorToMatrixMarketFile("Test_x.mm", x, "Official EpetraExt test initial guess",
"This is the official EpetraExt test initial guess generated by the EpetraExt regression tests"));
EPETRA_CHK_ERR(EpetraExt::MultiVectorToMatrixMarketFile("Test_mvX.mm", X, "Official EpetraExt test initial guess",
"This is the official EpetraExt test initial guess generated by the EpetraExt regression tests"));
EPETRA_CHK_ERR(EpetraExt::VectorToMatrixMarketFile("Test_xexact.mm", xexact, "Official EpetraExt test exact solution",
"This is the official EpetraExt test exact solution generated by the EpetraExt regression tests"));
EPETRA_CHK_ERR(EpetraExt::MultiVectorToMatrixMarketFile("Test_mvXexact.mm", Xexact, "Official EpetraExt test exact solution",
"This is the official EpetraExt test exact solution generated by the EpetraExt regression tests"));
EPETRA_CHK_ERR(EpetraExt::VectorToMatrixMarketFile("Test_b.mm", b, "Official EpetraExt test right hand side",
"This is the official EpetraExt test right hand side generated by the EpetraExt regression tests"));
EPETRA_CHK_ERR(EpetraExt::MultiVectorToMatrixMarketFile("Test_mvB.mm", B, "Official EpetraExt test right hand side",
"This is the official EpetraExt test right hand side generated by the EpetraExt regression tests"));
EPETRA_CHK_ERR(EpetraExt::MultiVectorToMatlabFile("Test_mvB.mat", B));
EPETRA_CHK_ERR(EpetraExt::RowMatrixToMatlabFile("Test_A.dat", A));
Epetra_Map * map1;
Epetra_CrsMatrix * A1;
Epetra_CrsMatrix * A2;
Epetra_CrsMatrix * A3;
Epetra_Vector * x1;
Epetra_Vector * b1;
Epetra_Vector * xexact1;
Epetra_MultiVector * X1;
Epetra_MultiVector * B1;
Epetra_MultiVector * Xexact1;
EpetraExt::MatrixMarketFileToMap("Test_map.mm", map.Comm(), map1);
if (map.SameAs(*map1)) {
if (verbose) std::cout << "Maps are equal. In/Out works." << std::endl;
}
else {
if (verbose) std::cout << "Maps are not equal. In/Out fails." << std::endl;
ierr += 1;
}
EPETRA_CHK_ERR(EpetraExt::MatrixMarketFileToCrsMatrix("Test_A.mm", *map1, A1));
// If map is zero-based, then we can compare to the convenient reading versions
if (map1->IndexBase()==0) EPETRA_CHK_ERR(EpetraExt::MatrixMarketFileToCrsMatrix("Test_A.mm", map1->Comm(), A2));
if (map1->IndexBase()==0) EPETRA_CHK_ERR(EpetraExt::MatlabFileToCrsMatrix("Test_A.dat", map1->Comm(), A3));
EPETRA_CHK_ERR(EpetraExt::MatrixMarketFileToVector("Test_x.mm", *map1, x1));
EPETRA_CHK_ERR(EpetraExt::MatrixMarketFileToVector("Test_xexact.mm", *map1, xexact1));
EPETRA_CHK_ERR(EpetraExt::MatrixMarketFileToVector("Test_b.mm", *map1, b1));
EPETRA_CHK_ERR(EpetraExt::MatrixMarketFileToMultiVector("Test_mvX.mm", *map1, X1));
EPETRA_CHK_ERR(EpetraExt::MatrixMarketFileToMultiVector("Test_mvXexact.mm", *map1, Xexact1));
EPETRA_CHK_ERR(EpetraExt::MatrixMarketFileToMultiVector("Test_mvB.mm", *map1, B1));
residual = A1->NormInf(); double rA1Inf = residual;
if (verbose) std::cout << "Inf Norm of A1 = " << residual << std::endl;
ierr += checkValues(rA1Inf,rAInf,"Inf Norm of A", verbose);
residual = A1->NormOne(); double rA1One = residual;
if (verbose) std::cout << "One Norm of A1 = " << residual << std::endl;
ierr += checkValues(rA1One,rAOne,"One Norm of A", verbose);
