///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
void
sasio::Files::
resize_array()
{
int nf = _number_of_frames() ;
Eigen::Array<float,Eigen::Dynamic,Eigen::Dynamic> temp_x(_natoms(),nf) ;
Eigen::Array<float,Eigen::Dynamic,Eigen::Dynamic> temp_y(_natoms(),nf) ;
Eigen::Array<float,Eigen::Dynamic,Eigen::Dynamic> temp_z(_natoms(),nf) ;
temp_x = _x() ;
temp_y = _y() ;
temp_z = _z() ;
_x().resize(_natoms(),_number_of_frames()+1) ;
_y().resize(_natoms(),_number_of_frames()+1) ;
_z().resize(_natoms(),_number_of_frames()+1) ;
// see: slice.cpp in retired_ideas/play_with_eigen/
// mat1.block(i,j,rows,cols)
// a.block(0, 0, 3, 1) = b.block(0,0,3,1) ;
_x().block(0, 0, _natoms(), nf) = temp_x.block(0,0,_natoms(),nf) ;
_y().block(0, 0, _natoms(), nf) = temp_y.block(0,0,_natoms(),nf) ;
_z().block(0, 0, _natoms(), nf) = temp_z.block(0,0,_natoms(),nf) ;
return ;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
int
sascalc::Prop::
self_overlap(float &cutoff, int &frame){
int check = 0 ; // overlapped == 1
// default == no overlap will return == 0
float dist ;
float this_x , that_x ;
float this_y , that_y ;
float this_z , that_z ;
float dx2, dy2, dz2 ;
int count = 1 ;
for(int i = 0 ; i != _natoms()-1 ; ++i)
{
this_x = _x()(i,frame) ;
this_y = _y()(i,frame) ;
this_z = _z()(i,frame) ;
for(int j = i+1 ; j != _natoms() ; ++j)
{
that_x = _x()(j,frame) ;
that_y = _y()(j,frame) ;
that_z = _z()(j,frame) ;
dx2 = (this_x - that_x)*(this_x - that_x) ;
dy2 = (this_y - that_y)*(this_y - that_y) ;
dz2 = (this_z - that_z)*(this_z - that_z) ;
dist = sqrt(dx2+dy2+dz2) ;
if(dist < cutoff)
{
std::cout << "count = " << count << std::endl ;
std::cout << "this_atom = " << _atom_name()[count-1] << std::endl ;
std::cout << "that_atom = " << _atom_name()[count] << std::endl ;
std::cout << "dist = " << dist << std::endl ;
std::cout << "this_x = " << this_x << std::endl ;
std::cout << "this_y = " << this_y << std::endl ;
std::cout << "this_z = " << this_z << std::endl ;
std::cout << "that_x = " << that_x << std::endl ;
std::cout << "that_y = " << that_y << std::endl ;
std::cout << "that_z = " << that_z << std::endl ;
check = 1 ;
return check ;
}
}
// std::cout << count << " " ;
count++ ;
}
std::cout << std::endl ;
return check ;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
void
sascalc::Prop::
calc_pmi(int &frame)
{
std::vector<float> com = calc_com(frame) ;
_x().col(frame) -= com[0] ;
_y().col(frame) -= com[1] ;
_z().col(frame) -= com[2] ;
float Ixx = (_atom_mass()*(_y().col(frame)*_y().col(frame) + _z().col(frame)*_z().col(frame))).sum() ;
float Iyy = (_atom_mass()*(_x().col(frame)*_x().col(frame) + _z().col(frame)*_z().col(frame))).sum() ;
float Izz = (_atom_mass()*(_x().col(frame)*_x().col(frame) + _y().col(frame)*_y().col(frame))).sum() ;
float Ixy = (-_atom_mass()*(_x().col(frame)*_y().col(frame))).sum() ;
float Ixz = (-_atom_mass()*(_x().col(frame)*_z().col(frame))).sum() ;
float Iyz = (-_atom_mass()*(_y().col(frame)*_z().col(frame))).sum() ;
float Iyx = (-_atom_mass()*(_y().col(frame)*_x().col(frame))).sum() ;
float Izx = (-_atom_mass()*(_z().col(frame)*_x().col(frame))).sum() ;
float Izy = (-_atom_mass()*(_z().col(frame)*_y().col(frame))).sum() ;
Eigen::Matrix3f I ;
I << Ixx, Ixy, Ixz,
Iyx, Iyy, Iyz,
Izx, Izy, Izz;
Eigen::SelfAdjointEigenSolver<Eigen::Matrix3f> eigensolver(I);
if (eigensolver.info() != Eigen::Success)
{
std::cout << "PMI calculation failed" << std::endl ;
return ;
}
_uk() = eigensolver.eigenvalues() ; // .col(0) ;
_ak() = eigensolver.eigenvectors() ;
// std::cout << "The eigenvalues of I are:\n" << eigensolver.eigenvalues() << std::endl;
// std::cout << "Here's a matrix whose columns are eigenvectors of I \n"
// << "corresponding to these eigenvalues:\n"
// << eigensolver.eigenvectors() << std::endl;
_x().col(frame) += com[0] ;
_y().col(frame) += com[1] ;
_z().col(frame) += com[2] ;
return ;
}
void Compute(gmp_randstate_t r) const {
// The algorithm is sample x and z from the exponential distribution; if
// (x-1)^2 < 2*z, return (random sign)*x; otherwise repeat. Probability
// of acceptance is sqrt(pi/2) * exp(-1/2) = 0.7602.
