/* SRC: classes/exception.php line 152 */
void c_Exception::t_inittrace() {
INSTANCE_METHOD_INJECTION_BUILTIN(Exception, Exception::initTrace);
Variant v_top;
Variant v_frame;
ObjectData *obj_tmp UNUSED;
{
const CallInfo *cit0 = NULL;
MethodCallPackage mcp0;
mcp0.staticMethodCall(NAMSTR(s_sys_ssf08d205d, "static"), NAMSTR(s_sys_ssc453e9e9, "getTraceOptions"));
mcp0.lateStaticBind(fi.getThreadInfo());
cit0 = mcp0.ci;
const Array &tmp1((x_debug_backtrace(toBoolean((cit0->getMeth0Args())(mcp0, 0)))));
m_trace = tmp1;
}
LOOP_COUNTER(1);
{
while (!(empty(m_trace))) {
LOOP_COUNTER_CHECK(1);
{
{
const Variant &tmp0((m_trace.rvalAt(0LL, AccessFlags::Error)));
v_top.assignVal(tmp0);
}
{
bool tmp0;
{
bool tmp1 = ((isset(v_top, NAMSTR(s_sys_ssc82dbd12, "class"), true) && isset(v_top, NAMSTR(s_sys_ss52403931, "function"), true)));
if (tmp1) {
const String &tmp2((toString(v_top.rvalAt(NAMSTR(s_sys_ssc82dbd12, "class"), AccessFlags::Error_Key))));
int64 tmp3((x_strcasecmp(tmp2, NAMSTR(s_sys_ssae8717ad, "exception"))));
tmp1 = (same(tmp3, 0LL));
}
bool tmp4 = (tmp1);
if (tmp4) {
const String &tmp5((toString(v_top.rvalAt(NAMSTR(s_sys_ss52403931, "function"), AccessFlags::Error_Key))));
int64 tmp6((x_strcasecmp(tmp5, NAMSTR(s_sys_ssa26bedd7, "__init__"))));
tmp4 = (same(tmp6, 0LL));
}
tmp0 = (tmp4);
}
if (tmp0) {
{
{
const Variant &tmp0((x_array_shift(ref(m_trace))));
v_frame.assignVal(tmp0);
}
if (isset(v_frame, NAMSTR(s_sys_ss8ce7db5b, "file"), true)) {
{
const Variant &tmp0((v_frame.rvalAt(NAMSTR(s_sys_ss8ce7db5b, "file"), AccessFlags::Error_Key)));
m_file.assignVal(tmp0);
}
}
if (isset(v_frame, NAMSTR(s_sys_ssddf8728c, "line"), true)) {
{
const Variant &tmp0((v_frame.rvalAt(NAMSTR(s_sys_ssddf8728c, "line"), AccessFlags::Error_Key)));
m_line.assignVal(tmp0);
}
}
return;
}
}
}
x_array_shift(ref(m_trace));
}
}
}
}
///
/// @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
*/
}
MatrixXf EMclustering::initialization(MatrixXf x, int k)
{
srand (1);
int n = x.cols();
int d = x.rows();
//cerr<<n<<"d "<<d<<endl;
VectorXi idx(k);
//idx.setRandom(k);
//cerr<<idx<<endl;
idx(0) = rand()%n;
for(int i=1;i<k;i++)
{
int random;// = rand()%n;
//cerr<<random<<endl;
bool flag2 = true;
while(flag2)
{
random = rand()%n;
flag2 = false;
for(int j=0;j<i;j++)
{
if(idx(j)==random)
{
flag2 = true;
break;
}
}
}
idx(i) = random;
}
//cerr<<"idx"<<idx<<endl<<endl;
int tmpsize = idx.size();
MatrixXf m(d,tmpsize);
for(int i=0;i<tmpsize;i++)
m.col(i) = x.col(idx(i));
