temptarget = 1.0
# wrapper on VMD window via Pizza.py vmd tool
# just proc 0 handles reading of dump file and viz
if me == 0:
from vmd import vmd
v = vmd()
v('menu main off')
v.rep('VDW')
from dump import dump
from pdbfile import pdbfile
d = dump('tmp.dump', 0)
p = pdbfile(d)
d.next()
d.unscale()
p.single(ntimestep)
v.new('tmp.pdb', 'pdb')
# display GUI with run/stop buttons and slider for temperature
if me == 0:
try:
from Tkinter import *
except:
from tkinter import *
tkroot = Tk()
tkroot.withdraw()
root = Toplevel(tkroot)
# (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)
temptarget = 1.0
# wrapper on VMD window via Pizza.py vmd tool
# just proc 0 handles reading of dump file and viz
if me == 0:
from vmd import vmd
v = vmd()
v('menu main off')
v.rep('VDW')
from dump import dump
from pdbfile import pdbfile
d = dump('tmp.dump',0)
p = pdbfile(d)
d.next()
d.unscale()
p.single(ntimestep)
v.new('tmp.pdb','pdb')
# display GUI with run/stop buttons and slider for temperature
if me == 0:
try:
from Tkinter import *
except:
from tkinter import *
tkroot = Tk()
tkroot.withdraw()
root = Toplevel(tkroot)
for line in pdbfile:
if isatom.match(line):
curatom = atom.Atom(line)
oldfile.write(curatom.write_line())
curatom.bfac = bfacdict[myindex[int(curatom.resseq.strip())]]
newfile.write(curatom.write_line())
else :
oldfile.write(line)
newfile.write(line)
newfile.flush()
oldfile.flush()
counts()
newfile.close()
oldfile.close()
if __name__=="__main__":
try:
p = OptionParser()
p.add_option("--infile","-i",dest="pdbfile",metavar="*.pdb")
p.add_option("--alignment" ,"-a",dest="alnfile",metavar="*.txt with alignment")
opttuple,spillover = p.parse_args()
pdb = pdbfile.pdbfile(opttuple.pdbfile)
ad = pdb.make_atom_dict()
read_clustal_make_dict(opttuple.alnfile)
dictunme = get_property_by_resn()
setbfac_property_clustal(open(opttuple.pdbfile))
except IOError:
p.print_help()
except TypeError:
p.print_help()
