def ion_dictionary(sequence):
std_aa_mass = {
'G': 57.02146,
'A': 71.03711,
'S': 87.03203,
'P': 97.05276,
'V': 99.06841,
'T': 101.04768,
'C': 103.00919,
'L': 113.08406,
'I': 113.08406,
'N': 114.04293,
'D': 115.02694,
'Q': 128.05858,
'K': 128.09496,
'E': 129.04259,
'M': 131.04049,
'H': 137.05891,
'F': 147.06841,
'R': 156.10111,
'Y': 163.06333,
'W': 186.07931,
}
getmassresult = getmass(sequence)
seq_nomod = getmassresult[0]
moddict = getmassresult[1]
seqlen = len(seq_nomod)
def getmodmass(resn):
return std_aa_mass[seq_nomod[resn-1]] + moddict[resn]
iondict = {'a': [0], 'a+': [0], 'b': [0], 'y': [0], 'y-': [0], 'y--': [0], 'x': [0], 'x+': [0], 'c': [0], 'z': [0]}
sum1 = 0
sum2 = 0
for i in range(1, len(seq_nomod)):
sum1 += getmodmass(i)
iondict['a'].append(sum1 - 27.9949)
iondict['a+'].append(sum1 - 27.9949 + 1.007825)
iondict['b'].append(sum1)
iondict['c'].append(sum1 + 17.026549)
i2 = seqlen - i +1
sum2 += getmodmass(i2)
iondict['x'].append(sum2 + 43.989830)
iondict['x+'].append(sum2 + 43.989830 + 1.007825)
iondict['y'].append(sum2 + 18.010565)
iondict['y-'].append(sum2 + 18.010565 - 1.007825)
iondict['y--'].append(sum2 + 18.010565 - 2 * 1.007825)
iondict['z'].append(sum2 + + 17.002740 - 14.003074 - 1.007825)
return iondict
def ion_dictionary(sequence, maxcharge):
std_aa_mass = {
'G': 57.02146,
'A': 71.03711,
'S': 87.03203,
'P': 97.05276,
'V': 99.06841,
'T': 101.04768,
'C': 103.00919,
'L': 113.08406,
'I': 113.08406,
'N': 114.04293,
'D': 115.02694,
'Q': 128.05858,
'K': 128.09496,
'E': 129.04259,
'M': 131.04049,
'H': 137.05891,
'F': 147.06841,
'R': 156.10111,
'Y': 163.06333,
'W': 186.07931,
}
getmassresult = getmass(sequence)
seq_nomod = getmassresult[0]
moddict = getmassresult[1]
seqlen = len(seq_nomod)
def getmodmass(resn):
return std_aa_mass[seq_nomod[resn-1]] + moddict[resn]
iondict = {}
for c in range(1, maxcharge+1):
sum1 = 0
for i in range(1, seqlen):
sum1 += getmodmass(i)
iondict[(sum1 - 27.994915 + (c * 1.007825)) / c] = [i, c]
return iondict
def assign(sequence,raw_input):
seqaa = getmass(sequence)[0]
lenseq = len(seqaa)
idict = ion_dictionary(sequence)
pkd = peakdict(raw_input)
intsbypos = {k:0 for k in range(1,lenseq+1)}
nterm_types = [k for k in idict if k[0] in('a', 'b', 'c')]
cterm_types = [k for k in idict if k[0] in('x', 'y', 'z')]
for iontype in nterm_types:
the_ions = idict[iontype]
for ion in pkd:
res = search(ion, the_ions, 10)
if res > 0:
intsbypos[res] += pkd[ion]
for iontype in cterm_types:
the_ions = idict[iontype]
for ion in pkd:
res = search(ion, the_ions, 10)
if res > 0:
intsbypos[lenseq - res + 1] += pkd[ion]
dictrange = range(1,len(intsbypos)+1)
outputformat =[]
for thing in dictrange:
outputformat.append(str(thing)+', '+str(intsbypos[thing]))
return '<br>'.join(outputformat)
def result_table(filename, seq, maxc):
themains = get_envelopes(filename, seq, maxc)
seq_aa = getmass(seq)[0]
a_ions = themains[0] # a ions and position/charge
discDist = themains[1] # discovered distributions
def maketd(text):
return "<td>" + str(text) + "</td>"
result = """<table border = "1"> <tr>
<td>a.a.</td>
<td>ion number</td>
<td>charge state</td>
<td>observed m/z</td>
<td>[observed intensities]<br>[fitted intensities]</td>
<td>(root square error)/(total signal)</td>
<td>Relative contributions <br>[a-1, a, a+1, a+2]</td>
<td> [a]/([a]+[a+1]) </td>
</tr>"""
for ion in discDist:
optResult = getratio(ion * a_ions[ion][1], discDist[ion])
if ((sqrt(optResult[1][1])) / sum(discDist[ion])) < 0.1:
#optResult = getratio(ion * a_ions[ion][1], discDist[ion])
result += "<tr>"
result += maketd(seq_aa[a_ions[ion][0]-1])
result += maketd(a_ions[ion][0])
result += maketd(str(a_ions[ion][1]) + "+")
result += maketd(ion)
result += "<td>" + str([round(k,3) for k in discDist[ion]]) + "<br>" + str([round(k, 3) for k in optResult[1][0]]) + "</td>"
result += maketd((sqrt(optResult[1][1])) / sum(discDist[ion]))
result += maketd([round(k / sum(optResult[0]),3) for k in optResult[0]])
result += maketd(float(optResult[0][1])/(optResult[0][1] + optResult[0][2]))
result += "</tr>"
return result