def test_1(self):
import base64
import StringIO
from itcc.tools import dmddat2mtxyz
from itcc.core.frame import parseframe
dmddatfile = StringIO.StringIO(base64.decodestring(test_in_dmddat_base64))
molfile = StringIO.StringIO(test_in_mol)
ofile = StringIO.StringIO()
frame = parseframe("1-3/2,4-8/3")
dmddat2mtxyz.dmddat2mtxyz(dmddatfile, molfile, ofile, frame)
self.assertEqual(ofile.getvalue(), test_out)
def main():
import sys
from optparse import OptionParser
usage = "usage: %prog [-h|options] dmddatfname molfname"
parser = OptionParser(usage)
parser.add_option(
"-f", "--frame", dest='frame_str',
default=None,
help="select frame, " \
"format is 'begin[-end[/step]](,begin[-end[/step]])*', " \
"for example '-f 2-40/3,71-91/2'")
(options, args) = parser.parse_args()
frame = parseframe(options.frame_str)
if len(args) != 2:
parser.error("incorrect number of arguments")
dmddat2mtxyz(file(args[0]), file(args[1]), sys.stdout, frame)
def test_1(self):
self.assertEqual(tuple(frame.parseframe('1,2')), (0,1))
self.assertEqual(tuple(frame.parseframe('1-3')), (0,1,2))
self.assertEqual(tuple(frame.parseframe('1-3/2')), (0,2))
self.assertEqual(tuple(frame.parseframe('3/2')), (2,))
self.assertEqual(tuple(frame.parseframe(None)), ())
def main_common(rmsd_func):
from optparse import OptionParser
usage = "\n" \
" %prog [options] xyzfname1 xyzfname2\n" \
" %prog [options] -F FILE\n" \
" %prog -h"
parser = OptionParser(usage=usage)
parser.set_default("no_h", False)
parser.add_option('-H', "--no-h", dest="no_h",
action="store_true",
help="does not include hydrogen")
parser.add_option('-a', "--atoms", dest="atoms",
help="only compare selected atoms, 1-based",
metavar="STRING")
parser.add_option('-A', "--atomsfile", dest="atomsfile",
help="read the selected atoms from file",
metavar="FILE")
parser.add_option('-b', "--atoms1", dest="atoms1",
help="the selected atoms for molecule 1",
metavar="STRING")
parser.add_option('-B', "--atoms1file", dest="atoms1file",
help="read the selected atoms from file",
metavar="FILE")
parser.add_option('-c', "--atoms2", dest="atoms2",
help="the selected atoms for molecule 2",
metavar="STRING")
parser.add_option('-C', "--atoms2file", dest="atoms2file",
help="read the selected atoms from file",
metavar="FILE")
parser.add_option('-F', "--files", dest="files",
help="read the compare file lists from FILE",
metavar="FILE")
parser.add_option('-s', '--loop-step',
dest='loop_step',
type='int',
help='logical symmetry: loop step')
parser.add_option('-m', '--mirror',
dest='mirror',
action='store_true',
help='also consider the mirror molecule')
parser.add_option('-v', '--verbose',
dest='verbose',
action='store_true',
help='be verbose')
(options, args) = parser.parse_args()
if len(args) == 2 and options.files is None:
pass
elif len(args) == 0 and options.files:
pass
else:
parser.error("incorrect number of arguments")
if (options.atoms and options.atomsfile) or \
(options.atoms1 and options.atoms1file) or \
(options.atoms2 and options.atoms2file):
parser.error("options conflict")
atoms1 = None
atoms2 = None
if options.atomsfile:
options.atoms = file(options.atomsfile).read()
if options.atoms:
atoms1 = list(frame.parseframe(options.atoms))
atoms2 = atoms1[:]
if options.atoms1file:
options.atoms1 = file(options.atoms1file).read()
if options.atoms1:
atoms1 = frame.parseframe(options.atoms1)
if options.atoms2file:
options.atoms2 = file(options.atoms2file).read()
if options.atoms2:
atoms2 = frame.parseframe(options.atoms2)
filelists = []
if options.files is not None:
filelists = [line.split() for line in file(options.files).readlines()]
else:
filelists = [args]
from itcc.molecule import read
mol_cache = {}
for filepair in filelists:
fname1 = filepair[0]
fname2 = filepair[1]
if options.verbose:
print fname1, fname2,
mol1 = cache_mol(fname1, mol_cache)
mol2 = cache_mol(fname2, mol_cache)
if options.no_h:
if atoms1 is None:
atoms1 = range(len(mol1))
atoms1 = [x for x in atoms1 if mol1.atoms[x].no != 1]
if options.no_h:
if atoms2 is None:
atoms2_new = range(len(mol2))
else:
atoms2_new = atoms2
atoms2_new = [x for x in atoms2_new if mol2.atoms[x].no != 1]
else:
atoms2_new = atoms2
print rmsd_func(mol1, mol2, atoms1, atoms2_new,
options.mirror, options.loop_step)
