dump2pdb.py
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	#!/usr/bin/env python

	# Script: dump2pdb.py
	# Purpose: convert a LAMMPS dump file to PDB format
	# Syntax: dump2pdb.py dumpfile Nid Ntype Nx Ny Nz pdbfile template
	# dumpfile = LAMMPS dump file in native LAMMPS format
	# Nid,Ntype,Nx,Ny,Nz = columns #s for ID,type,x,y,z
	# (usually 1,2,3,4,5)
	# pdbfile = new PDB file
	# template = PDB file to use as template for creating new PDB file
	# this arg is optional, if not used a generic PDB file is created
	# Author: Steve Plimpton (Sandia), sjplimp at sandia.gov

	import sys,os
	path = os.environ["LAMMPS_PYTHON_TOOLS"]
	sys.path.append(path)
	from dump import dump
	from pdbfile import pdbfile

	if len(sys.argv) != 8 and len(sys.argv) != 9:
	raise StandardError, "Syntax: dump2pdb.py dumpfile Nid Ntype Nx Ny Nz pdbfile template"

	dumpfile = sys.argv[1]
	nid = int(sys.argv[2])
	ntype = int(sys.argv[3])
	nx = int(sys.argv[4])
	ny = int(sys.argv[5])
	nz = int(sys.argv[6])
	pfile = sys.argv[7]
	if len(sys.argv) == 9: template = sys.argv[8]
	else: template = ""

	d = dump(dumpfile)
	d.map(nid,"id",ntype,"type",nx,"x",ny,"y",nz,"z")
	if template: p = pdbfile(template,d)
	else: p = pdbfile(d)
	p.one(pfile)