OBMoleculeFormat Class Reference

Static routine, which can be called from elsewhere.

Referenced by XMLMoleculeFormat::ReadChemObject().

Static routine, which can be called from elsewhere.

Referenced by XMLMoleculeFormat::WriteChemObject().

The "Convert" interface for reading a new molecule.

Reimplemented from OBFormat.

The "Convert" interface for writing a new molecule.

Reimplemented from OBFormat.

Defer output of a molecule until later, so it can be combined with others

Returns:

Success, or false if no molecule was read.

Instead of sending molecules for output via AddChemObject(), they are saved in here in OBMoleculeFormat or discarded. By default they are saved only if they are in the first input file. Parts of subsequent molecules, such as chemical structure, coordinates and OBGenericData can replace the parts in molecules with the same title that have already been stored, subject to a set of rules. After all input files have been read, the stored molecules (possibly now having augmented properties) are sent to the output format.

Is a static function with *this as parameter so that it can be called from other format classes like XMLMoleculeFormat which are not derived from OBMoleculeFormat.

Referenced by OBMoleculeFormat::ReadChemObjectImpl().

Write out all molecules queued with DeferMolOutput.

Referenced by OBMoleculeFormat::WriteChemObjectImpl().

Delete the list of queued molecules from DeferMolOutput.

Referenced by OBMoleculeFormat::DeferMolOutput(), and OBMoleculeFormat::OutputDeferredMols().

Returns:

the OBMol which combines pFirst and pSecond (i.e.)

Makes a new OBMol on the heap by combining two molecules according to the rule below. If both have OBGenericData of the same type, or OBPairData with the same attribute, the version from pFirst is used. Returns a pointer to a new OBMol which will need deleting by the calling program (probably by being sent to an output format). If the molecules cannot be regarded as being the same structure a NULL pointer is returned and an error message logged.

pFirst and pSecond and the objects they point to are not changed. (const modifiers difficult because class OBMol not designed appropriately)

Combining molecules: rules for each of the three parts Title: Use the title of pFirst unless it has none, when use that of pSecond. Warning if neither molecule has a title.

Structure

• a structure with atoms replaces one with no atoms
• a structure with bonds replaces one with no bonds, provided the formula is the same, else an error.
• structures with atoms and bonds are compared by InChI; error if not the same.
• a structure with 3D coordinates replaces one with 2D coordinates
• a structure with 2D coordinates replace one with 0D coordinates

OBGenericData OBPairData

Referenced by OBMoleculeFormat::DeferMolOutput().

Attempts to read the index file datafilename.obindx successively from the following directories:

• the current directory
• that in the environment variable BABEL_DATADIR or in the macro BABEL_DATADIR if the environment variable is not set
• in a subdirectory of the BABEL_DATADIR directory with the version of OpenBabel as its name An index of type NameIndexType is then constructed. NameIndexType is defined in obmolecformat.h and may be a std::tr1::unordered_map (a hash_map) or std::map. In any case it is searched by

        NameIndexType::iterator itr = index.find(molecule_name);
        if(itr!=index.end())
        unsigned pos_in_datafile = itr->second;
  

  pos_in_datafile is used as a parameter in seekg() to read from the datafile

If no index is found, it is constructed from the datafile by reading all of it using the format pInFormat, and written to the directory containing the datafile. This means that this function can be used without worrying whether there is an index. It will be slow to execute the first time, but subsequent uses get the speed benefit of indexed access to the datafile.

The serialization and de-serialization of the NameIndexType is entirely in this routine and could possibly be improved. Currently re-hashing is done every time the index is read.

Returns:

the type of data converted by this format (here, OBMol)

Reimplemented from OBFormat.

Referenced by OBFormat::RegisterFormat().

The "API" interface Read function.

Reads a single object. Does not make a new object on the heap; can be used with a pointer to an chem object on the heap or the stack.

Reimplemented in XMLMoleculeFormat.

Referenced by OBMoleculeFormat::DeferMolOutput(), OBConversion::Read(), and OBMoleculeFormat::ReadChemObjectImpl().

The "API" interface Write function.

Writes a single object Does not delete the object; can be used with a pointer to an chem object on the heap or the stack.

Returns:

false on error.

Referenced by OBMoleculeFormat::OutputDeferredMols(), OBConversion::Write(), and OBMoleculeFormat::WriteChemObjectImpl().

