def test_user_can_read_coord():
with tempfile.NamedTemporaryFile(mode="w+", encoding="utf-8", suffix=".xyz") as f:
f.write("$coord" + s)
f.write("0.00000000000000 0.00000000000000 -1.06176434496059 c" + s)
f.write("0.00000000000000 0.00000000000000 1.06176434496059 h" + s)
f.write("$end")
f.flush()
fname = open(f.name)
atoms = read(fname)
fname.close()
assert len(atoms) == 2
def test_ignore_coordinates_after_marker():
with tempfile.NamedTemporaryFile(mode="w+", encoding="utf-8", suffix=".xyz") as f:
f.write("test" + s)
f.write("$coord" + s)
f.write("0.00000000000000 0.00000000000000 -1.06176434496059 c" + s)
f.write("0.00000000000000 0.00000000000000 1.06176434496059 h" + s)
f.write("$end")
f.write("0.00000000000000 0.00000000000000 2.06176434496059 h" + s)
f.flush()
fname = open(f.name)
atoms = read(fname)
fname.close()
assert len(atoms) == 2
position = atoms[0].get("position")
assert position[0] == 0.0
def read(fileObject):
"""Method to first check the file type and then read
the structure accordingly
The returned atom coordinates will be in Bohr
"""
fname = fileObject.name.lower()
filetp = "unknown"
lines = fileObject.readlines()
if fname.endswith((".xyz")):
filetp = "xyz"
else:
for line in lines:
if line.strip().startswith("$coord"):
filetp = "turbomole"
break
fileObject.close()
atoms = []
newfile = open(fname, "r+")
if filetp == "turbomole":
atoms = tm.read(newfile)
elif filetp == "xyz":
atoms = xyz.read(newfile)
else:
print('Error: file type of input "{0}" not recognized'.format(fname))
exit(1)
newfile.close()
return atoms
def read(fileObject):
"""Method to first check the file type and then read
the structure accordingly
The returned atom coordinates will be in Bohr
"""
fname = fileObject.name.lower()
filetp = "unknown"
lines = fileObject.readlines()
if fname.endswith((".xyz")):
filetp = "xyz"
else:
for line in lines:
if line.strip().startswith("$coord"):
filetp = "turbomole"
break
fileObject.close()
atoms = []
newfile = open(fname, "r+")
if filetp == "turbomole":
atoms = tm.read(newfile)
elif filetp == "xyz":
atoms = xyz.read(newfile)
else:
errorbye("Input format erroneous or not implemented.")
newfile.close()
return atoms