<|file_name|>Parameter.py<|end_file_name|><｜fim▁begin｜>param = dict(
	useAIon=True,
	verbose=False,
	chargePreXlinkIons=[1, 3],
	chargePostXlinkIons=[2, 5],
	basepeakint = 100.0,
	dynamicrange = 0.001,
	missedsites = 2,
	minlength = 4,
	maxlength = 51,
	modRes = '',
	modMass = 0.0,
	linkermass = 136.10005,
	ms1tol = dict(measure='ppm', val=5),
	ms2tol = dict(measure='da', val=0.01),
	minmz = 200,
	maxmz = 2000,
	mode = 'conservative',
	patternstring = '^[ACDEFGHIKLMNPQRSTVWY]*K[ACDEFGHIKLMNPQRSTVWY]+$',
	fixedMod = [],
	neutralloss=dict(
		h2oLoss=dict(
			mass=-18.010565, 
			aa=set('ACDEFGHIKLMNPQRSTVWY')),
		nh3Loss=dict(
			mass=-17.026549,
			aa=set('ACDEFGHIKLMNPQRSTVWY')),
		h2oGain=dict(
			mass=18.010565,
			aa=set('ACDEFGHIKLMNPQRSTVWY'))))

mass = dict(
	A=71.037114,
	R=156.101111,
	N=114.042927,
	D=115.026943,<｜fim▁hole｜>	E=129.042593,
	Q=128.058578,
	G=57.021464,
	H=137.058912,
	I=113.084064,
	L=113.084064,
	K=128.094963,
	M=131.040485,
	F=147.068414,
	P=97.052764,
	S=87.032028,
	T=101.047678,
	W=186.079313,
	Y=163.063329,
	V=99.068414,
	Hatom=1.007825032,
	Oatom=15.99491462,
	neutronmass = 1.008701,
	BIonRes=1.0078246,
	AIonRes=-26.9870904,
	YIonRes=19.0183888,
	isotopeInc = [1.008701/4, 1.008701/3, 1.008701/2, 1.008701/1])

modification = dict(
	position=[],
	deltaMass=[])
for i in range(len(param['fixedMod'])):
	aa = param['fixedMod'][i][0]
	delta = param['fixedMod'][i][1]
	mass[aa] += delta<｜fim▁end｜>
	C=103.009184,