XMLConversion Class Reference

Three types of options set on the the command line by -a? , -x? , or -?

Enumerator:

INOPTIONS
OUTOPTIONS
GENOPTIONS

Existing OBConversion instance copied.

Frees reader and writer if necessary.

opens libxml2 reader

opens libxml2 writer

Parses the input xml stream and sends each element to the format's callback routines.

Read and discard XML text up to the next occurrence of the tag e.g."/molecule>" This is left as the current node. Returns 1 on success, 0 if not found, -1 if failed.

This static function returns a reference to the map Avoids "static initialization order fiasco"

Returns the extended OBConversion class, making it if necessary.

Because OBConversion::Convert is still using the unextended OBConversion object we need to obtain the conversion paramters from it when requested

Reimplemented from OBConversion.

Static callback functions for xmlReaderForIO().

Sets value to element content. Returns false if there is no content.

Sets value to element content as an integer. Returns false if there is no content.

Sets value to element content as an double. Returns false if there is no content.

Called once by each format class.

Class information on formats is collected by making an instance of the class derived from OBFormat(only one is usually required). RegisterFormat() is called from its constructor.

If the compiled format is stored separately, like in a DLL or shared library, the initialization code makes an instance of the imported OBFormat class.

Searches registered formats.

Searches registered formats for an ID the same as the file extension.

Searches registered formats for a MIME the same as the chemical MIME type passed.

Repeatedly called to recover available Formats.

Returns the ID + the first line of the description in str and a pointer to the format in pFormat. If called with str==NULL the first format is returned; subsequent formats are returned by calling with str!=NULL and the previous value of itr returns false, and str and pFormat NULL, when there are no more formats. Use like:

        const char* str=NULL;
        Formatpos pos;
        OBConversion conv; // dummy to make sure static data is available
        while(OBConversion::GetNextFormat(pos,str,pFormat))
        {
                // use str and pFormat
        }
   *

NOTE: Because of dynamic loading problems, it is usually necessary to declare a "dummy" OBConversion object to access this static method. (Not elegant, but will hopefully be fixed in the future.)

Sets the formats from their ids, e g CML.

Sets the formats from their ids, e g CML. If inID is NULL, the input format is left unchanged. Similarly for outID Returns true if both formats have been successfully set at sometime

Sets the input format from an id e.g. CML.

Sets the output format from an id e.g. CML.

Get the position in the input stream of the object being read.

Get the length in the input stream of the object being read.

Returns:

a default title which is the filename

Extension method: deleted in ~OBConversion().

Determine whether an option is set.

Returns:

NULL if option not and a pointer to the associated text if it is

Access the map with option name as key and any associated text as value.

Set an option of specified type, with optional text.

Set several single character options of specified type from string like ab"btext"c"ctext".

For example -h takes 0 parameters; -f takes 1. Call in a format constructor.

Returns:

the number of parameters registered for the option, or 0 if not found

Returns the list of supported input format

Returns the list of supported output format

Conversion for single input and output stream.

Conversion with existing streams.

Actions the "convert" interface. Calls the OBFormat class's ReadMolecule() which

• makes a new chemical object of its chosen type (e.g. OBMol)
• reads an object from the input file
• subjects the chemical object to 'transformations' as specified by the Options
• calls AddChemObject to add it to a buffer. The previous object is first output via the output Format's WriteMolecule(). During the output process calling IsFirst() and GetIndex() (the number of objects including the current one already output. allows more control, for instance writing <cml> and </cml> tags for multiple molecule outputs only.

AddChemObject does not save the object passed to it if it is NULL (as a result of a DoTransformation()) or if the number of the object is outside the range defined by StartNumber and EndNumber.This means the start and end counts apply to all chemical objects found whether or not they are output.

If ReadMolecule returns false the input conversion loop is exited.

Conversion with multiple input/output files: makes input and output streams, and carries out normal, batch, aggregation, and splitting conversion.

Makes input and output streams, and carries out normal, batch, aggregation, and splitting conversion.

Normal Done if FileList contains a single file name and OutputFileName does not contain a *.

Aggregation Done if FileList has more than one file name and OutputFileName does not contain * . All the chemical objects are converted and sent to the single output file.