while (true) {
_edist(_x, r);
_edist(_z, r);
for (mp_size_t k = 1; ; ++k) {
_x.ExpandTo(r, k - 1);
_z.ExpandTo(r, k - 1);
mpfr_prec_t prec = std::max(mpfr_prec_t(MPFR_PREC_MIN), k * bits);
mpfr_set_prec(_xf, prec);
mpfr_set_prec(_zf, prec);
// Try for acceptance first; so compute upper limit on (y-1)^2 and
// lower limit on 2*z.
if (_x.UInteger() == 0) {
_x(_xf, MPFR_RNDD);
mpfr_ui_sub(_xf, 1u, _xf, MPFR_RNDU);
} else {
_x(_xf, MPFR_RNDU);
mpfr_sub_ui(_xf, _xf, 1u, MPFR_RNDU);
}
mpfr_sqr(_xf, _xf, MPFR_RNDU);
_z(_zf, MPFR_RNDD);
mpfr_mul_2ui(_zf, _zf, 1u, MPFR_RNDD);
if (mpfr_cmp(_xf, _zf) < 0) { // (y-1)^2 < 2*z, so accept
if (_x.Boolean(r)) _x.Negate(); // include a random sign
return;
}
// Try for rejection; so compute lower limit on (y-1)^2 and upper
// limit on 2*z.
if (_x.UInteger() == 0) {
_x(_xf, MPFR_RNDU);
mpfr_ui_sub(_xf, 1u, _xf, MPFR_RNDD);
} else {
_x(_xf, MPFR_RNDD);
mpfr_sub_ui(_xf, _xf, 1u, MPFR_RNDD);
}
mpfr_sqr(_xf, _xf, MPFR_RNDD);
_z(_zf, MPFR_RNDU);
mpfr_mul_2ui(_zf, _zf, 1u, MPFR_RNDU);
if (mpfr_cmp(_xf, _zf) > 0) // (y-1)^2 > 2*z, so reject
break;
// Otherwise repeat with more precision
}
// Reject and start over with a new y and z
}
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
std::vector<float>
sascalc::Prop::
calc_com(int &frame)
{
if(_total_mass() <= 0.0) {
calc_mass() ;
std::cout << "com tot mass = " << _total_mass() << std::endl ;
}
float comx = 0.0, comy = 0.0, comz = 0.0 ;
try
{
comx = (_atom_mass()*_x().col(frame)).sum() / _total_mass() ;
comy = (_atom_mass()*_y().col(frame)).sum() / _total_mass() ;
comz = (_atom_mass()*_z().col(frame)).sum() / _total_mass() ;
}
catch(std::overflow_error e) {
std::cout << "failed in calc_com" << std::endl ;
std::cout << "total_mass = " << _total_mass() << std::endl ;
std::cout << e.what() << " -> ";
std::vector<float> com = {comx, comy, comz} ;
return com ;
}
std::vector<float> com = {comx, comy, comz} ;
return com ;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
void
sasio::Files::
read_dcd(std::string &dcd_input_file_name)
{
int input_natoms, input_nset, input_reverseEndian ;
FILE *dcd_file_pointer ;
dcd_file_pointer = sasio::open_dcd_read(dcd_input_file_name, input_natoms, input_nset, input_reverseEndian) ;
int input_frame = 0 ;
_number_of_frames() = 0 ;
_x().setZero(_natoms(), input_nset);
_y().setZero(_natoms(), input_nset);
_z().setZero(_natoms(), input_nset);
std::cout << "_x().cols() = " << _x().cols() << std::endl ;
std::cout << "input_nset = " << input_nset << std::endl ;
for(int i = 0 ; i < input_nset ; ++i)
{
std::cout << "." ;
read_dcd_step(dcd_file_pointer, i, input_natoms, input_reverseEndian) ;
}
int result = close_dcd_read(dcd_file_pointer) ;
std::cout << std::endl ;
return ;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
void
sasio::Files::
read_dcd_step(FILE *dcd_infile, int &frame, int &natoms, int &reverseEndian)
{
int charmm = 0 ;
int num_fixed = 0 ;
int result ;
std::vector<float> vector_x(natoms) ;
std::vector<float> vector_y(natoms) ;
std::vector<float> vector_z(natoms) ;
result = read_dcdstep(dcd_infile,natoms,&vector_x[0],&vector_y[0],&vector_z[0],num_fixed,frame,reverseEndian,charmm) ;
if(_x().cols() < frame)
{
std::cout << "resizing array: cols() = " << _x().cols() << " frame = " << frame << std::endl ;
resize_array() ;
}
for(int i = 0 ; i < _natoms() ; ++i)
{
_x()(i,frame) = vector_x[i] ;
_y()(i,frame) = vector_y[i] ;
_z()(i,frame) = vector_z[i] ;
}
