bussiere / 3dstructureclustering Goto Github PK

DESCRIPTION
This software can be used to find cluster in biological structures (PDB and
Dynamics trajectories like Gromacs and Amber). 

SYNTAXE : 
/!\ NEVER USE SPACES
The Basic Syntaxe is => CHAIN:RES_NUM:ATOMS_NAME
chain, amino acids and atoms are separed with ":"
You can select an amino acid interval with RES_NUM-RES_NUM 
    => 1-30
You can select several atoms type with "-" to (it's apply on the selected AAs)
    => CA-CB
If you wan to select all elements of a group : use "." or nothing.
    => A:.:. (means all atoms of all residues of the chain A)
    => A:: is the same as A:.:.
You can have several selection if you put a "," between them
    => A:.:.,B:1-30:CA (the Entire chain A and only the carbon alpha of the firth
        30 aa of the chain B)

exemples : 
:20-30:CA-CB => Alpha and beta carbon of the amino acids 20 to 30 of all chains
A:1-100:.,B:200-300:CA => alpha carbons of aa 200 to 300 of the chain B AND all
                          atoms of aa 1 to 100 of the chain A.
    
ARGUMENTS : 
    -f : a list of pdb (like "/structure/*.pdb") 
    -l : list of pdb code! /!\ IF YOU USED THAT : -f as to be the PATH of your pdb files
    -s : Selection string
    -a : Alignement type (g = Global, l = Local (on selection string))
    -o : output name for the log file (default is cluster.log)
    
USAGE : 
python Cluster_Analysis.py -f *.pdb -s [SELECTION] -a Alignement_type -o output_log