config_masses.py

Read in the masses file.

#!/usr/bin/python
 
 
import msparser
import sys
if len(sys.argv) < 3:
    print("Usage: %s UNIMOD  SCHEMA [SESSION_ID]" % sys.argv[0])
    print("UNIMOD is the file path to the unimod.xml file, e.g., ../config/unimod.xml or a fully formed URL such as http://www.matrixscience.com/cgi .")
    print("SCHEMA is the unimod schema file path, e.g., ../html/xmlns/schema/unimod_2/unimod_2.xsd")
    print("SESSION_ID is the session id. Only needed if UNIMOD is a URL.")
    sys.exit(1)
 
def checkErrorHandler(obj) :
    print("Last error description                   ")
    print("=========================================")
    print("Error: %s" % obj.getLastErrorString())
    print("=========================================")
    print("Testing the error handling...            ")
    print("=========================================")
 
    err = obj.getErrorHandler()
 
    for i in range(1, 1 + err.getNumberOfErrors()) :
        print("Error number: %d (%d times): %s" % (
            err.getErrorNumber(i),
            err.getErrorRepeats(i) + 1,
            err.getErrorString(i)
            ))
    
    print(" ") 
 
    obj.clearAllErrors()    
 
# A sessionID can optionally be passed as the second parameter.
# This will only be required if the 'file' is a URL.
if len(sys.argv) > 3:
    cs = msparser.ms_connection_settings()
    cs.setSessionID(sys.argv[3])
    umodFile = msparser.ms_umod_configfile(sys.argv[1], sys.argv[2], cs)
else :
    umodFile = msparser.ms_umod_configfile(sys.argv[1], sys.argv[2])
file = msparser.ms_masses(umodFile)
 
 
if not file.isValid() :
    print("Error when reading file: %s" % file.getFileName())
    checkErrorHandler(file)
    sys.exit(1)
 
 
print("Name of the file: %s" % file.getFileName())
print("-------------------------------------------------------------")
print("---   Content of masses file                              ---")
print("-------------------------------------------------------------")
print("# Amino acid masses (monoisotopic and average)")
 
for i in range(0, 26) :
    res = chr(ord('A') + i)
    print("%1s:%5.5f,%5.5f" % (
        res, 
        file.getResidueMass(msparser.MASS_TYPE_MONO, res),
        file.getResidueMass(msparser.MASS_TYPE_AVE, res)
        ))
 
print (" ")
print("# Atomic masses used for terminus values")
 
print("HYDROGEN:%5.5f,%5.5f" % (
    file.getHydrogenMass(msparser.MASS_TYPE_MONO),
    file.getHydrogenMass(msparser.MASS_TYPE_AVE)
    ))
 
print("CARBON:%5.5f,%5.5f" % (
    file.getCarbonMass(msparser.MASS_TYPE_MONO),
    file.getCarbonMass(msparser.MASS_TYPE_AVE)
    ))
 
print("NITROGEN:%5.5f,%5.5f" % (
    file.getNitrogenMass(msparser.MASS_TYPE_MONO),
    file.getNitrogenMass(msparser.MASS_TYPE_AVE)
    ))
 
print("OXYGEN:%5.5f,%5.5f" % (
    file.getOxygenMass(msparser.MASS_TYPE_MONO),
    file.getOxygenMass(msparser.MASS_TYPE_AVE)
    ))
 
print("ELECTRON:%5.7f" % (
    file.getElectronMass()
    ))
 
 
 
 
"""
 
Running the program as 
 
python config_masses.pl /usr/local/mascot/config/masses
 
will give the following output under Mascot Server 2.3:
 
 
Name of the file: /usr/local/mascot/config/masses
-------------------------------------------------------------
---   Content of masses file                              ---
-------------------------------------------------------------
# Amino acid masses (monoisotopic and average)
A:71.03711,71.07790
B:114.53494,114.59500
C:103.00919,103.14290
D:115.02694,115.08740
E:129.04259,129.11400
F:147.06841,147.17390
G:57.02146,57.05130
H:137.05891,137.13930
I:113.08406,113.15760
J:0.00000,0.00000
K:128.09496,128.17230
L:113.08406,113.15760
M:131.04048,131.19610
N:114.04293,114.10260
O:0.00000,0.00000
P:97.05276,97.11520
Q:128.05858,128.12920
R:156.10111,156.18570
S:87.03203,87.07730
T:101.04768,101.10390
U:150.95363,150.03790
V:99.06841,99.13110
W:186.07931,186.20990
X:111.00000,111.00000
Y:163.06333,163.17330
Z:128.55059,128.62160
 
# Atomic masses used for terminus values
HYDROGEN:1.00783,1.00794
CARBON:12.00000,12.01070
NITROGEN:14.00307,14.00670
OXYGEN:15.99491,15.99940
ELECTRON:0.0005490
 
 
"""