dump2pdb.py
0553f4af2b94lammps-icms

dump2pdb.py
View Options

			#!/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)