def test1(self):
current_dir = os.path.dirname(__file__)
db = Database()
converter = OptimDBConverter(db,
mindata=os.path.join(current_dir, "min.data"),
tsdata=os.path.join(current_dir, "ts.data"),
pointsmin=os.path.join(current_dir, "points.min"),
pointsts=os.path.join(current_dir, "points.ts"),
endianness="<")
converter.convert()
self.assertEqual(db.number_of_minima(), 2)
self.assertEqual(db.number_of_transition_states(), 1)
ts = db.transition_states()[0]
self.assertAlmostEqual(ts.coords[0], 1.548324, 5)
self.assertAlmostEqual(ts.coords[2], 0.18178001, 5)
self.assertAlmostEqual(ts.coords[-1], -0.50953229, 5)
self.assertEqual((180,), ts.coords.shape)
m = db.minima()[0]
print(repr(m.coords))
self.assertAlmostEqual(m.coords[0], 1.53700142, 5)
self.assertAlmostEqual(m.coords[2], 0.87783657, 5)
self.assertAlmostEqual(m.coords[-1], -0.50953229, 5)
self.assertEqual((180,), m.coords.shape)
def main():
parser = argparse.ArgumentParser(description=desc,
formatter_class=argparse.RawDescriptionHelpFormatter)
# parser.add_argument('--ndof', help='Number of total degrees of freedom (e.g. 3*number of atoms). This is simply the length of a coordinates vector.',
# type=int, default=1)
# parser.add_argument('--Database','-d', help = 'Name of database to write into', type = str, default="optimdb.sqlite")
# parser.add_argument('--Mindata','-m', help = 'Name of min.data file', type = str, default="min.data")
# parser.add_argument('--Tsdata','-t', help = 'Name of ts.data file', type = str, default="ts.data")
# parser.add_argument('--Pointsmin','-p', help = 'Name of points.min file', type = str, default="points.min")
# parser.add_argument('--Pointsts','-q', help = 'Name of points.ts file', type = str, default="points.ts")
parser.add_argument('--endianness', help = 'set the endianness of the binary data. Can be "<" for little-endian or ">" for big-endian', type = str, default="=")
args = parser.parse_args()
system = AMBERSystem(prmtopFname="coords.prmtop", inpcrdFname="coords.inpcrd")
db = system.create_database()
converter = OptimDBConverter(db, mindata="min.data",
tsdata="ts.data", pointsmin="points.min", pointsts="points.ts",
endianness=args.endianness)
converter.convert()
# system.get_ndof = lambda : args.ndof
run_gui(system, db=db)
print db.number_of_minima()
def test1(self):
current_dir = os.path.dirname(__file__)
db = Database()
converter = OptimDBConverter(
db,
mindata=os.path.join(current_dir, "min.data"),
tsdata=os.path.join(current_dir, "ts.data"),
pointsmin=os.path.join(current_dir, "points.min"),
pointsts=os.path.join(current_dir, "points.ts"),
endianness="<")
converter.convert()
self.assertEqual(db.number_of_minima(), 2)
self.assertEqual(db.number_of_transition_states(), 1)
ts = db.transition_states()[0]
self.assertAlmostEqual(ts.coords[0], 1.548324, 5)
self.assertAlmostEqual(ts.coords[2], 0.18178001, 5)
self.assertAlmostEqual(ts.coords[-1], -0.50953229, 5)
self.assertEqual((180, ), ts.coords.shape)
m = db.minima()[0]
print repr(m.coords)
self.assertAlmostEqual(m.coords[0], 1.53700142, 5)
self.assertAlmostEqual(m.coords[2], 0.87783657, 5)
self.assertAlmostEqual(m.coords[-1], -0.50953229, 5)
self.assertEqual((180, ), m.coords.shape)
def main():
parser = argparse.ArgumentParser(description="""
convert an OPTIM database to a pele sqlite database. Four files are needed. Normally they are called:
points.min : the coordinates of the minima in binary format
min.data : additional information about the minima (like the energy)
points.ts : the coordinates of the transition states
min.ts : additional information about transition states (like which minima they connect)
Other file names can optionally be passed. Some fortran compilers use non-standard endianness to save the
binary data. If your coordinates are garbage, try changing the endianness.
""", formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('--ndof', help='Number of total degrees of freedom (e.g. 3*number of atoms). This is simply the length of a coordinates vector.',
type=int, default=None)
parser.add_argument('--Database','-d', help = 'Name of database to write into', type = str, default="optimdb.sqlite")
parser.add_argument('--Mindata','-m', help = 'Name of min.data file', type = str, default="min.data")
parser.add_argument('--Tsdata','-t', help = 'Name of ts.data file', type = str, default="ts.data")
parser.add_argument('--Pointsmin','-p', help = 'Name of points.min file', type = str, default="points.min")
parser.add_argument('--Pointsts','-q', help = 'Name of points.ts file', type = str, default="points.ts")
parser.add_argument('--endianness', help = 'set the endianness of the binary data. Can be "<" for little-endian or ">" for big-endian', type = str, default="=")
args = parser.parse_args()
db = Database(args.Database)
cv = OptimDBConverter(database=db, ndof=args.ndof, mindata=args.Mindata,
tsdata=args.Tsdata, pointsmin=args.Pointsmin, pointsts=args.Pointsts,
endianness=args.endianness)
cv.setAccuracy()
cv.convert()
cv.db.session.commit()
def main():
parser = argparse.ArgumentParser(
description=desc, formatter_class=argparse.RawDescriptionHelpFormatter)
# parser.add_argument('--ndof', help='Number of total degrees of freedom (e.g. 3*number of atoms). This is simply the length of a coordinates vector.',
# type=int, default=1)
# parser.add_argument('--Database','-d', help = 'Name of database to write into', type = str, default="optimdb.sqlite")
# parser.add_argument('--Mindata','-m', help = 'Name of min.data file', type = str, default="min.data")
# parser.add_argument('--Tsdata','-t', help = 'Name of ts.data file', type = str, default="ts.data")
# parser.add_argument('--Pointsmin','-p', help = 'Name of points.min file', type = str, default="points.min")
# parser.add_argument('--Pointsts','-q', help = 'Name of points.ts file', type = str, default="points.ts")
parser.add_argument(
'--endianness',
help=
'set the endianness of the binary data. Can be "<" for little-endian or ">" for big-endian',
type=str,
default="=")
args = parser.parse_args()
system = AMBERSystem(prmtopFname="coords.prmtop",
inpcrdFname="coords.inpcrd")
db = system.create_database()
converter = OptimDBConverter(db,
mindata="min.data",
tsdata="ts.data",
pointsmin="points.min",
pointsts="points.ts",
endianness=args.endianness)
converter.convert()
# system.get_ndof = lambda : args.ndof
run_gui(system, db=db)
print db.number_of_minima()
def test_nocoords(self):
current_dir = os.path.dirname(__file__)
db = Database()
converter = OptimDBConverter(db,
mindata=os.path.join(current_dir, "min.data"),
tsdata=os.path.join(current_dir, "ts.data"),
pointsmin="poo",
pointsts="poo",
assert_coords=False,
endianness="<")
converter.convert()
def test_nocoords(self):
current_dir = os.path.dirname(__file__)
db = Database()
converter = OptimDBConverter(
db,
mindata=os.path.join(current_dir, "min.data"),
tsdata=os.path.join(current_dir, "ts.data"),
pointsmin="poo",
pointsts="poo",
assert_coords=False,
endianness="<")
converter.convert()
def test_nocoords_Fails(self):
current_dir = os.path.dirname(__file__)
db = Database()
converter = OptimDBConverter(db,
mindata=os.path.join(current_dir, "min.data"),
tsdata=os.path.join(current_dir, "ts.data"),
pointsmin="poo",
pointsts="poo",
assert_coords=True,
endianness="<")
with self.assertRaises(IOError):
converter.convert()
def test_nocoords_Fails(self):
current_dir = os.path.dirname(__file__)
db = Database()
converter = OptimDBConverter(
db,
mindata=os.path.join(current_dir, "min.data"),
tsdata=os.path.join(current_dir, "ts.data"),
pointsmin="poo",
pointsts="poo",
assert_coords=True,
endianness="<")
with self.assertRaises(IOError):
converter.convert()
def main():
parser = argparse.ArgumentParser(description="""
convert an OPTIM database to a pele sqlite database. Four files are needed. Normally they are called:
points.min : the coordinates of the minima in binary format
min.data : additional information about the minima (like the energy)
points.ts : the coordinates of the transition states
min.ts : additional information about transition states (like which minima they connect)
Other file names can optionally be passed. Some fortran compilers use non-standard endianness to save the
binary data. If your coordinates are garbage, try changing the endianness.
""", formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('--ndof', help='Number of total degrees of freedom (e.g. 3*number of atoms). This is simply the length of a coordinates vector.',
type=int, default=None)
parser.add_argument('--parentDB', help = 'Name of parent pinned database from which the system properties will be copied. Choose a small one!')
parser.add_argument('--Database','-d', help = 'Name of database to write into', type = str, default="optimdb.sqlite")
parser.add_argument('--Mindata','-m', help = 'Name of min.data file', type = str, default="min.data")
parser.add_argument('--Tsdata','-t', help = 'Name of ts.data file', type = str, default="ts.data")
parser.add_argument('--Pointsmin','-p', help = 'Name of points.min file', type = str, default="points.min")
parser.add_argument('--Pointsts','-q', help = 'Name of points.ts file', type = str, default="points.ts")
parser.add_argument('--endianness', help = 'set the endianness of the binary data. Can be "<" for little-endian or ">" for big-endian', type = str, default="=")
parser.add_argument('--nopoints', help = 'Load the metadata for minima and transition states without reading the coordinates (usually to save storage space)', action = 'store_true')
args = parser.parse_args()
system, basedb, x0 = create_frozenblj_system_from_db(args.parentDB)
db = Database(args.Database)
props = basedb.properties(as_dict=True)
for key, prop in props.iteritems():
db.add_property(key, prop)
cv = OptimDBConverter(database=db, ndof=args.ndof, mindata=args.Mindata,
tsdata=args.Tsdata, pointsmin=args.Pointsmin, pointsts=args.Pointsts,
endianness=args.endianness, coords_converter=system.coords_converter.get_reduced_coords)
cv.setAccuracy()
if args.nopoints:
cv.convert_no_coords()
else:
cv.convert()
cv.db.session.commit()
def test1(self):
current_dir = os.path.dirname(__file__)
db = Database()
converter = OptimDBConverter(
db,
mindata=os.path.join(current_dir, "min.data"),
tsdata=os.path.join(current_dir, "ts.data"),
pointsmin=os.path.join(current_dir, "points.min"),
pointsts=os.path.join(current_dir, "points.ts"),
endianness="<")
converter.convert()
mdata = tempfile.NamedTemporaryFile(delete=True)
tsdata = tempfile.NamedTemporaryFile(delete=True)
pm = tempfile.NamedTemporaryFile(delete=True)
pts = tempfile.NamedTemporaryFile(delete=True)
print mdata.name, tsdata.name
writer = WritePathsampleDB(db,
mindata=mdata.name,
tsdata=tsdata.name,
pointsmin=pm.name,
pointsts=pts.name,
endianness="<")
writer.write_db()
d1 = np.genfromtxt(os.path.join(current_dir, "min.data"))[:, :3]
d2 = np.genfromtxt(mdata.name)[:, :3]
_base_test.assert_arrays_almost_equal(self, d1, d2)
d1 = np.genfromtxt(os.path.join(current_dir,
"ts.data")).reshape(-1, 8)[:, :5]
d2 = np.genfromtxt(tsdata.name).reshape(-1, 8)[:, :5]
print d1, d2
_base_test.assert_arrays_almost_equal(self, d1, d2)
self.assertEqual(sha1_of_file(os.path.join(current_dir, "points.min")),
sha1_of_file(pm.name))
self.assertEqual(sha1_of_file(os.path.join(current_dir, "points.ts")),
sha1_of_file(pts.name))
def test2(self):
from pele.utils.tests.test_disconnectivity_graph import create_random_database
db = create_random_database(nmin=20, nts=15)
delete = False
mdata = tempfile.NamedTemporaryFile(delete=delete, suffix=".min.data")
tsdata = tempfile.NamedTemporaryFile(delete=delete, suffix=".ts.data")
pm = tempfile.NamedTemporaryFile(delete=delete)
pts = tempfile.NamedTemporaryFile(delete=delete)
print mdata.name, tsdata.name
writer = WritePathsampleDB(db,
mindata=mdata.name,
tsdata=tsdata.name,
pointsmin=pm.name,
pointsts=pts.name,
endianness="<")
writer.write_db()
newdb = Database()
reader = OptimDBConverter(newdb,
mindata=mdata.name,
tsdata=tsdata.name,
pointsmin=pm.name,
pointsts=pts.name,
endianness="<")
reader.convert()
for m1, m2 in izip(db.minima(), newdb.minima()):
self.assertAlmostEqual(m1.energy, m2.energy)
_base_test.assert_arrays_almost_equal(self, m1.coords, m2.coords)
for ts1, ts2 in izip(db.transition_states(),
newdb.transition_states()):
self.assertAlmostEqual(ts1.energy, ts2.energy)
_base_test.assert_arrays_almost_equal(self, ts1.coords, ts2.coords)
self.assertAlmostEqual(ts1.minimum1.energy, ts2.minimum1.energy)
self.assertAlmostEqual(ts1.minimum2.energy, ts2.minimum2.energy)
