bool
test_valid()
{
for (unsigned int i = 0; i < ArrayLength(ValidStrings); ++i) {
nsDependentCString str8(ValidStrings[i].m8);
nsDependentString str16(ValidStrings[i].m16);
if (!NS_ConvertUTF16toUTF8(str16).Equals(str8))
return false;
if (!NS_ConvertUTF8toUTF16(str8).Equals(str16))
return false;
nsCString tmp8("string ");
AppendUTF16toUTF8(str16, tmp8);
if (!tmp8.Equals(NS_LITERAL_CSTRING("string ") + str8))
return false;
nsString tmp16(NS_LITERAL_STRING("string "));
AppendUTF8toUTF16(str8, tmp16);
if (!tmp16.Equals(NS_LITERAL_STRING("string ") + str16))
return false;
if (CompareUTF8toUTF16(str8, str16) != 0)
return false;
}
return true;
}
PRBool
test_valid()
{
for (unsigned int i = 0; i < NS_ARRAY_LENGTH(ValidStrings); ++i) {
nsDependentCString str8(ValidStrings[i].m8);
nsDependentString str16(ValidStrings[i].m16);
if (!NS_ConvertUTF16toUTF8(str16).Equals(str8))
return PR_FALSE;
if (!NS_ConvertUTF8toUTF16(str8).Equals(str16))
return PR_FALSE;
nsCString tmp8("string ");
AppendUTF16toUTF8(str16, tmp8);
if (!tmp8.Equals(NS_LITERAL_CSTRING("string ") + str8))
return PR_FALSE;
nsString tmp16(NS_LITERAL_STRING("string "));
AppendUTF8toUTF16(str8, tmp16);
if (!tmp16.Equals(NS_LITERAL_STRING("string ") + str16))
return PR_FALSE;
if (CompareUTF8toUTF16(str8, str16) != 0)
return PR_FALSE;
}
return PR_TRUE;
}
// -----------------------------------------------------------------------------
// AppendBufL
// -----------------------------------------------------------------------------
//
void AppendBufL( TPtr8& aDest, HBufC* aSrc )
{
TInt length = aSrc ? aSrc->Length() * 2 : KNullBuffer;
APPEND_BUF_INT( aDest, length );
if( length > 0 )
{
TPtr8 tmp8( (TUint8*)aSrc->Ptr(), length, length);
__ASSERT_DEBUG( (aDest.MaxLength() - aDest.Length()) > tmp8.Length() , User::Panic( KNullDesC, KErrTooBig ) );
aDest.Append( tmp8 );
}
}
TEST(UTF, Invalid16)
{
for (unsigned int i = 0; i < ArrayLength(Invalid16Strings); ++i) {
nsDependentString str16(Invalid16Strings[i].m16);
nsDependentCString str8(Invalid16Strings[i].m8);
EXPECT_TRUE(NS_ConvertUTF16toUTF8(str16).Equals(str8));
nsCString tmp8("string ");
AppendUTF16toUTF8(str16, tmp8);
EXPECT_TRUE(tmp8.Equals(NS_LITERAL_CSTRING("string ") + str8));
EXPECT_EQ(CompareUTF8toUTF16(str8, str16), 0);
}
}
///
/// @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() ;
}