//cerr<<m<<endl<<endl;
VectorXf tmp1(m.cols());
tmp1 = m.cwiseProduct(m).colwise().sum();
//cerr<<tmp1<<endl<<endl;
tmp1 = tmp1.adjoint()/2;
//cerr<<tmp1<<endl<<endl;
MatrixXf tmp2(m.adjoint().rows(),x.cols());
tmp2 = m.adjoint() * x;
//cerr<<tmp2<<endl<<endl;
MatrixXf tmp3(tmp2.rows(),tmp2.cols());
tmp3 = tmp2.colwise() - tmp1;
//cerr<<tmp3<<endl<<endl;
double tmp4;
int tmp5;
int tmpd = tmp3.cols();
VectorXi label(tmpd);
for(int i=0;i<tmpd;i++)
{
tmp4 = tmp3.col(i).maxCoeff(&tmp5);
label(i) = tmp5;
}
//cerr<<label<<endl<<endl;
VectorXi tmp6(label.size());
VectorXi u = unique(label, tmp6);
//cerr<<u<<endl<<endl;
//cerr<<tmp6<<endl<<endl;
int max = 100;
int t=0;
while(k!=u.size()&&t<max)
{
t++;
//cerr<<"-----------"<<endl;
//idx.setRandom(k);
idx(0) = rand()%n;//cerr<<k<<" "<<u.size()<<" "<<idx(0)<<endl;
for(int i=1;i<k;i++)
{
int random;// = rand()%n;
bool flag2 = true;
while(flag2)
{random = rand()%n;
flag2 = false;
for(int j=0;j<i;j++)
{
if(idx(j)==random||x.col(idx(j))==x.col(random))
{
flag2 = true;
break;
}
}
}
idx(i) = random;//cerr<<idx(i)<<" ";
}//cerr<<endl;
//cerr<<"idx"<<idx<<endl<<endl;;
//cerr<<"u"<<u<<endl<<endl;
for(int i=0;i<tmpsize;i++)
m.col(i) = x.col(idx(i));
//cerr<<m<<endl<<endl;
tmp1 = m.cwiseProduct(m).colwise().sum();
//cerr<<tmp1<<endl<<endl;
tmp1 = tmp1.adjoint()/2;
//cerr<<tmp1<<endl<<endl;
tmp2 = m.adjoint() * x;
//cerr<<tmp2<<endl<<endl;
tmp3 = tmp2.colwise() - tmp1;
//cerr<<tmp3<<endl<<endl;
tmpd = tmp3.cols();
for(int i=0;i<tmpd;i++)
{
tmp4 = tmp3.col(i).maxCoeff(&tmp5);
label(i) = tmp5;
}
//cerr<<"label"<<label.size()<<endl<<endl;
//cerr<<"end"<<endl;
u = unique(label, tmp6);
label = tmp6;
//cerr<<"u"<<u<<endl<<endl;
//cerr<<tmp6<<endl<<endl;
}//cerr<<k<<" "<<u.size()<<endl;
//cerr<<t<<endl;
//cerr<<u.size()<<endl;
MatrixXf r(n,k);
r.setZero(n,k);
int j=0;
int tmplabel[k];
for(int i=0;i<k;i++)
tmplabel[i] = 0;
for(int i=0;i<n;i++)
{
r(i,label(j)) = 1;
tmplabel[label(j)] = 1;
j++;
}
//for(int i=0;i<n;i++)
//{
// if(tmplabel[i]==0)
// {
// r(i,0) = 1;
// }
//}
j = 0;
for(int i=0;i<k;i++)
{
if(tmplabel[i]==0)
{
//cerr<<i<<endl;
for(int ii=0;ii<n/k;ii++)
{
int ttt = rand()%n;
//for(int jj=0;jj<k;jj++)
// r(ttt,jj)=0;
r(ttt,i) = 1;
}
//j ++;//cerr<<j<<endl;
}
}
//cerr<<r.cols()<<endl;
//cerr<<r<<endl;
//delete [] tmplabel;
idx.resize(0);
m.resize(0,0);
tmp1.resize(0);
tmp2.resize(0,0);
tmp3.resize(0,0);
tmp6.resize(0);
u.resize(0);
label.resize(0);
return r;
}
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() ;
}
