Class Scine::Utils::ChemicalFileHandler

class ChemicalFileHandler

Handles the reading and writing of chemical file formats.

Matches suffixes to chemical file formats and then dispatches the calls to appropriate streaming I/O handlers. Catches I/O errors.

Public Static Functions

static std::pair<AtomCollection, BondOrderCollection> read(const std::string &filename)

Reads an atom collection and tries to read a bond order collection from a file.

Supported file formats are currently:

  • mol

  • xyz

Parameters

  • filename: The path to the file to read

If obabel is found in your path, all formats that openbabel supports are also available.

Note

The format of a file is deduced from its suffix.

Return

an AtomCollection and a BondOrderCollection read from the file. The BondOrderCollection may be empty if the file format does not include such information

Exceptions

  • FileInaccessibleException: if the file does not exist or cannot be opened

  • FormatUnsupportedException: if the file suffix cannot be matched to a supported file format

  • FormatMismatchException: if the file’s format does not match the parser’s expectations (e.g. if the suffix does not match the format)

  • NoBondInformationException: if the format does not contain bond order information

static void write(const std::string &filename, const AtomCollection &atoms)

Writes an atom collection to a file.

Supported file formats are currently

  • xyz

  • mol

Note

Overwrites existing files

Parameters

  • filename: The path to the file to write

  • atoms: The atom collection to commit to a file

Exceptions

  • FormatUnsupportedException: if the file suffix cannot be matched to a supported file format

  • FileInaccessibleException: if the file cannot be created

static void write(const std::string &filename, const AtomCollection &atoms, const BondOrderCollection &bondOrders)

Writes an atom collection and a bond order collection to a file.

Supported file formats are currently

  • mol

Note

Overwrites existing files

Parameters

  • filename: The path to the file to write

  • atoms: The atom collection to commit to a file

Exceptions

  • FormatUnsupportedException: if the file suffix cannot be matched to a supported file format

  • FileInaccessibleException: if the file cannot be created

struct FileInaccessibleException : public exception

Exception thrown if the file does not exist or cannot be opened.