Dragon script file

The script file should be produced by using the Script wizard available in the Graphic User Interface version of Dragon. However, the script file is a plain XML file that contains all the information needed for the task, thus the user can manually edit or build from scratch it with any XML or text editor. As the script file could be quite complex, it is strongly suggested always to use the Script wizard.

 

The full reference to the syntax of script files is here reported. Note that all options are the same that could be set while using Dragon GUI, so please refer to the concerning section of this help manual for more details on each issue.

 

1. Main root structure:

 

<DRAGON version="6.0.0">

 <OPTIONS>

   …

 </OPTIONS>

 <DESCRIPTORS>

   …

 </DESCRIPTORS>

 <MOLFILES>

   …

 </MOLFILES>

 <OUTPUT>

   …

 </OUTPUT>

 <EXTERNAL>

   …

 </EXTERNAL>

</DRAGON>

 

All reported nodes are mandatory, except the <EXTERNAL> tag.

 

2. <OPTIONS> tag

 

This section contains all general options for the calculation of descriptors and for the format of saved output files. The following tags are available:

 

<Decimal_Separator value="[VALUE]"/>

Sets the decimal separator to be used.

<Missing_String value="[VALUE]"/>

Sets the string (can be both a number, like “-999”, or a alphanumeric value, like “n.a.”) to be used.

<RejectUnusualValence value="[true/false]"/>

Sets if molecules with unusual valences should be rejected or not.

<Add2DHydrogens value="[true/false]"/>

Sets if hydrogen should be added or not.

<LogPathWalk value="[true/false]"/>

Sets if Path and Walk descriptors should be given in log form or not.

<LogEdge value="[true/false]"/>

Sets if Edge Adjacency descriptors should be given in log form or not.

<Weights>

 <weight name="[Mass/VdWVolume/

                          Electronegativity/Polarizability/

                          Ionization/I-State]"/>

 …

</Weights>

Sets the weights to be used. The <weight> tag can be added several times, each time with a different weight.

<SaveOnlyData value="[true/false]"/>

Sets if saved text file should contain only raw data (no headers).

<SaveLabelsOnSeparateFile value="[true/false]"/>

Sets if data label (headers) should be saved in a separate text file.

<SaveFormatBlock value="[VALUE]"/>

Sets the string for creating names of file when saving by blocks.

<SaveFormatSubBlock value="[VALUE]"/>

Sets the string for creating names of file when saving by sub-blocks.

<SaveExcludeMisVal value="[true/false]"/>

Sets if descriptors with at least one missing value should be excluded when saving results.

<SaveExcludeAllMisVal value="[true/false]"/>

Sets if descriptors with all missing value should be excluded when saving results.

<SaveExcludeConst value="[true/false]"/>

Sets if descriptors with constant value should be excluded when saving results.

<SaveExcludeNearConst value="[true/false]"/>

Sets if descriptors with near constant value should be excluded when saving results.

<SaveExcludeStdDev value="[true/false]"/>

Sets if descriptors with standard deviation values lower than the given threshold should be excluded when saving results.

<SaveStdDevThreshold value="0.0001"/>

Sets the standard deviation threshold.

<SaveExcludeCorrelated value="[true/false]"/>

Sets if descriptors with a pair correlation value higher than the given threshold should be excluded when saving results.

<SaveCorrThreshold value="0.98"/>

Sets the correlation threshold.

<SaveExclusionOptionsToVariables value="="[true/false]"/>

Sets if the above mentioned options for exclusions should be applied also to imported variables.

<SaveExcludeMisMolecules value="[true/false]"/>

Sets if molecules with at least one missing value should be excluded when saving results.

<SaveExcludeRejectedMolecules value="[true/false]"/>

Sets if rejected molecules should be excluded when saving results.

 

3. <DESCRIPTORS> tag

 

This section contains the list of all descriptors selected for calculation. The following tags are available:

 

<block id="[VALUE]" [SelectAll="true"]>

 <descriptor name="[NAME]">

 …

</block>

Selects a descriptor block and the descriptors to be used. The <descriptor> tag can be added several times, the value of the parameter name should be a valid descriptor name from the given block. If  the parameter SelectAll="true" is given, it is not necessary to add <descriptor> tags, and all the descriptors of the given block will be used.

 

4. <MOLFILES> tag

 

This section contains the list of all input molecule files chosen for calculation. The following tags are available:

 

<molInput value="[file/stdin]"/>

Sets if the input molecules should be read from one or more files (file option) or from the Standard Input stream (stdin option)

<molFile value="[FILE]"/>

Selects a file with molecules to be used as input. This tag can be added several times. Note that this tag should be used only when the <molInput> tag is set with the parameter "file".

<molInputFormat value="[SYBYL/MDL/

                                     HYPERCHEM/SMILES

                                     MACROMODEL]"/>

Selects the molecule format to be used while reading from Standard Input stream. Note that this tag should be used only when the <molInput> tag is set with the parameter "stdin".

 

5. <OUTPUT> tag

 

This section contains the specification about how and where the resulting descriptors will be saved. The following tags are available:

 

<SaveStdOut value="[true/false]"/>

Sets if results should be sent to Standard Output stream.

<SaveProject value="[true/false]"/>

Sets if results should be saved as a Dragon project (.drp).

<SaveProjectFile value="[FILE]"/>

Specifies the file name for saving results as a Dragon project (.drp), if this option is set.

<SaveFile value="[true/false]"/>

Sets if results should be saved as plain text file(s).

<SaveType value="[singlefile/block/subblock]"/>

Specifies how to save results as a plain text file(s), if this option is set. Available options are "singlefile" (all results saved in a single file), "block" (results divided in several files, one per descriptors block), "subblock" (results divided in several files, one per descriptors sub-block).

<SaveFilePath value="[FILE]"/>

Specifies the file name for saving results as a plan text file(s), if the "singlefile" option is set; if "block" or "subblock" are set, specifies the path in which results files will be saved.

<logMode value="[none/stderr/file]"/>

Specifies how the log should be produced. Available options are "none" (no log is produced), "stderr" (log is sent to Standard Error stream) or "file" (log is saved to a plain text file)

<logFile value="[FILE]"/>

Specifies the file name for saving the log, if the option is set.

 

6. <EXTERNAL> tag

 

This section contains information about external variables to be imported from a file. This section is not mandatory, thus if the user does not intend to import any external variables file, the <EXTERNAL> tag can be omitted. The following tags are available:

 

<fileName value="[VALUE]"/>

Specifies the plain text file to be imported for external variables.

<delimiter value="[VALUE]"/>

Sets the delimiter character.

<consecutiveDelimiter value="[true/false]"/>

Sets if consecutive delimiter should be reduced to a single one or not.

<MissingValue value="[VALUE]"/>

Specifies the value to be interpreted as missing value.