Information on this format. Printed out in response to -Hxxx option where xxx id the id of the format.

Must be provided by each format class. Can include a list of command line Options. These may be used to construction check boxes, radio buttons etc for GUI interface.

Reimplemented from OBPlugin.

Referenced by OBFormat::Display(), OBConversion::GetNextFormat(), OBMoleculeFormat::OutputDeferredMols(), OBMoleculeFormat::ReadChemObjectImpl(), OBConversion::RegisterOptionParam(), and OBMoleculeFormat::WriteChemObjectImpl().

A decription of the chemical object converted by this format.

If not provided, the object type used by the default format is used (usually OBMol).

Referenced by OBConversion::ReportNumberConverted().

Web address where the format is defined.

Referenced by OBFormat::Display().

Chemical MIME type associated with this file type (if any).

Decribes the capabilities of the format (Read only etc.).

Currently, can be a bitwise OR of any of the following NOTREADABLE READONEONLY NOTWRITABLE WRITEONEONLY DEFAULTFORMAT READBINARY WRITEBINARY READXML

Referenced by OBConversion::AddChemObject(), OBConversion::Convert(), OBFormat::Display(), OBConversion::FullConvert(), OBConversion::GetNextFormat(), OBConversion::InstallStreamFilter(), OBConversion::OpenAndSetFormat(), OBMoleculeFormat::ReadChemObjectImpl(), OBConversion::ReadFile(), OBFormat::RegisterFormat(), OBConversion::SetInFormat(), OBConversion::SetOutFormat(), and OBConversion::WriteFile().

Skip past first n objects in input stream (or current one with n=0).

Returns:

1 on success, -1 on error and 0 if not implemented

Reimplemented in XMLBaseFormat.

Referenced by OBConversion::Convert(), and OBConversion::SetStartAndEnd().

Returns:

a pointer to a new instance of the format, or NULL if fails. Normally a single global instance is used but this may cause problems if there are member variables and the format is used in more than one place in the program.

Referenced by OBConversion::RegisterFormat().

Provides a description in txt of the format specified by itr. If param starts with "in", read", "out" or "write" only the appropriate formats are output. The others return false. If param contains "verbose", the whole description is output.

Reimplemented from OBPlugin.

Referenced by OBConversion::FormatFromMIME().

Make a new instance of the class. See OpTransform, OBGroupContrib, SmartsDescriptor classes for derived versions. Usually, the first parameter is the classname, the next three are parameters(ID, filename, description) for a constructor, and the rest data.

Reimplemented in OBGroupContrib, and OpTransform.

Referenced by OBConversion::LoadFormatFiles().

Get a pointer to a plugin from its type and ID. Return NULL if not found. Not cast to Type*.

Referenced by OBConversion::LoadFormatFiles().

Return the ID of the sub-type instance.

Referenced by OBPlugin::Display(), OBFormat::Display(), and OBDescriptor::PredictAndSave().

Output a list of sub-type classes of the the type PluginID, or, if PluginID is "plugins" or empty, a list of the base types. If PluginID is not recognized or is NULL, the base types are output and the return is false.

Referenced by OBConversion::GetSupportedInputFormat(), OBConversion::GetSupportedOutputFormat(), and OBPlugin::List().

As ListAsVector but sent to an ostream with a default of cout if not specified.

Referenced by OBPlugin::ListAsString().

As ListAsVector but returns a string containing the list.

Utility function to return only the first line of a string.

Referenced by OBPlugin::Display(), OBFormat::Display(), and OBOp::OpOptions().

Return an iterator at the start of the map of the plugin types PluginID or, if there is no such map, the end of the top level plugin map.

Referenced by OBConversion::GetNextFormat(), and OBOp::OpOptions().

Referenced by OBConversion::GetNextFormat(), and OBOp::OpOptions().

Returns the map of the subtypes.

Referenced by OBFormat::RegisterFormat().

Returns a reference to the map of the plugin types. Is a function rather than a static member variable to avoid initialization problems.

Referenced by OBPlugin::GetTypeMap(), OBPlugin::ListAsVector(), and OBFormat::RegisterFormat().

Returns the map of a particular plugin type, e.g. GetMapType("fingerprints").

Returns the type with the specified ID, or NULL if not found. Will be cast to the appropriate class in the calling routine.

Referenced by OBFormat::RegisterFormat().