def averagineCalc(avgMass, charge = 1):
elemList = ['H','C','N','O','S']
numIsotopes = N.array([2, 2, 2, 3, 5])
maxDim1 = numIsotopes.max()
maxDim2 = len(elemList)
elemMasses = N.array([[1.0078246, 2.0141021, 0, 0, 0],
[12.0000000, 13.0033554, 0, 0, 0],
[14.0030732, 15.0001088, 0, 0, 0],
[15.9949141, 16.9991322, 17.9991616, 0, 0],
[31.972070, 32.971456, 33.967866, 34, 35.967080]])
elemAbundances = N.array([[0.99985, 0.00015, 0, 0, 0],
[0.988930, 0.011070, 0, 0, 0],
[0.996337, 0.003663, 0, 0, 0],
[0.997590, 0.000374, 0.002036, 0, 0],
[0.9502, 0.0075, 0.0421, 0, 0.0002]])
avgDict = {}
avgDict['H']=7.7583
avgDict['C']=4.9384
avgDict['N']=1.3577
avgDict['O']=1.4773
avgDict['S']=0.0417
avgMassDict = {}#this is the averagine mass dictionary not the average mass!
avgMassDict['H']=1.00794
avgMassDict['C']=12.011
avgMassDict['N']=14.00670
avgMassDict['O']=15.99940
avgMassDict['S']=32.06600
avgMonomerMass = 111.1254
#n = int(N.round(avgMass/avgMonomerMass))
n = avgMass/avgMonomerMass
modelComp = []
modelComp.append(int(N.round(avgDict['H']*n)))
modelComp.append(int(N.round(avgDict['C']*n)))
modelComp.append(int(N.round(avgDict['N']*n)))
modelComp.append(int(N.round(avgDict['O']*n)))
modelComp.append(int(N.round(avgDict['S']*n)))
modelMass = 0.0
for i,elem in enumerate(elemList):
modelMass+=avgMassDict[elem]*modelComp[i]
actualMass = avgMonomerMass*n
modelDev = actualMass - modelMass
print "Actual Mass, Deviation: ", actualMass, modelDev
if libmercuryOk:
mercAns = LMI.mercury(modelComp, numIsotopes, elemMasses, elemAbundances, charge, 1e-3)
if mercAns[0] == 0:
return mercAns
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]