User-Specified descriptors from Command Line


This option allows the user to compute specific ProtDCal descriptors using the Index Definition Language(IDL) file. IDL is represented by a file with the extension ".idl" with one descriptors name per line, an example could be:

Mw_NO_ALA_N1
ISA_NO_ALA_N1
...

The output generated using IDL interface will be a Prot file containing only the descriptor described in the IDL file. This option is executed only for CLI mode, using the next parameters:

i [/path/to/input/folder] for specify the input folder for calculations, by default this option use the Datasets folder in ProtDCal workspace.
f specify the dataset format (PDB-> pdb or FASTA-> fasta).
x [/path/to/projects/folder] for specify a file containing a list of specific descriptors, each descriptor must be a line. For use this option is necesary indicate to ProtDCal additional parameters(input and output directory, and the format of dataset(PDB or FASTA)).

In addition the parameters "o" for output directory is necessary. An example for use this command will be:


java -jar ProtDCal.jar -i Datasets/Fasta_Protein_Format/Stability -f fasta -x Projects -o Output/example