import sys

###############################################################################
# Read a spectrum from a file and return it as a dictionary.
def readSpectrum (fileName):

  # Create an empty spectrum.
  mySpectrum = {}

  # Open the file for reading.
  myFile = open(fileName, "r")

  # Read line by line.
  for line in myFile:
    line = line.rstrip()
  
    # Parse the line.
    words = line.split()
    if (len(words) != 2):
      print "Invalid line (%s)." % line
      sys.exit(1)
    
    # Round m/z to the nearest integer.
    mz = int(float(words[0]) + 0.5)
  
    # Store this peak.
    mySpectrum[mz] = float(words[1])

  myFile.close()
  print "Read %d peaks from %s." % (len(mySpectrum.keys()), fileName)
  return(mySpectrum)

###############################################################################
# MAIN
###############################################################################

USAGE = """USAGE: compare-spectra.py <observed> <theoretical>

This program computes the scalar product between two spectra.  The
spectra are provided in two files, with two columns per file.  The
first column is the m/z and the second is the corresponding intensity.
The spectra are placed into 1-Da bins on the m/z axis before the
scalar product is computed.

"""


# Parse the command line.
if (len(sys.argv) != 3):
  print "
  sys.exit(1)
observedFileName = sys.argv[1]
theoreticalFileName = sys.argv[2]

# Read both spectra.
observedSpectrum = readSpectrum(observedFileName)
theoreticalSpectrum = readSpectrum(theoreticalFileName)

# Compute the scalar product.
score = 0.0
for mz in theoreticalSpectrum.keys():
  if (observedSpectrum.has_key(mz)):
    score += observedSpectrum[mz] * theoreticalSpectrum[mz]
print score