void stimulus::entry() {
reset.write(true);
wait();
reset.write(false);
sc_signed tmp1(8);
sc_signed tmp2(8);
long tmp3;
int tmp4;
short tmp5;
char tmp6;
char tmp7;
bool tmp8;
sc_unsigned tmp9(4);
sc_unsigned tmp10(4);
tmp1 = "0b01010101";
tmp2 = "0b00000010";
tmp3 = 12345678;
tmp4 = -123456;
tmp5 = 20000;
tmp6 = '$';
tmp7 = 'A';
tmp8 = "0";
tmp9 = "0b0001";
tmp10 = "0b0010";
while(true){
out_valid.write(true);
out_value1.write(tmp1);
out_value2.write(tmp2);
out_value3.write(tmp3);
out_value4.write(tmp4);
out_value5.write(tmp5);
out_value6.write(tmp6);
out_value7.write(tmp7);
out_value8.write(tmp8);
out_value9.write(tmp9);
out_value10.write(tmp10);
cout << "Stimuli: " << tmp1 << " " << tmp2 << " " << tmp3 << " " << tmp4 << " "
<< tmp5 << " " << tmp6 << " " << tmp7 << " " << tmp8 << " " << tmp9 << " " << tmp10 <<endl;
tmp1 = tmp1 + 2;
tmp2 = tmp2 + 1;
tmp3 = tmp3 + 5;
tmp4 = tmp4 + 3;
tmp5 = tmp5 + 6;
tmp7 = tmp7 + 1;
tmp8 = !tmp8;
tmp9 = tmp9 + 1;
tmp10 = tmp10 + 1;
do { wait(); } while (in_ack==false);
out_valid.write(false);
wait();
}
}
///
/// @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
*/
}
