# Script:  dump2pdb.py

# Purpose: convert a LAMMPS dump file to PDB format

# Syntax:  dump2pdb.py dumpfile Nid Ntype Nx Ny Nz pdbfile

# 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

from dump import dump

from pdbfile import pdbfile

if len(sys.argv) != 8:

  raise StandardError, "Syntax: dump2pdb.py dumpfile Nid Ntype Nx Ny Nz 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])

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")

p = pdbfile(d)

if template: p = pdbfile(template,d)

else: p = pdbfile(d)

p.one(pfile)