def getAtoms(formula):
formula = validateStr(formula)
if '))' in formula:
return False
atoms = []
numAtoms = []
while (len(formula) > 0):
#First computes the molecular weight of all parenthetical formulas from left to right
while (len(re.findall('\(\w*\)[0-9]+', formula)) != 0):
parenthetical = re.findall('\(\w*\)[0-9]+', formula)
for i in range(0, len(parenthetical)):
parenMult1 = re.findall('\)[0-9]+', parenthetical[i])
# print "ParenMult1", parenMult1, parenthetical[i]
parenMult2 = re.findall('[0-9]+', parenMult1[0])
# print "ParentMult2", parenMult2
segments = parseFormula(parenthetical[i])
# print "Segments", segments
for i in range(0, len(segments)):
multFactor = re.findall('[0-9]+', segments[i])
subSegs = re.findall('[A-Z][a-z]*', segments[i])
# print "MultiFactor: ", multFactor
# print "Subsegs: ", subSegs
for seg in subSegs:
atoms.append(seg)
if len(parenMult2) > 0:
coreNum = int(parenMult2[0])
else:
coreNum = 1
if len(multFactor) > 0:
multNum = int(multFactor[0])
numAtoms.append(coreNum * multNum)
else:
numAtoms.append(coreNum)
formula = re.sub('\(\w*\)[0-9]+', '', formula)
#Sums nonparenthetical molecular weights when all parenthetical molecular weights have been summed
segments = parseFormula(formula)
# print "Segments", segments
for i in range(0, len(segments)):
multFactor = re.findall('[0-9]+', segments[i])
subSegs = re.findall('[A-Z][a-z]*', segments[i])
# print "MultiFactor: ", multFactor
# print "Subsegs: ", subSegs
for seg in subSegs:
atoms.append(seg)
if len(multFactor) > 0:
multNum = int(multFactor[0])
numAtoms.append(1 * multNum)
else:
numAtoms.append(1)
formula = re.sub(formula, '', formula)
elemOk = True
for elem in atoms:
if not elemDict.has_key(elem):
elemOk = False
return elemOk, atoms, numAtoms
return elemOk, atoms, numAtoms
def plotElementParameter(self, elemKey, plotType):#plot electronic affinities
paramVals = []
elemList = []
try:
if elemKey == 'ionenergy':
for elem in TableofElementsList:
if elemDict.has_key(elem):
elemList.append(elem)
paramVals.append(elemDict[elem].__dict__[elemKey][0])
else:
for elem in TableofElementsList:
if elemDict.has_key(elem):
elemList.append(elem)
paramVals.append(elemDict[elem].__dict__[elemKey])
self.addPlot(paramVals, elemList, plotType, 'Element #', 'Parameter Value')
except:
print elemDict[elem].name, elemDict[elem].ionenergy
raise
def plotElementParameter(self, elemKey,
plotType): #plot electronic affinities
paramVals = []
elemList = []
try:
if elemKey == 'ionenergy':
for elem in TableofElementsList:
if elemDict.has_key(elem):
elemList.append(elem)
paramVals.append(elemDict[elem].__dict__[elemKey][0])
else:
for elem in TableofElementsList:
if elemDict.has_key(elem):
elemList.append(elem)
paramVals.append(elemDict[elem].__dict__[elemKey])
self.addPlot(paramVals, elemList, plotType, 'Element #',
'Parameter Value')
except:
print elemDict[elem].name, elemDict[elem].ionenergy
raise
def isoCalc(elemList, elemComp, charge = 0):
'''
interface to mercury calc to get user defined isotope patterns
Limiting the maximum isotopes to be considered to 5
'''
try:
if len(elemList)== 0 or len(elemComp) == 0:
return False
if len(elemList) != len(elemComp):
return False
maxIsotopes = 7
numElements = len(elemList)
numIsotopes = N.zeros(maxIsotopes, dtype = N.int)
elemMasses = N.zeros((numElements, maxIsotopes))
elemAbundances = N.zeros((numElements, maxIsotopes))
for i,elem in enumerate(elemList):
if elemDict.has_key(elem):
tempIsos = elemDict[elem].isotopes
tempOrder = []
tempOrder = N.array(tempOrder)
orderInd = tempOrder.argsort()
# print orderInd
# tempIsos = tempIsos[maxOrder]
maxIso = len(tempIsos)
if maxIso > maxIsotopes:
maxIso = maxIsotopes
numIsotopes[i] = int(maxIso)
for j in xrange(maxIso):
#each iso is a tuple that is the (nominal mass, isotope mass, isotope abundance)
iso = tempIsos[j]
# print elem, iso[1], iso[2]
elemMasses[i][j]=iso[1]
elemAbundances[i][j]=iso[2]
except:
return [False, None]
# print elemList
# print elemMasses
# print elemAbundances
# print numIsotopes
if libmercuryOk:
print "Libmercury OK"
