def getDim(value, ndim):
obj = dimRe.match(value)
if not obj:
raise AnsigParseException('dim = "%s", must be "F" followed by integer (e.g. "F2")' % value)
dim = int(obj.group(1))
if dim < 1 or dim > ndim:
raise AnsigParseException('dim = "%s", must be between "F1" and "F%d"' % (value, ndim))
return ndim-dim+1 # Ansig dimensions are backwards
def callback(key, values, comment):
if key == 'control':
if project.foundControl:
raise AnsigParseException('control found twice')
project.foundControl = True
controlKeywordDict = {
'help_dir': (False, 1, (None, )),
'html_viewer': (False, 1, (None, )),
'dictionary': (False, 1, (None, )),
'gr_translate': (False, 1, (None, )),
'sequence': (False, 1, (None, )),
'spectra': (False, 1, (None, )),
'crosspeaks': (False, 1, (None, )),
'backup': (False, 1, (None, )),
'initialize': (False, 1, (None, )),
'exit': (False, 1, (None, )),
'binaryformat': (False, 1, (None, )),
'font': (False, 1, (None, )),
}
return controlKeywordDict
elif key in ('sequence', 'spectra', 'crosspeaks', 'binaryformat'):
value = values[0]
if key != 'binaryformat':
key = key + 'File'
if not os.path.isabs(value):
base = os.path.dirname(project.projectFile)
value = joinPath(base, value)
setattr(project, key, value)
def getNdim(value):
obj = ndimRe.match(value)
if not obj:
raise AnsigParseException('ndim = "%s", must be integer followed by "D" (e.g. "3D")' % value)
ndim = int(obj.group(1))
return ndim
def callback(key, values, comment):
if key == 'sequence':
if project.sequence:
raise AnsigParseException('second sequence found')
name = values[0]
AnsigSequence(project, name)
sequenceKeywordDict = {
'residue': (False, 2, (None, None)),
}
return sequenceKeywordDict
elif key == 'residue':
project.sequence.addResidue(values[0], values[1], comment)
def callback(key, values, comment):
if key in ('picket_fence_bug', 'ppm_range', 'end_spectrum'):
return
if key == 'spectrum':
ndim = getNdim(values[0])
name = values[1]
spectrum = AnsigSpectrum(project, ndim, name)
spectrumKeywordDict = {
'expnucleus': (False, (2, 5), (None, None, None, None, None)),
'experiment': (False, (1, 3, 5), (None, None, None, None, ANSIG_FLOAT)),
###'symmetry': (False, ndim, ndim*(None,)), # have ( and ) around strings and not sure if white space is allowed or not
'symmetry': (False, -1, (None,)),
'solvent': (False, 1, (None,)),
'temperature': (False, 1, (ANSIG_FLOAT,)),
'pH': (False, 1, (ANSIG_FLOAT,)),
'equivalent': (False, 1, (None,)),
'scale': (False, 1, (ANSIG_FLOAT,)),
'contour_file': (False, -1, (None,)),
'matrix_file': (True, 0, ()),
}
return spectrumKeywordDict
spectrum = project.spectra[-1]
ndim = spectrum.ndim
if key == 'matrix_file':
rr = tuple(range(2,2*(ndim+1),2))
matrixKeywordDict = {
'parameter_file': (False, 1, (None,)),
'ndim': (False, 1, (ANSIG_INT,)),
'file': (False, 1, (None,)),
'head': (False, 1, (ANSIG_INT,)),
'deflate': (False, 1, (ANSIG_FLOAT,)),
'reflate': (False, 1, (ANSIG_FLOAT,)),
'dim': (False, 1, (ANSIG_INT,)),
'npts': (False, 1, (ANSIG_INT,)),
'block': (False, 1, (ANSIG_INT,)),
'sw': (False, 1, (ANSIG_FLOAT,)),
'sf': (False, 1, (ANSIG_FLOAT,)),
'refppm': (False, 1, (ANSIG_FLOAT,)),
'refpt': (False, 1, (ANSIG_FLOAT,)),
'nuc': (False, 1, (None,)),
'aliased': (False, 1, (None,)),
'folded': (False, 1, (None,)),
'linewidth': (False, rr, ndim*(None, ANSIG_FLOAT)),
'noise_level': (False, 1, (ANSIG_FLOAT,)),
'contour_levels': (False, -1, (ANSIG_FLOAT,)),
'contour_base': (False, 3, (ANSIG_FLOAT, ANSIG_FLOAT, ANSIG_INT)),
}
spectrum.currentDim = None
return matrixKeywordDict
elif key == 'end_matrix_file':
del spectrum.currentDim
# spectrum attributes
elif key == 'expnucleus':
dim = getDim(values[0], ndim)
nuc = values[1]
spectrum.nuc[dim-1] = nuc
if len(values) == 5:
pass # TBD: "associate other_spectrum, other_dim" gives mapping to some other dataDim
elif key == 'experiment':
if len(values) == 5:
dim1 = getDim(values[0], ndim)
dim2 = getDim(values[1], ndim)
expName = values[2]
if values[3] != 'mixing_time':
raise AnsigParseException('fourth argument = "%s", must be "mixing_time"' % values[3])
mixing_time = getFloat(values[4], 'mixing_time = "%s", must be float')
elif len(values) == 3:
if ndim == 2 and values[1] == 'mixing_time':
dim1 = 1
dim2 = 2
expName = values[0]
mixing_time = getFloat(values[2], 'mixing_time = "%s", must be float')
else:
dim1 = getDim(values[0], ndim)
dim2 = getDim(values[1], ndim)
expName = values[2]
mixing_time = None
else: # len(values) = 1
if ndim != 2:
raise AnsigParseException('ndim != 2 but unspecified dims in "experiment" statement')
dim1 = 1
dim2 = 2
expName = values[0]
mixing_time = None
spectrum.transfers.append((dim1, dim2, expName, mixing_time))
elif key == 'symmetry':
pass # TBD
elif key in ('solvent', 'temperature', 'pH', 'equivalent', 'scale'):
setattr(spectrum, key, values[0])
elif key == 'contour_file':
pass # TBD
# matrix_file attributes
elif key == 'parameter_file':
parFile = values[0]
spectrum.parFile = parFile
if os.path.exists(parFile):
try:
readParFile(parFile)
except IOError, e:
raise AnsigParseException(str(e))
def getFloat(value, errorMsg):
try:
x = float(value)
except ValueError, e:
raise AnsigParseException(errorMsg % value)
pass # TBD
# matrix_file attributes
elif key == 'parameter_file':
parFile = values[0]
spectrum.parFile = parFile
if os.path.exists(parFile):
try:
readParFile(parFile)
except IOError, e:
raise AnsigParseException(str(e))
elif key == 'ndim':
if values[0] != ndim:
raise AnsigParseException('spectrum "%s": ansig spd file has ndim=%d but also have set ndim=%d' % (spectrum.name, ndim, values[0]))
elif key == 'file':
spectrum.dataFile = values[0]
elif key == 'head':
spectrum.head = values[0]
elif key in ('deflate', 'reflate'):
pass # TBD: not sure what to do about this (but should not be common)
elif key == 'dim':
spectrum.currentDim = values[0]
elif key in ('npts', 'block', 'sw', 'sf', 'refppm', 'refpt'):
x = getattr(spectrum, key)