Post-download file conversion / processing (Basics)


As we mentioned before in Application Objectives, it is also known that in Bioinformatics most of the data files need also further processing after being downloaded. Frequently the downlaoded files have to undergo archive extracting and/or file copying, and/or moving, and/or renaming. In other cases it is a more complicated user-designed algorithm that has to be applied to each downloaded file. Those algorithms are implemented using different computer language scripts or compiled into independent binary applications.

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For any set of downloaded or stored files on the user's computer, the user can apply any file conversion or processing using an executable, batch or script file (*.exe; *.bat; *.pl and etc). Such executable has to be able to process a single file as input.

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In the following screens you should specify:

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1) In the Main toolbar click Convert button or use Main Menu Tools Convert:




2) The docked Files conversion window will be shown.

The window consists of several sections:


Under activity we understand a group of variables uniquely identifying the file conversion / processing (or all values of the input fields on the window form above).

In Predefined activities section: you can open a previously saved conversion / processing activity, save the current activity as an external file (*.convert), and write the activity memo.

3) Open a previously saved activity supplied with BioDownloader package by clicking:



4) Files conversion window form will be filled out with the previously-saved values:


This conversion activity extracts

  1. remediated PDB-formatted coordinates files
  2. s2c files
  3. pdbaa files
  4. pdbnt files


with an external utility XML2PDB provided with BioDownloader installation package.

In this activity Filename field contains "xml2pdb.exe". Input files Mask is "*.xml". Executable argument line defined as "-i %FULLNAME -c -s -p -n".

In Executable argument line field "%FULLNAME" is substituted with "%IDIR + %INAME" which are in their turn replaced with the input files directory path and the names of the files contained within this directory and satisfying the input files Mask.

5) Specify input files Path and Output directory:

As you can see, those two fields have the red balloons next to them and are notifying the user that such paths don't exist:






6) Check the input fields for the red balloons, check the command line, check the input files, specify optional parameters, click Launch button to launch the file conversion.

There are no red balloons anymore; the file conversion action is ready to be launched. It will apply the following command to every input file in the input folder with the xml extension:


Check files in the input folder:



Optionally you can specify the timeout per each file conversion:


Please lauch the files conversion now:


7) The input xml files will be processed and converted to pdb, s2c, pdbaa, and pdbnt files:




8) You may wish to save the modified activity under a different filename:

You've made changes to the xml2pdb.convert task when you changed the default input files Path and Output directory to your own values. You may wish to change the Memo and save the modified activity under a different filename by clicking Save As button:



Later you can return to this activity by using a) the drop-down list, or b) clicking Open button, or c) double-clicking the required conversion activity file in Windows Explorer (it will start a new instance of BioDowloader):




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