ProCKSI

= Standardising Results with XML =

ProCKSI utilises a variety of similarity comparison methods (e.g. USM, MaxCMO, TMaling, ...) producing different similarity measures (e.g. Zscore, TMscore, RMSD, ...) each. Each of the comparison methods produces output with different formats and additional content such as alignments, rotation matrix, etc. Some of them produce just one output file, others a set of linked HTML files.

''Optional tags'': '''exclude''' (measure, result), '''log''' (no log is generated if not specified) BR
''Optional attributes'': '''description'''

{{{
<job id="ID" description="TEXT">
<log filename="FILENAME" />

<input type="structure|tree|contact map|similarity matrix">
    <item id="ID" label="TEXT" filename="FILENAME" />
    ...
    <item id="ID" label="TEXT" filename="FILENAME" />
  </input>

<method id="ID" name="TEXT">
    <param name="TEXT">VALUE</param>
    ...
    <param name="TEXT">VALUE</param>

<exclude>
      <measure>NAME</measure>
      ...
      <measure>NAME</measure>

<result>NAME</result>
      ...
      <result>NAME</result>
    </exclude>
  </method>
  ...
  <method>
    ...
  </method>
</job>
}}}

The data used as an input could be protein structures, similarity trees, contact maps or similarity matrices. All specified methods should be able to operate on given data files. This dependency could be verified automatically using XML Schema.