xexact1->Norm2(&residual); double rxx1 = residual;
if (verbose) std::cout << "Norm of xexact1 = " << residual << std::endl;
ierr += checkValues(rxx1,rxx,"Norm of xexact", verbose);
Xexact1->Norm2(&residualmv[0]); std::vector<double> rXX1(residualmv);
if (verbose) std::cout << "Norm of Xexact1 = (" << residualmv[0] <<", " <<residualmv[1]<<")"<< std::endl;
ierr += checkValues(rXX1[0],rXX[0],"Norm of Xexact", verbose);
ierr += checkValues(rXX1[1],rXX[1],"Norm of Xexact", verbose);
Epetra_Vector tmp11(*map1);
A1->Multiply(false, *xexact1, tmp11);
Epetra_MultiVector tmp11mv(*map1,2,false);
A1->Multiply(false, *Xexact1, tmp11mv);
tmp11.Norm2(&residual); double rAx1 = residual;
if (verbose) std::cout << "Norm of A1*x1 = " << residual << std::endl;
ierr += checkValues(rAx1,rAx,"Norm of A1*x", verbose);
tmp11mv.Norm2(&residualmv[0]); std::vector<double> rAX1(residualmv);
if (verbose) std::cout << "Norm of A1*X1 = (" << residualmv[0] <<", "<<residualmv[1]<<")"<< std::endl;
ierr += checkValues(rAX1[0],rAX[0],"Norm of A1*X", verbose);
ierr += checkValues(rAX1[1],rAX[1],"Norm of A1*X", verbose);
if (map1->IndexBase()==0) {
Epetra_Vector tmp12(*map1);
A2->Multiply(false, *xexact1, tmp12);
tmp12.Norm2(&residual); double rAx2 = residual;
if (verbose) std::cout << "Norm of A2*x1 = " << residual << std::endl;
ierr += checkValues(rAx2,rAx,"Norm of A2*x", verbose);
Epetra_Vector tmp13(*map1);
A3->Multiply(false, *xexact1, tmp13);
tmp13.Norm2(&residual); double rAx3 = residual;
if (verbose) std::cout << "Norm of A3*x1 = " << residual << std::endl;
ierr += checkValues(rAx3,rAx,"Norm of A3*x", verbose);
}
b1->Norm2(&residual); double rb1 = residual;
if (verbose) std::cout << "Norm of b1 (should equal norm of Ax) = " << residual << std::endl;
ierr += checkValues(rb1,rb,"Norm of b", verbose);
B1->Norm2(&residualmv[0]); std::vector<double> rB1(residualmv);
if (verbose) std::cout << "Norm of B1 (should equal norm of AX) = (" << residualmv[0] <<", "<<residualmv[1]<<")"<< std::endl;
ierr += checkValues(rB1[0],rB[0],"Norm of B", verbose);
ierr += checkValues(rB1[1],rB[1],"Norm of B", verbose);
tmp11.Update(1.0, *b1, -1.0);
tmp11.Norm2(&residual);
if (verbose) std::cout << "Norm of difference between computed A1x1 and A1x1 from file = " << residual << std::endl;
ierr += checkValues(residual,0.0,"Norm of difference between computed A1x1 and A1x1 from file", verbose);
tmp11mv.Update(1.0, *B1, -1.0);
tmp11mv.Norm2(&residualmv[0]);
if (verbose) std::cout << "Norm of difference between computed A1X1 and A1X1 from file = (" << residualmv[0] << ", "<<residualmv[1]<<")"<< std::endl;
ierr += checkValues(residualmv[0],0.0,"Norm of difference between computed A1X1 and A1X1 from file", verbose);
ierr += checkValues(residualmv[1],0.0,"Norm of difference between computed A1X1 and A1X1 from file", verbose);
if (map1->IndexBase()==0) {delete A2; delete A3;}
delete A1;
delete x1;
delete b1;
delete xexact1;
delete X1;
delete B1;
delete Xexact1;
delete map1;
return(ierr);
}
void
sasio::Files::
write_pdb(const std::string &filename, int &frame)
{
std::ofstream outfile(filename) ;
std::string time_and_user_string ;