_number_of_frames()++ ;
return ;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
std::vector<std::vector<float >>
sascalc::Prop::
calc_minmax(int &frame){
float min_x = _x().col(frame).minCoeff() ; float max_x = _x().col(frame).maxCoeff() ;
float min_y = _y().col(frame).minCoeff() ; float max_y = _y().col(frame).maxCoeff() ;
float min_z = _z().col(frame).minCoeff() ; float max_z = _z().col(frame).maxCoeff() ;
std::vector<float> min_vector ;
std::vector<float> max_vector ;
min_vector.push_back(min_x) ; min_vector.push_back(min_y) ; min_vector.push_back(min_z) ;
max_vector.push_back(max_x) ; max_vector.push_back(max_y) ; max_vector.push_back(max_z) ;
std::vector<std::vector<float >> minmax ;
minmax.push_back(min_vector) ; minmax.push_back(max_vector) ;
return minmax ;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
void
sasio::Files::
write_dcd_step(FILE *outfile, int &frame, int &step)
{
int step_result = 0 ;
step_result = write_dcdstep(outfile,_natoms(),&_x()(0,frame),&_y()(0,frame),&_z()(0,frame),step+1) ;
return ;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
float
sascalc::Prop::
calc_rmsd(sasmol::SasMol &mol, int &frame){
float dx = (_x().col(frame)-mol._x().col(frame)).pow(2.0).sum() ;
float dy = (_y().col(frame)-mol._y().col(frame)).pow(2.0).sum() ;
float dz = (_z().col(frame)-mol._z().col(frame)).pow(2.0).sum() ;
float rmsd = sqrt((dx + dy + dz)/_natoms()) ;
return rmsd ;
}
Parser::Parser(const vector<Production>& productions, const string& parserTablePath) : BasicParser(productions), parserTablePath(parserTablePath)
{
#ifdef _DEBUG
stream.open("ParserResult.txt", fstream::out | fstream::binary);
#endif
// String Begin
Rule quotationMarks = Rule('\"', &context);
Rule ruleString = quotationMarks + *!quotationMarks + quotationMarks;
ruleString.buildDFA();
ruleString.setShowName("\"{String}\"");
Production::Item itemString(ruleString);
// String End
// Digit Start
Rule _0('0', &context);
Rule _9('9', &context);
Rule _0_9 = _0 - _9;
Rule ruleDigit = +_0_9;
ruleDigit.buildDFA();
ruleDigit.setShowName("\"{Digit}\"");
Production::Item itemDigit(ruleDigit);
// Digit End
// Real Start
Rule _point('.', &context);
Rule ruleReal = *_0_9 + _point + +_0_9;
ruleReal.buildDFA();
ruleReal.setShowName("\"{Real}\"");
Production::Item itemReal(ruleReal);
// Real End
// Letter Start
Rule _('_', &context);
Rule _a('a', &context);
Rule _z('z', &context);
Rule _A('A', &context);
Rule _Z('Z', &context);
Rule _a_z = _a - _z;
Rule _A_Z = _A - _Z;
Rule ruleLetter = ((+_ + ruleDigit) |
(+(_ | _a_z | _A_Z))) +
*(_ | ruleDigit | _a_z | _A_Z);
ruleLetter.buildDFA();
ruleLetter.setShowName("\"{Letter}\"");
Production::Item itemLetter(ruleLetter);
// Letter End
vts.push_back(pair<string, Production::Item>("{String}", itemString));
vts.push_back(pair<string, Production::Item>("{Digit}", itemDigit));
vts.push_back(pair<string, Production::Item>("{Real}", itemReal));
vts.push_back(pair<string, Production::Item>("{Letter}", itemLetter));
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
float
sascalc::Prop::
calc_rg(int &frame){
std::vector<float> com = calc_com(frame) ;
float rgx = ((_x().col(frame) - com[0]).pow(2.0)).sum() ;
float rgy = ((_y().col(frame) - com[1]).pow(2.0)).sum() ;
float rgz = ((_z().col(frame) - com[2]).pow(2.0)).sum() ;
float rg = sqrt((rgx + rgy + rgz) / _natoms()) ;
return rg ;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
Eigen::Matrix3f
sasmath::Math::