def test1(self):
current_dir = os.path.dirname(__file__)
db = Database()
converter = OptimDBConverter(db,
mindata=os.path.join(current_dir, "min.data"),
tsdata=os.path.join(current_dir, "ts.data"),
pointsmin=os.path.join(current_dir, "points.min"),
pointsts=os.path.join(current_dir, "points.ts"),
endianness="<")
converter.convert()
mdata = tempfile.NamedTemporaryFile(delete=True)
tsdata = tempfile.NamedTemporaryFile(delete=True)
pm = tempfile.NamedTemporaryFile(delete=True)
pts = tempfile.NamedTemporaryFile(delete=True)
print(mdata.name, tsdata.name)
writer = WritePathsampleDB(db,
mindata=mdata.name,
tsdata=tsdata.name,
pointsmin=pm.name,
pointsts=pts.name,
endianness="<")
writer.write_db()
d1 = np.genfromtxt(os.path.join(current_dir, "min.data"))[:,:3]
d2 = np.genfromtxt(mdata.name)[:,:3]
_base_test.assert_arrays_almost_equal(self, d1, d2)
d1 = np.genfromtxt(os.path.join(current_dir, "ts.data")).reshape(-1,8)[:,:5]
d2 = np.genfromtxt(tsdata.name).reshape(-1,8)[:,:5]
print(d1, d2)
_base_test.assert_arrays_almost_equal(self, d1, d2)
self.assertEqual(sha1_of_file(os.path.join(current_dir, "points.min")),
sha1_of_file(pm.name))
self.assertEqual(sha1_of_file(os.path.join(current_dir, "points.ts")),
sha1_of_file(pts.name))
def test2(self):
from pele.utils.tests.test_disconnectivity_graph import create_random_database
db = create_random_database(nmin=20, nts=15)
delete=False
mdata = tempfile.NamedTemporaryFile(delete=delete, suffix=".min.data")
tsdata = tempfile.NamedTemporaryFile(delete=delete, suffix=".ts.data")
pm = tempfile.NamedTemporaryFile(delete=delete)
pts = tempfile.NamedTemporaryFile(delete=delete)
print(mdata.name, tsdata.name)
writer = WritePathsampleDB(db,
mindata=mdata.name,
tsdata=tsdata.name,
pointsmin=pm.name,
pointsts=pts.name,
endianness="<")
writer.write_db()
newdb = Database()
reader = OptimDBConverter(newdb,
mindata=mdata.name,
tsdata=tsdata.name,
pointsmin=pm.name,
pointsts=pts.name,
endianness="<")
reader.convert()
for m1, m2 in zip(db.minima(), newdb.minima()):
self.assertAlmostEqual(m1.energy, m2.energy)
_base_test.assert_arrays_almost_equal(self, m1.coords, m2.coords)
for ts1, ts2 in zip(db.transition_states(), newdb.transition_states()):
self.assertAlmostEqual(ts1.energy, ts2.energy)
_base_test.assert_arrays_almost_equal(self, ts1.coords, ts2.coords)
self.assertAlmostEqual(ts1.minimum1.energy, ts2.minimum1.energy)
self.assertAlmostEqual(ts1.minimum2.energy, ts2.minimum2.energy)
def main():
parser = argparse.ArgumentParser(
description="""
convert an OPTIM database to a pele sqlite database. Four files are needed. Normally they are called:
points.min : the coordinates of the minima in binary format
min.data : additional information about the minima (like the energy)
points.ts : the coordinates of the transition states
min.ts : additional information about transition states (like which minima they connect)
Other file names can optionally be passed. Some fortran compilers use non-standard endianness to save the
binary data. If your coordinates are garbage, try changing the endianness.
""",
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument(
'--ndof',
help=
'Number of total degrees of freedom (e.g. 3*number of atoms). This is simply the length of a coordinates vector.',
type=int,
default=None)
parser.add_argument('--Database',
'-d',
help='Name of database to write into',
type=str,
default="optimdb.sqlite")
parser.add_argument('--Mindata',
'-m',
help='Name of min.data file',
type=str,
default="min.data")
parser.add_argument('--Tsdata',
'-t',
help='Name of ts.data file',
type=str,
default="ts.data")
parser.add_argument('--Pointsmin',
'-p',
help='Name of points.min file',
type=str,
default="points.min")
parser.add_argument('--Pointsts',
'-q',
help='Name of points.ts file',
type=str,
default="points.ts")
parser.add_argument(
'--endianness',
help=
'set the endianness of the binary data. Can be "<" for little-endian or ">" for big-endian',
type=str,
default="=")
args = parser.parse_args()
db = Database(args.Database)
cv = OptimDBConverter(database=db,
ndof=args.ndof,
mindata=args.Mindata,
tsdata=args.Tsdata,
pointsmin=args.Pointsmin,
pointsts=args.Pointsts,
endianness=args.endianness)
cv.setAccuracy()
cv.convert()
cv.db.session.commit()
