This option allows to do calculations without the GUI. First is necessary start a console and then move to the ProtDCal folder using command cd /path/to/ProtDCal. Second execute the follow command:
java [Java parameters] [ProtDCal parameters]
This command has divide in two parts (Java and ProtDCal) for configure Java and ProtDCal parameters in a separated way. In the first part (Java) you configure all Java parameters, but we recommend just the next parameter:
-Xms[RAM]M | for increase the memory for calculations. RAM is the quantity in Megabytes, for example: -Xms256M -Xms512M |
In other way, the second part (ProtDCal) you can configure the next options:
p | [/path/to/project/folder] for specify the projects to be processed, by default we recommend put the projects in the Projects folder in the ProtDCal workspace. |
o | [/path/to/output/folder] for specify the output folder for calculations, by default this option use the Outputs folder in ProtDCal workspace. |
i | [/path/to/input/folder] for specify the input folder for calculations. |
f | for specify the dataset format: (PDB-> pdb or FASTA-> fasta) |
x | [/path/to/features/list/folder] for specify the path to a file containing a list of specific descriptors, each descriptor label must be in a different line. For using this option it is necessary to indicate additional parameters(-i, -f and -o). |
ppi | [/path/to/ppi/file/combinations] for specify the PPI file combinations path for protein pairs descriptors calculations. |
v | 1 or 0 for including the project name in the descriptor name. The "1" include the name "0" not. |
The formats for using this CLI are::
java -Xmx1000m -jar ProtDCal.jar -p [/path/to/project/folder] -o [/path/to/output/folder]
java -Xmx1000m -jar ProtDCal.jar -f [fasta o pdb] -i [/path/to/input/folder] -x [/path/to/features/list/folder] -o [/path/to/output/folder]
java -Xmx1000m -jar ProtDCal.jar -f fasta -i [/path/to/input/folder] -x [/path/to/features/list/folder] -o [/path/to/output/folder] -ppi [/path/to/ppi/file/combinations]
java -Xmx1000m -jar ProtDCal.jar -i [/path/to/input/folder] -p [/path/to/project/folder] -o [/path/to/output/folder] -ppi [/path/to/ppi/file/combinations]