find_u(sasmol::SasMol &mol, int &frame)
{
Eigen::Matrix3f r ;
float rxx = (mol._x().col(frame)*_x().col(frame)).sum() ;
float rxy = (mol._x().col(frame)*_y().col(frame)).sum() ;
float rxz = (mol._x().col(frame)*_z().col(frame)).sum() ;
float ryx = (mol._y().col(frame)*_x().col(frame)).sum() ;
float ryy = (mol._y().col(frame)*_y().col(frame)).sum() ;
float ryz = (mol._y().col(frame)*_z().col(frame)).sum() ;
float rzx = (mol._z().col(frame)*_x().col(frame)).sum() ;
float rzy = (mol._z().col(frame)*_y().col(frame)).sum() ;
float rzz = (mol._z().col(frame)*_z().col(frame)).sum() ;
r << rxx,rxy,rxz,
ryx,ryy,ryz,
rzx,rzy,rzz;
Eigen::Matrix3f rtr = r.transpose() * r ;
Eigen::SelfAdjointEigenSolver<Eigen::Matrix3f> eigensolver(rtr);
if (eigensolver.info() != Eigen::Success)
{
std::cout << "find_u calculation failed" << std::endl ;
}
Eigen::Matrix<float,3,1> uk ; // eigenvalues
Eigen::Matrix3f ak ; // eigenvectors
uk = eigensolver.eigenvalues() ;
ak = eigensolver.eigenvectors() ;
Eigen::Matrix3f akt = ak.transpose() ;
Eigen::Matrix3f new_ak ;
new_ak.row(0) = akt.row(2) ; //sort eigenvectors
new_ak.row(1) = akt.row(1) ;
new_ak.row(2) = akt.row(0) ;
// python ak0 --> ak[2] ; ak1 --> ak[1] ; ak2 --> ak[0]
//Eigen::Matrix<float,3,1> ak2 = akt.row(2).cross(akt.row(1)) ;
Eigen::MatrixXf rak0 = (r * (akt.row(2).transpose())) ;
Eigen::MatrixXf rak1 = (r * (akt.row(1).transpose())) ;
Eigen::Matrix<float,3,1> urak0 ;
if(uk[2] == 0.0)
{
urak0 = 1E15 * rak0 ;
}
else
{
urak0 = (1.0/sqrt(fabs(uk[2])))*rak0 ;
}
Eigen::Matrix<float,3,1> urak1 ;
if(uk[1] == 0.0)
{
urak1 = 1E15 * rak1 ;
}
else
{
urak1 = (1.0/sqrt(fabs(uk[1])))*rak1 ;
}
Eigen::Matrix<float,3,1> urak2 = urak0.col(0).cross(urak1.col(0)) ;
Eigen::Matrix3f bk ;
bk << urak0,urak1,urak2;
Eigen::Matrix3f u ;
u = (bk * new_ak).transpose() ;
return u ;
/*
u = array([[-0.94513198, 0.31068658, 0.100992 ],
[-0.3006246 , -0.70612572, -0.64110165],
[-0.12786863, -0.63628635, 0.76078203]])
check:
u =
-0.945133 0.310686 0.100992
-0.300624 -0.706126 -0.641102
-0.127869 -0.636287 0.760782
*/
}
///
/// @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
*/
}
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() ;
}
///
/// @par Detailed description
/// ...
/// @param [in, out] (param1) ...
/// @return ...
/// @note ...
void
sasio::Files::
read_xyz(const std::string &filename)
{
/* NOT CHECKED FOR MULTIPLE FRAMES */
std::string line, word ;
std::ifstream infile(filename) ;
std::string local_natoms ;
infile >> local_natoms ;
_natoms() = stoi(local_natoms) ;
_number_of_frames() = 1 ; // HARDWIRED
// #### need to cleanly read the end of the first line
// #### and the next line
getline(infile,line) ;
std::istringstream record(line) ;
while(record >> word) ;
getline(infile,line) ;
while(record >> word) ;
std::vector<float> vector_x;
std::vector<float> vector_y;
std::vector<float> vector_z;
std::vector<float> coor;
while(getline(infile,line))
{
std::istringstream record(line) ;
record >> word ;
_atom_name().push_back(word) ;
while(record >> word)
{
coor.push_back(stod(word));
}
}
auto begin = coor.begin() ;
auto end = coor.end() ;
std::vector<float>::iterator ii ;
for(ii = begin ; ii != end ; ii+=3)
{
vector_x.push_back(*ii) ;
vector_y.push_back(*(ii+1)) ;
vector_z.push_back(*(ii+2));
}
infile.close() ;
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] ;
}
_number_of_frames()++ ;
return ;
/*
5
test
N -3.259000 -5.011000 -14.360000
*/
} // end of read_xyz
