From 13643a8314c2feb5155a9eab03b4ea610a24e70f Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 31 Mar 2008 22:39:55 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1693 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- tools/python/dump2pdb.py | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/tools/python/dump2pdb.py b/tools/python/dump2pdb.py index aff5cbf8ca..ec7c2d6bf4 100755 --- a/tools/python/dump2pdb.py +++ b/tools/python/dump2pdb.py @@ -2,11 +2,13 @@ # 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 @@ -15,8 +17,8 @@ sys.path.append(path) 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]) @@ -25,8 +27,11 @@ 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") -p = pdbfile(d) +if template: p = pdbfile(template,d) +else: p = pdbfile(d) p.one(pfile)