/// Writes \p molecule to the file with \p fileName.
///
/// This static convenience method allows for the writing of molecule
/// to a file without explicitly creating a file object.
void MoleculeFile::quickWrite(const Molecule *molecule, const std::string &fileName)
{
MoleculeFile file;
file.addMolecule(const_cast<Molecule *>(molecule));
file.write(fileName);
// remove the molecule from the file so that it does
// not get deleted when this function returns
file.removeMolecule(const_cast<Molecule *>(molecule));
}
/// Downloads and returns the file containing the compounds with ID's
/// in the list \p ids. If an error occurs \c 0 is returned.
///
/// The ownership of the file is passed to the caller.
///
/// For example, to download the file containing %PubChem Compounds
/// 1, 2, 3, 42 and 57:
/// \code
/// QStringList ids;
/// ids << "1" << "2" << "3" << "42" << "57";
/// MoleculeFile *file = pubchem.downloadFile(ids);
/// \endcode
MoleculeFile* PubChem::downloadFile(const QStringList &ids) const
{
QByteArray data = downloadFileData(ids, "sdf");
if(data.isEmpty()){
return 0;
}
std::stringstream buffer(std::string(data.constData(), data.size()));
MoleculeFile *file = new MoleculeFile;
file->read(buffer, "sdf");
return file;
}
/// Downloads and returns the file containing the compounds with ID's
/// in the list \p ids. If an error occurs \c 0 is returned.
///
/// The ownership of the file is passed to the caller.
///
/// For example, to download the file containing %PubChem Compounds
/// 1, 2, 3, 42 and 57:
/// \code
/// QStringList ids;
/// ids << "1" << "2" << "3" << "42" << "57";
/// MoleculeFile *file = pubchem.downloadFile(ids);
/// \endcode
MoleculeFile* PubChem::downloadFile(const QStringList &ids) const
{
QByteArray data = downloadFileData(ids, "sdf");
if(data.isEmpty()){
return 0;
}
QBuffer buffer;
buffer.setData(data);
buffer.open(QBuffer::ReadOnly);
MoleculeFile *file = new MoleculeFile;
file->read(&buffer, "sdf");
return file;
}
/// Downloads and returns the ligand molecule with \p name. If an
/// error occurs \c 0 is returned.
///
/// The ownership of the returned molecule is passed to the caller.
///
/// For example, to download the heme ligand (named "HEM"):
/// \code
/// Molecule *heme = pdb.downloadLigand("HEM");
/// \endcode
Molecule* ProteinDataBank::downloadLigand(const QString &name) const
{
QString url("%1/pdb/files/ligand/%2_ideal.sdf");
QByteArray data = DownloadThread::download(url.arg(d->url.toString()).arg(name.toUpper()));
if(data.isEmpty()){
return 0;
}
std::stringstream buffer(std::string(data.constData(), data.size()));
MoleculeFile file;
bool ok = file.read(buffer, "sdf");
if(!ok || file.isEmpty()){
return 0;
}
Molecule *molecule = file.molecule();
file.removeMolecule(molecule);
return molecule;
}