//------------------------------------------------------------------------------
bool OBOpenDXCubeFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
char buffer[BUFF_SIZE];
string str;
stringstream errorMsg;
OBGridData *gd = (OBGridData*)mol.GetData(OBGenericDataType::GridData);
if (gd == NULL) {
errorMsg << "The molecule has no grid.";
obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obWarning);
return false;
}
// APBS-style OpenDX Multigrid
// First some comments
ofs << "# Data from Open Babel " << BABEL_VERSION << "\n";
str = mol.GetTitle();
if (str.empty())
ofs << "# Molecule Title: *****" << "\n";
else
ofs << "# Molecule Title: " << str << "\n";
int nx, ny, nz;
double origin[3], xAxis[3], yAxis[3], zAxis[3];
gd->GetAxes(xAxis, yAxis, zAxis);
gd->GetNumberOfPoints(nx, ny, nz);
gd->GetOriginVector(origin);
// data line 1: # of points in x, y, z (nx, ny, nz)
snprintf(buffer, BUFF_SIZE, "object 1 class gridpositions counts %5d %5d %5d", nx, ny, nz);
ofs << buffer << "\n";
// data line 2: origin (x, y, z)
snprintf(buffer, BUFF_SIZE,"origin %12.6f %12.6f %12.6f",
origin[0], origin[1], origin[2]);
ofs << buffer << "\n";
// data line 3: x-displacement
snprintf(buffer, BUFF_SIZE,"delta %12.6f %12.6f %12.6f",
xAxis[0], xAxis[1], xAxis[2]);
ofs << buffer << "\n";
// data line 4: y-displacement
snprintf(buffer, BUFF_SIZE,"delta %12.6f %12.6f %12.6f",
yAxis[0], yAxis[1], yAxis[2]);
ofs << buffer << "\n";
// data line 5: z-displacement
snprintf(buffer, BUFF_SIZE,"delta %12.6f %12.6f %12.6f",
zAxis[0], zAxis[1], zAxis[2]);
ofs << buffer << "\n";
// data line 6: # of points in x, y, z (nx, ny, nz)
snprintf(buffer, BUFF_SIZE, "object 2 class gridconnections counts %5d %5d %5d", nx, ny, nz);
ofs << buffer << "\n";
// data line 7: total # of points
snprintf(buffer, BUFF_SIZE, "object 3 class array type double rank 0 items %5d data follows", nx*ny*nz);
ofs << buffer << "\n";
// The cube(s)
double value;
unsigned int count = 1;
for (int i = 0; i < nx; ++i)
{
for (int j = 0; j < ny; ++j)
{
for (int k = 0; k < nz; ++k)
{
value = gd->GetValue(i, j, k);
snprintf(buffer, BUFF_SIZE," %12.5E", value);
if (count % 3 == 0)
ofs << buffer << "\n";
else
ofs << buffer;
count++;
} // z-axis
} // y-axis
} // x-axis
if (count % 3 != 0)
ofs << "\n";
ofs << "attribute \"dep\" string \"positions\"\n";
ofs << "object \"regular positions regular connections\" class field\n";
ofs << "component \"positions\" value 1\n";
ofs << "component \"connections\" value 2\n";
ofs << "component \"data\" value 3\n";
return true;
}
//------------------------------------------------------------------------------
bool OBGaussianCubeFormat::WriteMolecule(OBBase* pOb, OBConversion* pConv)
{
OBMol* pmol = dynamic_cast<OBMol*>(pOb);
if(pmol==NULL)
return false;
ostream &ofs = *pConv->GetOutStream();
OBMol &mol = *pmol;
char buffer[BUFF_SIZE];
string str;
stringstream errorMsg;
// first two lines are comments
str = mol.GetTitle();
if (str.empty())
ofs << "*****" << endl;
else
ofs << str << endl;
ofs << endl; // line 2
OBGridData *gd = (OBGridData*)mol.GetData(OBGenericDataType::GridData);
if (gd == NULL) {
errorMsg << "The molecule has no grid.";
obErrorLog.ThrowError(__FUNCTION__, errorMsg.str(), obWarning);
return false;
}
int nx, ny, nz;
double origin[3], xAxis[3], yAxis[3], zAxis[3];
gd->GetAxes(xAxis, yAxis, zAxis);
gd->GetNumberOfPoints(nx, ny, nz);
gd->GetOriginVector(origin);
// line 3: number of atoms, origin x y z
snprintf(buffer, BUFF_SIZE,"%5d%12.6f%12.6f%12.6f", - static_cast<signed int> (mol.NumAtoms()),
origin[0]*ANGSTROM_TO_BOHR, origin[1]*ANGSTROM_TO_BOHR, origin[2]*ANGSTROM_TO_BOHR);
ofs << buffer << endl;
// line 4: number of points x direction, axis x direction x y z
snprintf(buffer, BUFF_SIZE,"%5d%12.6f%12.6f%12.6f", nx,
xAxis[0]*ANGSTROM_TO_BOHR, xAxis[1]*ANGSTROM_TO_BOHR, xAxis[2]*ANGSTROM_TO_BOHR);
ofs << buffer << endl;
// line 5: number of points y direction, axis y direction x y z
snprintf(buffer, BUFF_SIZE,"%5d%12.6f%12.6f%12.6f", ny,
yAxis[0]*ANGSTROM_TO_BOHR, yAxis[1]*ANGSTROM_TO_BOHR, yAxis[2]*ANGSTROM_TO_BOHR);
ofs << buffer << endl;
// line 6: number of points z direction, axis z direction x y z
snprintf(buffer, BUFF_SIZE,"%5d%12.6f%12.6f%12.6f", nz,
zAxis[0]*ANGSTROM_TO_BOHR, zAxis[1]*ANGSTROM_TO_BOHR, zAxis[2]*ANGSTROM_TO_BOHR);
ofs << buffer << endl;
// Atom lines: atomic number, ?, X, Y, Z
FOR_ATOMS_OF_MOL (atom, mol) {
double *coordPtr = atom->GetCoordinate();
snprintf(buffer, BUFF_SIZE,"%5d%12.6f%12.6f%12.6f%12.6f", atom->GetAtomicNum(),
static_cast<double>(atom->GetAtomicNum()),
coordPtr[0]*ANGSTROM_TO_BOHR, coordPtr[1]*ANGSTROM_TO_BOHR, coordPtr[2]*ANGSTROM_TO_BOHR);
ofs << buffer << endl;
}