Utilities used for reading XML files

These utilities are used for dealing with specific XML output from specific CCP4 programs.

Argument list: None

Returns the current value of the XML_OUTPUT logical parameter in the user's preferences. If XML_OUTPUT is not defined in the preferences then 0 is returned.

Argument list: <xmlfile>

Returns 1 if data from the named XML file has already been parsed and loaded into the xmldata array, otherwise returns 0

xmlfile Full pathname of the XML file to check

Argument list: None

Resets XML_LOADED to zero, to force rereading of XML files next time data is requested.

Argument list: <attlist> <attribute>

Returns the values an XML attribute given the attribute list passed to the handling commands by the XML parser. If the attribute cannot be found in the list, or if no corresponding value can be found then an empty string is returned.

attlist Attribute list passed from the XML parser

attribute The attribute whose value is required

Argument list: <xmlfile> <element>

Returns the value of an element in the xmldata global array which is populated by parsing the named CCP4 XML file.

xmlfile Full path name of the CCP4 XML file

element Name of the element in the array of which to return the value

Argument list: <xmlfile>

Parse a CCP4 XML file and load the data into the global array xmldata.

This is a generic version which will read any XML file.

xmlfile Full path name of the XML file to be parsed.

Argument list: <name> <attlist>

See also HandleEndCCP4Xml

name Name of the XML element

attlist Attribute list for that element

Argument list: <name>

See also HandleStartCCP4Xml

name Name of the XML element

Argument list: <xmlfile>

If ALMN has produced an XML output file then this command returns the reindexing operator specified in the attribute list of the reindex_operator element.

If no reindexing operator is specified then the command returns None. If there is an error reading the XML file then an empty string is returned.

xmlfile The full path name of the ALMN XML file to be read.

Argument list: <xmlfile>

Returns the ideal number of monomers based on data extracted from the Matthews XML output file. The Matthews results are analysed and the number of monomers giving a solvent content closest to 50% is returned as the ideal number of monomers in the asu.

xmlfile Full path name of the Matthews XML file

Argument list: <xmlfile>

Returns the peak number of pseudotranslation extracted from an XML file written by the mr_analyse task

xmlfile Full path name of the mr_analyse XML file

Argument list: <xmlfile> <peak_no>

Returns the pseudotranslation vector extracted from an XML file written by the mr_analyse task

xmlfile Full path name of the mr_analyse XML file