time_and_user_string = util::time_and_user();
std::string temp_remark = "REMARK PDB FILE WRITTEN ";
temp_remark += time_and_user_string ;
std::string remark(temp_remark,0,80) ;
std::cout << remark << std::endl ;
outfile << remark << std::endl;
//std::string dum1 =" 1 2 3 4 5 6 7 8";
//std::string dum2 ="12345678901234567890123456789012345678901234567890123456789012345678901234567890";
//outfile << dum1 << std::endl;
//outfile << dum2 << std::endl;
std::stringstream line ;
std::stringstream my_stringstream;
for(int i = 0 ; i < _natoms() ; ++i)
{
line.str( std::string() );
line.clear() ;
std::string tmp(_atom_record()[i],0,6) ;
line << std::setfill(' ') << std::setw(6) << tmp ;
if(_atom_index()[i] > 99999)
{
std::string tmp2(std::to_string(99999),0,5) ;
line << std::setfill(' ') << std::setw(5) << std::right << tmp2 ;
}
else if(_atom_index()[i] < -9999)
{
std::string tmp2(std::to_string(-9999),0,5) ;
line << std::setfill(' ') << std::setw(5) << std::right << tmp2 ;
}
else
{
std::string tmp2(std::to_string(_atom_index()[i]),0,5) ;
line << std::setfill(' ') << std::setw(5) << std::right << tmp2 ;
}
std::string tmp0 = " ";
line << tmp0 ;
std::string tmp3(_atom_name()[i],0,4) ;
line << std::setfill(' ') << std::setw(4) << std::left << tmp3 ;
std::string tmp4(_atom_altloc()[i],0,1) ;
line << std::setw(1) << tmp4 ;
std::string tmp5(_atom_resname()[i],0,3) ;
line << std::setfill(' ') << std::setw(4) << std::left << tmp5 ;
std::string tmp6(_atom_chain()[i],0,1) ;
line << std::setfill(' ') << std::setw(1) << std::left << tmp6 ;
if(_atom_resid()[i] > 9999)
{
std::string tmp7(std::to_string(9999),0,4) ;
line << std::setfill(' ') << std::setw(4) << std::right << tmp7 ;
}
else if(_atom_resid()[i] < -999)
{
std::string tmp7(std::to_string(-999),0,4) ;
line << std::setfill(' ') << std::setw(4) << std::right << tmp7 ;
}
else
{
std::string tmp7(std::to_string(_atom_resid()[i]),0,4) ;
line << std::setfill(' ') << std::setw(4) << std::right << tmp7 ;
}
std::string tmp8(_atom_icode()[i],0,1) ;
line << std::setw(4) << std::left << tmp8 ;
//std::string f_str = std::to_string(f);
//here
//
my_stringstream << _x()(i,frame) ;
//my_stringstream << std::to_string(_x()(i,frame)) ;
//line << std::setfill(' ') << std::setw(8) << std::right << my_stringstream.str() ;
line << std::setfill(' ') << std::setw(8) << std::right << my_stringstream.str() ;
my_stringstream << _y()(i,frame) ;
line << my_stringstream.str() ;
my_stringstream << _z()(i,frame) ;
line << my_stringstream.str() ;
std::string tmp12(_atom_occupancy()[i],0,6) ;
line << std::setfill(' ') << std::setw(6) << std::right << tmp12 ;
std::string tmp13(_atom_beta()[i],0,6) ;
line << std::setfill(' ') << std::setw(6) << std::right << tmp13 ;
std::string tmp14(_atom_segname()[i],0,4) ;
line << std::setfill(' ') << std::setw(10) << std::right << tmp14 ;
std::string tmp15(_atom_element()[i],0,2) ;
line << std::setfill(' ') << std::setw(2) << std::right << tmp15 ;
std::string tmp16(_atom_charge()[i],0,2) ;
line << std::setfill(' ') << std::setw(2) << std::right << tmp16 ;
outfile << line.str() << std::endl ;
}
outfile << "END" << std::endl;
outfile.close() ;
}
