APPENDIX D - Score XML

The Score XML is a file generated by VEGA when you want to evaluate and analyze the interaction energy (score) of two molecules included in a complex that can be obtained through molecular docking procedures (see -f option). The following scheme highlight the meaning of each XML tag:

Configuration file

 

Description


<score version="1.0">
     

Main tag:
- version Version number of file format.


  <type id="SCORETYP" value="SCOREVAL">
 

Score section (one for each calculated score/energy type):
- id identification string (BROTO, BROTO2, BROTO3, BROTOF, CHARMM, CHARMM22, CHARMM36, CVFF, ELECT and ELECTDD).
- value total score/interaction energy.


    <description>Score description</description>
 

Score/energy type description.


    <atoms number="atmnum">
 

Begin of the section containing the contribution of each atom to the total score/energy.
- number number of the atoms in the complex.


      ...
 

Unformatted floating point numbers separated by one ore more spaces or by line feeds.


    </atoms>
 

End of the atom contributions.


    <residues number="resnum">
 

Begin of the section containing the contribution of each residue to the total score/energy.
- number number of the residues in the complex.


      <residue name="resname" number="resnum"
       chain="cid" mol="molnum" energy="eneval"/>
      ...
 

In this section, there is one record for each residue in the complex. More in detail:
- name residue name (max. 4 characters).
- number residue number (max. 4 digits).
- chain chain id (1 character, * if the chain id is undefined).
- mol number of the molecule containing the residue.
- energy energy contribution of the residue.
The residues are sorted by energy.


    </residues>
 

End of residues section.


  </type>
 

End of score/energy type section.


  ...
  Here can be repeated the sections between type one time for each type of calculated score/energy.

</score>
  End of Score XML file.