Contact Residues 1.2
--------------------

REQUIREMENTS: VMD Version 1.1 or greater (?)

CHANGELOG:
	1.1 fixed some wrong variable names
	1.2 added parameter for output filenames prefix

DESCRIPTION:
	Script analyzing contacts between 2 groups of residues, e.g.
	contacts between residues of a protein and ions.

HOW IT WORKS:
	Script uses VMD measure contacts command to find all contacts between
	residues from 2 different selections fulfilling the distance criterion.
	All atom contacts between 1 pair of residues in 1 frame are tken as
	a single residue contact.
	Please make sure that your structure is imaged and centered. VMD doesn't 
	support handling PBC in "measure" and similar commands yet.
	See the script itself for more information.

PROCEDURES:
	fResContactSingle - analyzes contacts for single (active) frame, prints
			    output to vmd console
	fResContact - analyzes the whole trajectory, prints output to files

EXAMPLE USAGE AND OUTPUT:
	usage:
	fResContactSingle "sel1" "sel2" cutoff
	fResContact "sel1" "sel2" cutoff output_name_prefix <startframe <endframe>>
	Optional startframe/endframe parameters define range of frames from
	the trajectory, that should be analyzed. If omitted, whole trajectory
	is parsed
	
	example:
	fResContactSingle "protein" "resname CL" 3.5
	finds all contacts between protein and CL residues (distance <=3.5A)
	output:
   	38 ARG -    81  CL - 2.393458
    	7 PRO -   113  CL - 3.178880
   	16 ARG -   110  CL - 2.513435
    	0 ARG -   105  CL - 2.424728
   	40 LYS -    86  CL - 3.424543
    	6 GLU -   113  CL - 3.340827
	i.e. sel1 residue + name - sel2 residue + name - smallest contact distance
	between these 2 residues
	one pair per line

	example 2:
	fResContact "protein" "resname CL" 3.5 1 100 "cl"
	performs the same analysis for frames 1 to 100, prints output to 4 files:
	
	1) cl-contact_all.dat
	1 line per contact and frame
	frame number, contacting residues, minimal distance

	2) cl-contactAB.dat
	1 line per residue pair
	contacting residues, number of frames when these residues were in contact 
	and percentage of the analyzed trajectory

	3),4) cl-contactA.dat, cl-contactB.dat
	1 line per residue
	total number of contacts for each residue + percentage 
	percentage values: 1 residue is expected to have max. 
	1 contact in 1 frame; i.e. percentage = contacts/frames
	these values can be misleading, since 1 res from sel1 can interact
	with 2 residues from sel2 - depending on size and character
	of the residues
	
	example 3:
	protein residues 1 (ARG), 5 (LYS) are in contact with 10 (CL)
	cl-contact_all.dat: (frame, res1, res2, distance)
	    1 1 ARG - 10 CL 3.50000
	    1 5 LYS - 10 CL 2.90000
	cl-contact_AB.dat:	(res1, res2, contact percentage, contact length)
	    1 ARG - 10 CL 100% (1 frame(s))
	    5 LYS - 10 CL 100% (1 frame(s))
	cl-contactA.dat: (res1, total contact percentage, total contact length)
	    1 ARG - 100% (1 contact(s))
	    5 LYS - 100% (1 contact(s))
	cl-contactB.dat: (res2, total contact percentage, total contact length)
	    10 CL - 200% (2 contact(s))

DOWNLOAD FILE:
	_contact.tcl

AUTHOR:
	Lubos Vrbka (lubos (dot) vrbka (at) gmail (dot) com)