Class Scine::Utils::OpenBabelStreamHandler¶
-
class
OpenBabelStreamHandler
: public Scine::Utils::FormattedStreamHandler¶ If obabel is in the PATH, supports IO to range of OpenBabel’s file formats.
- Note
Concerning the GPLv2 OpenBabel license, this StreamHandler very much communicates ‘at arms length’ with OpenBabel (https://www.gnu.org/licenses/old-licenses/gpl-2.0-faq.en.html#TOCGPLInProprietarySystem) by merely calling it via system process-level interaction, if present.
Public Functions
-
std::pair<AtomCollection, BondOrderCollection>
read
(std::istream &is, const std::string &format) const¶ Reads from an input stream, extracting element types, positions and bond orders (if present)
- Return
An Atomcollection and BondOrderCollection
- Parameters
is
: The input stream to read
- Exceptions
FormatUnsupportedException
: If the desired format is unsupported
-
void
write
(std::ostream &os, const std::string &format, const AtomCollection &atoms) const¶ Writes element types and positional information to an arbitrary filetype.
- Parameters
os
: The output stream to write toformat
: The format to writeatoms
: The element type and positional information to write to a file
- Exceptions
FormatUnsupportedException
: If the desired format is unsupported
-
void
write
(std::ostream &os, const std::string &format, const AtomCollection &atoms, const BondOrderCollection &bondOrders) const¶ Writes element types and positional information to an arbitrary filetype.
- Parameters
os
: The output stream to write to.format
: The format to writeatoms
: The element type and positional information to write to a filebondOrders
: The bond order collection to write to file
- Exceptions
FormatUnsupportedException
: If the desired filetype is unsupportedNoBondInformationException
: If the specified filetype does not contain bond order information
-
std::vector<FormatSupportPair>
formats
() const¶ Returns a list of supported file formats.
- Note
These may, but do not have to be identical to each format’s conventional file suffix
-
bool
formatSupported
(const std::string &format, SupportType operation) const¶ Check whether a particular operation for a format is supported.
- Return
true if the operation is supported for that format
- Parameters
format
: The format filetype suffix to check foroperation
: The operation for which support is queried
-
std::string
name
() const¶ Getter for the name of the FormattedStreamHandler.
- Return
Returns the name of the FormattedStreamHandler.
Public Static Functions
-
static const std::vector<FormatSupportPair> &
getSupportedFormats
()¶ List of checked and supported file formats.
- Note
This list is po
-
static bool
checkForBinary
()¶ Checks for the presence of ‘obabel’ in the PATH.
- Return
Whether ‘obabel’ is found and can be used
-
static int
indirect
(std::istream &is, std::ostream &os, const std::string &inFormat, const std::string &outFormat)¶ Converts between two formats using openbabel with two streams.
- Note
For supported formats,
- See
openBabelFormats
- Warning
This does not check whether obabel is present. Do not use this function without a pre-pended
checkForBinary
call.- Pre
is
populated with data of formatinFormat
- Post
os
is populated with data of formatoutFormat
- Return
The exit code of obabel execution
- Parameters
is
: The input stream for obabelos
: The output stream for obabelinFormat
: The format string ofis
outFormat
: The format string ofos