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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)
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