Splitting Done if FileList contains a single file name and OutputFileName contains a * . Each chemical object in the input file is converted and sent to a separate file whose name is OutputFileName with the replaced by 1, 2, 3, etc. OutputFileName must have at least one character other than the * before the extension. For example, if OutputFileName is NEW*.smi then the output files are NEW1.smi, NEW2.smi, etc.

Batch Conversion Done if FileList has more than one file name and contains a * . Each input file is converted to an output file whose name is OutputFileName with the * replaced by the inputfile name without its path and extension. So if the input files were inpath/First.cml, inpath/Second.cml and OutputFileName was NEW*.mol, the output files would be NEWFirst.mol, NEWSecond.mol.

If FileList is empty, the input stream that has already been set (usually in the constructor) is used. If OutputFileName is empty, the output stream already set is used.

On exit, OutputFileList contains the names of the output files.

Returns the number of Chemical objects converted.

Adds to internal array during input.

Called by ReadMolecule() to deliver an object it has read from an input stream. Used in two modes:

• When Count is negative it is left negative and the routine is just a store for an OBBase object. The negative value returned tells the calling routine that no more objects are required.
• When count is >=0, probably set by Convert(), it acts as a queue of 2: writing the currently stored value before accepting the supplied one. This delay allows output routines to respond differently when the written object is the last. Count is incremented with each call, even if pOb=NULL. Objects are not added to the queue if the count is outside the range StartNumber to EndNumber. There is no upper limit if EndNumber is zero. The return value is the return code from WriteChemObject - false on error.

Retrieve from internal array during output.

Retrieves an object stored by AddChemObject() during output

True if the first input object is being processed.

Retrieves number of ChemObjects that have been actually output.

Returns the number of objects which have been output or are currently being output. The outputindex is incremented when an object for output is fetched by GetChemObject(). So the function will return 1 if called from WriteMolecule() during output of the first object.

Sets ouput index (maybe to control whether seen as first object).

Used with multiple input files. Off by default.

Used with multiple input files. Off by default.

The default format is set in a single OBFormat class (generally it is OBMol).

Outputs an object of a class derived from OBBase.

Part of "API" interface. The output stream can be specified and the change is retained in the OBConversion instance

Outputs an object of a class derived from OBBase as a string.

Part of "API" interface. The output stream is temporarily changed to the string and then restored This method is primarily intended for scripting languages without "stream" classes The optional "trimWhitespace" parameter allows trailing whitespace to be removed (e.g., in a SMILES string or InChI, etc.)

Outputs an object of a class derived from OBBase as a file (with the supplied path).

Part of "API" interface. The output stream is changed to the supplied file and the change is retained in the OBConversion instance. This method is primarily intended for scripting languages without "stream" classes

Manually closes and deletes the output stream The file is closed anyway when in the OBConversion destructor or when WriteFile is called again.

Since:

version 2.1

Reads an object of a class derived from OBBase into pOb.

Part of "API" interface. The input stream can be specified and the change is retained in the OBConversion instance

Returns:

false and pOb=NULL on error

Reads an object of a class derived from OBBase into pOb from the supplied string.

Part of "API" interface.

Returns:

false and pOb=NULL on error This method is primarily intended for scripting languages without "stream" classes

Reads an object of a class derived from OBBase into pOb from the file specified.

Part of "API" interface. The output stream is changed to the supplied file and the change is retained in the OBConversion instance.

Returns:

false and pOb=NULL on error This method is primarily intended for scripting languages without "stream" classes

Replaces * in BaseName by InFile without extension and path.

Replaces * in BaseName by Count.

Checks for misunderstandings when using the -m option.

contains ID and pointer to all OBFormat classes

This static function returns a reference to the FormatsMap which, because it is a static local variable is constructed only once. This fiddle is to avoid the "static initialization order fiasco" See Marshall Cline's C++ FAQ Lite document, www.parashift.com/c++-faq-lite/".

contains MIME and pointer to all OBFormat classes

This static function returns a reference to the FormatsMIMEMap which, because it is a static local variable is constructed only once. This fiddle is to avoid the "static initialization order fiasco" See Marshall Cline's C++ FAQ Lite document, www.parashift.com/c++-faq-lite/".

input stream is gzip-encoded

position in the input stream of the object being written

position in the input stream of the object being read

length in the input stream of the object being written

length in the input stream of the object being read

Way to extend OBConversion.

list of supported input format

list of supported output format