#!/usr/bin/python

'''
This small python script lists atoms of a given pdb file that are 
in the proximity of given coordinates.

Usage:
closeup.py <pdbfile> <x y z> <max distance>

'''

import sys, math 

__copyright__ = """
-----------------------------------------------------------------
(c) Copyright by Christian Fufezan, 2007  (christian@fufezan.net)

    Permission to use, copy, modify, and distribute this 
    software and its documentation for any purpose and 
    without fee or royalty is hereby granted, provided 
    that the above copyright notice appear in all copies 
    and that both that copyright notice and this permission 
    notice appear in supporting documentation or portions 
    thereof, including modifications, that you make.

"""
__version__   = '1.0'
__author__    = 'Christian Fufezan'
__date__      = '7th March 2007'
__url__       = 'http://www.fufezan.net/contact.php'

class ATOM:
	def __init__(self,x,y,z):
		self.x = x
		self.y = y
		self.z = z

	def distanceTo(self, zeOther):
		SumOfSquares = ((self.x-zeOther.x)**2) + ((self.y-zeOther.y)**2) + ((self.z-zeOther.z)**2)
		formated = '%(d).3f' % {'d' :math.sqrt(SumOfSquares)	}
		return float(formated)
		
		
def bp():
	sys.exit(0)

if (__name__ == "__main__"):
	if (len(sys.argv)) != 6:
		print __doc__
		print " script location:",str(sys.argv[0])
		print " Version",__version__,"\n"
		bp()
	else:
		pdbfile = sys.argv[1]
		x = float(sys.argv[2])
		y = float(sys.argv[3])
		z = float(sys.argv[4])
		d = float(sys.argv[5])
		centre = ATOM(x,y,z)
		complete_pdb=open(pdbfile).xreadlines()
		neighbours = []
		
		for line in complete_pdb:
			if (line[:6] == 'HETATM') or (line[:6] == 'ATOM  '):
				tmpAtom=ATOM(float(line[31:38]),float(line[39:46]),float(line[47:54]))
				distance = tmpAtom.distanceTo(centre)
				if distance < d:
					tmpAtom.idx = int(line[6:11])
					tmpAtom.atype = str(line[11:16]).strip()
					tmpAtom.aa = str(line[17:20]).strip()
					tmpAtom.chain = str(line[21:22])
					tmpAtom.resid = int(line[22:26])
					tmpAtom.distance = distance
					neighbours.append(tmpAtom)
		
		for atom in neighbours:
			print '%(distance).2f %(idx)5s %(atype)3s %(aa)s %(chain)s%(resid)4s %(x).3f %(y).3f %(z).3f' % {
			'distance'	: atom.distance,
			'idx'		: atom.idx,
			'atype'		: atom.atype,
			'aa'		: atom.aa,
			'chain'		: atom.chain,
			'resid'		: atom.resid,
			'x'			: atom.x,
			'y'			: atom.y,
			'z'			: atom.z
			}