//------------------------------------------------------------------------------
bool OBOpenDXCubeFormat::ReadMolecule( OBBase* pOb, OBConversion* pConv )
{
OBMol* pmol = pOb->CastAndClear<OBMol>();
if(pmol == 0)
return false;
istream& ifs = *pConv->GetInStream();
const char* title = pConv->GetTitle();
char buffer[BUFF_SIZE];
stringstream errorMsg;
if (!ifs)
return false; // We are attempting to read past the end of the file
pmol->SetTitle(title);
while (ifs.good() && ifs.getline(buffer,BUFF_SIZE)) {
if (buffer[0] == '#')
continue; // comment line
if (EQn(buffer, "object", 6))
break;
}
if (!ifs)
return false; // ran out of lines
vector<string> vs;
tokenize(vs, buffer);
// Number of grid points (voxels)
vector<int> voxels(3);
if (!EQn(buffer, "object", 6) || vs.size() != 8)
return false;
else {
voxels[0] = atoi(vs[5].c_str());
voxels[1] = atoi(vs[6].c_str());
voxels[2] = atoi(vs[7].c_str());
}
double x, y, z;
if (!ifs.getline(buffer, BUFF_SIZE) || !EQn(buffer, "origin", 6))
return false;
else {
tokenize(vs, buffer);
if (vs.size() != 4)
return false;
x = atof(vs[1].c_str());
y = atof(vs[2].c_str());
z = atof(vs[3].c_str());
}
vector3 origin(x, y, z);
// now three lines with the x, y, and z axes
vector<vector3> axes;
for (unsigned int i = 0; i < 3; ++i) {
if (!ifs.getline(buffer, BUFF_SIZE) || !EQn(buffer, "delta", 5))
return false;
else {
tokenize(vs, buffer);
if (vs.size() != 4)
return false;
x = atof(vs[1].c_str());
y = atof(vs[2].c_str());
z = atof(vs[3].c_str());
axes.push_back(vector3(x, y, z));
}
}
// Two remaining header lines before the data:
/*
object 2 class gridconnections counts nx ny nz
object 3 class array type double rank 0 times n data follows
*/
if (!ifs.getline(buffer, BUFF_SIZE) || !EQn(buffer, "object", 6))
return false;
if (!ifs.getline(buffer, BUFF_SIZE) || !EQn(buffer, "object", 6))
return false;
pmol->BeginModify();
pmol->SetDimension(3);
OBGridData *gd = new OBGridData;
gd->SetAttribute("OpenDX");
// get all values as one vector<double>
char *endptr;
vector<double> values;
int n = voxels[0]*voxels[1]*voxels[2];
int line = 0;
values.reserve(n);
while (ifs.getline(buffer, BUFF_SIZE))
{
++line;
if (EQn(buffer, "attribute", 9))
break; // we're finished with reading data -- although we should probably have a voxel check in here too
tokenize(vs, buffer);
if (vs.size() == 0)
{
errorMsg << "Problem reading the OpenDX grid file: cannot"
<< " read line " << line
<< ", there does not appear to be any data in it.\n"
<< buffer << "\n";
obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obError);
return false;
}
for (unsigned int l = 0; l < vs.size(); ++l)
{
values.push_back(strtod(static_cast<const char*>(vs[l].c_str()), &endptr));
}
}
gd->SetNumberOfPoints(voxels[0], voxels[1], voxels[2]);
gd->SetLimits(origin, axes[0], axes[1], axes[2]);
gd->SetUnit(OBGridData::ANGSTROM);
gd->SetOrigin(fileformatInput); // i.e., is this data from a file or determined by Open Babel
gd->SetValues(values); // set the values
pmol->SetData(gd); // store the grids in the OBMol
pmol->EndModify();
// Trailing control lines
/*
attribute "dep" string "positions"
object "regular positions regular connections" class field
component "positions" value 1
component "connections" value 2
component "data" value 3
*/
if (!ifs.getline(buffer, BUFF_SIZE) || !EQn(buffer, "object", 6))
return false;
if (!ifs.getline(buffer, BUFF_SIZE) || !EQn(buffer, "component", 9))
return false;
if (!ifs.getline(buffer, BUFF_SIZE) || !EQn(buffer, "component", 9))
return false;
if (!ifs.getline(buffer, BUFF_SIZE) || !EQn(buffer, "component", 9))
return false;
// clean out any remaining blank lines
std::streampos ipos;
do
{
ipos = ifs.tellg();
ifs.getline(buffer,BUFF_SIZE);
}
while(strlen(buffer) == 0 && !ifs.eof() );
ifs.seekg(ipos);
return true;
}
