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This is what I have so far:

AminoDict={

'A':89.09,

'R':174.20,

'N':132.12,

'D':133.10,

'C':121.15,

'Q':146.15,

'E':147.13,

'G':75.07,

'H':155.16,

'I':131.17,

'L':131.17,

'K':146.19,

'M':149.21,

'F':165.19,

'P':115.13,

'S':105.09,

'T':119.12,

'W':204.23,

'Y':181.19,

'V':117.15,

'X':0.0,

'-':0.0,

'*':0.0 }

import re

sequence = open(raw_input('Enter amino acid sequence: '), 'r')

headers = 0

seq = 

aa_seq = 

AveMolWeight=0

for line in sequence:

    if line.startswith('>'):

        headers = headers + 1

    else:

        seq.append(headers)

        line=line.strip('rn')

        aa_seq.append(seq)

cA = aa_seq.count('A')

cR = aa_seq.count('R')

cN = aa_seq.count('N')

cD = aa_seq.count('D')

cC = aa_seq.count('C')

cQ = aa_seq.count('Q')

cE = aa_seq.count('E')

cG = aa_seq.count('G')

cH = aa_seq.count('H')

cI = aa_seq.count('I')

cL = aa_seq.count('L')

cK = aa_seq.count('K')

cM = aa_seq.count('M')

cF = aa_seq.count('F')

cP = aa_seq.count('P')

cS = aa_seq.count('S')

cT = aa_seq.count('T')

cW = aa_seq.count('W')

cV = aa_seq.count('V')

cY = aa_seq.count('Y')

total = cA + cR + cN + cD + cC + cQ + cE + cG + cH + cI + cL + cK + cM + cF + cP + cS + cT + cW + cV + cY

for rando in aa_seq:

    AveMolWeight = AveMolWeight + float(total*110)

print headers

print "Molecular Weight by Average: %.1f" % (AveMolWeight)

It outputs this:

`4242

Molecular Weight by Average: 0.0`

The problem is that the input file has multiple fasta headers, I can make a code that can do one single protein sequence with one header. But I can't figure out how to do each protein sequence individual and output the sequence header and molecular weight of each.