mercAns = LMI.mercury(elemComp, numIsotopes, elemMasses, elemAbundances, charge, 1e-3)
# mercAns = LMI.mercury(modelComp, numIsotopes, elemMasses, elemAbundances, charge, 1e-3)
if mercAns[0] == 0:
return [True, scaleIsos(mercAns[1])]
else:
return [False, None]
def getMass(x):
atom=re.findall('[A-Z][a-z]*',x)
number=re.findall('[0-9]+', x)
if len(number) == 0:
multiplier = 1
else:
multiplier = float(number[0])
if elemDict.has_key(atom[0]):
# atomic_mass=TableofElements[atom[0]]
# atomic_mass=elemDict[atom[0]].mass#TableofElements[atom[0]]
atomic_mass=elemDict[atom[0]].isotopes[0][1]#get monoisotopic mass
else:
atomic_mass = 0.0
return (atomic_mass*multiplier)
def getMass(x):
atom = re.findall('[A-Z][a-z]*', x)
number = re.findall('[0-9]+', x)
if len(number) == 0:
multiplier = 1
else:
multiplier = float(number[0])
if elemDict.has_key(atom[0]):
# atomic_mass=TableofElements[atom[0]]
# atomic_mass=elemDict[atom[0]].mass#TableofElements[atom[0]]
atomic_mass = elemDict[atom[0]].isotopes[0][1] #get monoisotopic mass
else:
atomic_mass = 0.0
return (atomic_mass * multiplier)
def mousePressEvent(self, event):
'''
The SVG coordinates are reversed in the y dimension so we need to subtract
'''
# print event.button(), event.x(), self.origH-event.y()
xP = N.round(event.x()/self.xMod)#event.x()+
yP = N.round(self.origH-(event.y()/self.yMod))
# print xP, yP, event.x(), self.origH-(event.y())
crit = (xP >= self.xLo) & (xP <= self.xHi) & (yP >= self.yLo) & (yP <= self.yHi)
Ans = N.where(crit)[0]
if len(Ans)>0:
curAtom = self.elems[Ans]
# print curAtom
if elemDict.has_key(curAtom):
elem = elemDict[curAtom]
print elem.name, elem.mass
self.emit(QtCore.SIGNAL("elementSelected(PyQt_PyObject)"),elem)
def mousePressEvent(self, event):
'''
The SVG coordinates are reversed in the y dimension so we need to subtract
'''
# print event.button(), event.x(), self.origH-event.y()
xP = N.round(event.x() / self.xMod) #event.x()+
yP = N.round(self.origH - (event.y() / self.yMod))
# print xP, yP, event.x(), self.origH-(event.y())
crit = (xP >= self.xLo) & (xP <= self.xHi) & (yP >= self.yLo) & (
yP <= self.yHi)
Ans = N.where(crit)[0]
if len(Ans) > 0:
curAtom = self.elems[Ans]
# print curAtom
if elemDict.has_key(curAtom):
elem = elemDict[curAtom]
print elem.name, elem.mass
self.emit(QtCore.SIGNAL("elementSelected(PyQt_PyObject)"),
elem)
def getAtoms(formula):
formula = validateStr(formula)
if '))' in formula:
return False
atoms = []
numAtoms = []
while (len(formula)>0):
#First computes the molecular weight of all parenthetical formulas from left to right
while (len(re.findall('\(\w*\)[0-9]+', formula))!=0):
parenthetical=re.findall('\(\w*\)[0-9]+',formula)
for i in range(0,len(parenthetical)):
parenMult1 = re.findall('\)[0-9]+', parenthetical[i])
# print "ParenMult1", parenMult1, parenthetical[i]
parenMult2 = re.findall('[0-9]+', parenMult1[0])
# print "ParentMult2", parenMult2
segments =parseFormula(parenthetical[i])
# print "Segments", segments
for i in range(0, len(segments)):
multFactor = re.findall('[0-9]+', segments[i])
subSegs = re.findall('[A-Z][a-z]*',segments[i])
# print "MultiFactor: ", multFactor
# print "Subsegs: ", subSegs
for seg in subSegs:
atoms.append(seg)
if len(parenMult2)>0:
coreNum = int(parenMult2[0])
else:
coreNum = 1
if len(multFactor)>0:
multNum = int(multFactor[0])
numAtoms.append(coreNum*multNum)
else:
numAtoms.append(coreNum)
formula=re.sub('\(\w*\)[0-9]+', '', formula)
#Sums nonparenthetical molecular weights when all parenthetical molecular weights have been summed
segments = parseFormula(formula)
# print "Segments", segments
for i in range(0, len(segments)):
multFactor = re.findall('[0-9]+', segments[i])
subSegs = re.findall('[A-Z][a-z]*',segments[i])
# print "MultiFactor: ", multFactor
# print "Subsegs: ", subSegs
for seg in subSegs:
atoms.append(seg)
if len(multFactor)>0:
multNum = int(multFactor[0])
numAtoms.append(1*multNum)
else:
numAtoms.append(1)
formula=re.sub(formula, '', formula)
elemOk = True
for elem in atoms:
if not elemDict.has_key(elem):
elemOk = False
return elemOk, atoms, numAtoms
return elemOk, atoms, numAtoms