def __init__(self, frameStr=None):
"""
If second parameter is not given, constructs empty frame, otherwise
constructs frame from the string which satisfies following pattern
<number of atoms>
comment line
atom_symbol11 x-coord11 y-coord11 z-coord11
atom_symbol12 x-coord12 y-coord11 z-coord12
...
"""
Frame.__init__(self)
if not frameStr is None:
lines = frameStr.split('\n')
if lines[-1] == '': del (lines[-1])
if len(lines) < 3:
raise InputError(
frameStr, 'Wrong number of arguments while \
constructing the XYZFrame')
length = int(lines[0])
self._comment = lines[1]
for line in lines[2:]:
self.atoms.append(XYZAtom(line))
if len(self.atoms) != length:
raise InputError(
frameStr,
"Wrong number of lines in file: length=%d and len(self.atoms) %d"
% (length, len(self.atoms)))
def __init__(self, xyzFile, R = 1.9859, T = 310):
self.xyzFile = xyzFile
self.frame = self.xyzFile.nextFrame()
self.R, self.T = R, T
if self.frame is None:
raise InputError(xyzFile, "no frames in file")
self.hexLatticeLoader = HexLatticeLoader(self.frame)
def openFiles(options):
try:
xyzFile = XYZFile(options.xyzFilename)
datFile = open(options.datFilename, 'w')
except:
raise(InputError(options.xyzFilename, "error while opening xyz or output file"))
return xyzFile, datFile
def openFiles(options):
try:
outFile = open(options.outFilename, 'w')
datFile = open(options.datFilename)
except:
raise(InputError(options.outFilename, "error while opening output file"))
return datFile, outFile
def _construct(self, atomStr):
atomList = atomStr.split()
if len(atomList) != 4:
raise InputError(
atomStr, 'Wrong number of arguments while \
constructing the XYZAtom')
self.symbol, self.x = atomList[0].strip(), float(atomList[1])
self.y, self.z = float(atomList[2]), float(atomList[3])
def boxVectors(self):
try:
vList = [float(size) for size in self.comment.split(",")]
for _ in range(len(vList), 9):
vList.append(0)
v1 = [vList[0], vList[3], vList[4]]
v2 = [vList[5], vList[1], vList[6]]
v3 = [vList[7], vList[8], vList[2]]
return [v1, v2, v3]
except:
raise (InputError(self.comment,
"Cannot read size of box from comment."))
def boxSize(self):
"""
Returns size of the box from frame.
This property is only present in specific kind of xyz files (stored in
comment).
If boxSize is not present, raises input exception
"""
try:
return [float(size) for size in self.comment.split(",")]
except:
raise (InputError(self.comment,
"Cannot read size of box from comment."))
def __init__(self, filename):
"""
"""
self._filename = filename
if self._filename[-3:] == 'gro':
self._frameCreator = self._createGroFrame
self._countNum = 1
elif self._filename[-3:] == 'xyz':
self._frameCreator = self._createXYZFrame
self._countNum = 0
else:
raise InputError(self._filename, "Wrong filename type")
self._frames = None
self.currentFrame = None
self.file = None
def load(self):
""" Loads whole file into memory."""
if self._frames is None:
self._frames = []
try:
xyzFile = open(self.filename, 'r')
except:
self._frames = []
return
lines = xyzFile.readlines()
if len(lines) < 2:
raise (InputError(lines, 'Not enough lines in frame file'))
atomsCount = int(lines[0])
step = atomsCount + 2
i = 0
while (i + step) < len(lines) + 1:
step = int(lines[i]) + 2
self._frames.append(XYZFrame(''.join(lines[i:i + step])[:-1]))
i += step
self.currentFrame = len(self.frames) - 1
def load(self):
""" Loads whole file into memory."""
#FIXME: write loaders for both files
if self._frames is None:
self._frames = []
try:
structFile = open(self.filename, 'r')
except:
self._frames = []
return
lines = structFile.readlines()
if len(lines) < 2:
raise (InputError(lines, 'Not enough lines in frame file'))
atomsCount = int(lines[self._countNum])
step = atomsCount + 2
i = 0
while (i + step) < len(lines) + 1:
step = int(lines[i + self._countNum]) + 2
self._frames.append(
self._frameCreator(''.join(lines[i:i + step +
self._countNum])[:-1]))
i += step
self.currentFrame = len(self.frames) - 1
def nextFrame(self):
"""
Returns next frame from the file. If file has ended returns None
value
"""
if self.currentFrame is None:
self.currentFrame = 0
self.file = open(self.filename, 'r')
else:
self.currentFrame += 1
frameLst = [self.file.readline()]
if frameLst[0] == '':
self.file.close()
return None
atomsCount = int(frameLst[0])
for _ in range(atomsCount + 1):
lineStr = self.file.readline()
if lineStr == '':
print frameLst
self.file.close()
raise InputError('lineStr == '
'', "Wrong number of lines in file")
frameLst.append(lineStr)
return XYZFrame(''.join(frameLst))