DCI Analysis CLI¶

This tutorial familiarises users with the Command-line Interface (CLI) of the DCI Analysis. The same functionality is also available in the PACKMAN API ( tutorials_dci_api )

PACKMAN DCI Analysis Web Server:

How to cite:

Paper Under Review.

CLI INSTRUCTIONS¶

Following is the PACKMAN hinge prediction interface description:

usage: packman dci [-h] [-pdbid PDB_ID] [-chain CHAIN] [-cutoff CUTOFF]
                    [-n_com N_COM]
                    FILENAME

positional arguments:
FILENAME              Path and filename of the PDB file.

optional arguments:
-h, --help            show this help message and exit
-pdbid PDB_ID, --pdbid PDB_ID
                        If provided, the PBD with this ID will be downloaded
                        and saved to FILENAME.
-chain CHAIN, --chain CHAIN
                        Enter The Chain ID
-cutoff CUTOFF, --cutoff CUTOFF
                        Enter the cutoff for DCI. (Read the Publication for
                        more details)
-n_com N_COM, --n_com N_COM
                        Enter the number of communities. (Read the Publication
                        for more details)

EXAMPLES¶

python -m packman dci 1prw.pdb –chain A The options are self-explanatory. This is the example where PDB file is already present.
python -m packman dci 1prw.pdb Chains are not defined, and therefore DCI is calculated for all the chains.