UPDATE: see here for an isotopic calculator written in python -- it calculates mass as well: http://verahill.blogspot.com.au/2012/10/isotopic-pattern-caculator-in-python.html
The best molecular weight calculator which I've encountered is Matthew Monroe's Molecular Weight Calculator, which can be found at http://ncrr.pnnl.gov/software/
It does everything. Molecular weights. Isotopic patterns. And so, so, so much more.
It has one major drawback though - it's written for Windows. Luckily, it sort of works under Wine after you've done a bit of wine-trick-ery.
As great as the calculator is, sometimes you only need to calculate the molecular weight of something, and nothing else. Searching the debian repos I can' t find a single dedicated molecular weight calculator. In particular, a command-line driven calculator would be nice.
Seriously - it's a crying shame that the distribution with the largest repos, i.e. Debian, does not have a single passable molecular weight calculator. It is even more surprising given the number of chemistry-related packages which are present.
So, here's what I did:
a quick google on "python molecular weight calculator" brought me to http://pygments.org
A little bit of editing gave the code below, which was saved as molcalc, copied to /usr/bin, followed by sudo chmod +x /usr/bin/molcalc. It can now be called using
molcalc "(Co(CO)5)2"
and returns
The mass of (Co(CO)5)2 is 257.916890.
Here's the code, which is 99.9% the original and 0.1% my modification. All credit thus due to Lee, Freitas and Tucker.
NOTE: it doesn't handle layered parentheses. (Al(NO3)3)2 gets interpreted as Al2(NO3)3.
#!/usr/bin/python2.6
#########################################################################
# Author: Toni Lee with the help of Guilherme Freitas and Becky Tucker. Minor changes by Lindqvist
# Copyright: This module has been placed in the public domain
#########################################################################
#Import regular expressions
import re
import sys
try:
test=sys.argv[1]
except:
quit()
#Create the dictionary (From Becky with a value of 0 inserted for Uus(mass not measurable))
TableofElements ={ 'H':1.00794,'He':4.002602,'Li':6.941,'Be':9.012182,
'B':10.811,'C':12.0107,'N':14.0067,'O':15.9994,'F':18.9984032,'Ne':20.1797,
'Na':22.98976928,'Mg':24.3050,'Al':26.9815386,'Si':28.0855,
'P':30.973762,'S':32.065,'Cl':35.453,'Ar':39.948,'K':39.0983,'Ca':40.078,
'Sc':44.955912,'Ti':47.867,'V':50.9415,'Cr':51.9961,'Mn':54.938045,
'Fe':55.845,'Ni':58.6934,'Co':58.933195,'Cu':63.546,'Zn':65.38,'Ga':69.723,
'Ge':72.64,'As':74.92160,'Se':78.96,'Br':79.904,'Kr':83.798,'Rb':85.4678,
'Sr':87.62,'Y':88.90585,'Zr':91.224,'Nb':92.90638,'Mo':95.96,'Tc':98,
'Ru':101.07,'Rh':102.90550,'Pd':106.42,'Ag':107.8682,'Cd':112.411,
'In':114.818,'Sn':118.710,'Sb':121.760,'Te':127.60,'I':126.90447,
'Xe':131.293,'Cs':132.9054519,'Ba':137.327,'La':138.90547,'Ce':140.116,
'Pr':140.90765,'Nd':144.242,'Pm':145,'Sm':150.36,'Eu':151.964,'Gd':157.25,
'Tb':158.92535,'Dy':162.500,'Ho':164.93032,'Er':167.259,'Tm':168.93421,
'Yb':173.054,'Lu':174.9668,'Hf':178.49,'Ta':180.94788,'W':183.84,
'Re':186.207,'Os':190.23,'Ir':192.217,'Pt':195.084,'Au':196.966569,
'Hg':200.59,'Tl':204.3833,'Pb':207.2,'Bi':208.98040,'Po':210,'At':210,
'Rn':220,'Fr':223,'Ra':226,'Ac':227,'Th':232.03806,'Pa':231.03588,
'U':238.02891,'Np':237,'Pu':244,'Am':243,'Cm':247,'Bk':247,'Cf':251,
'Es':252,'Fm':257,'Md':258,'No':259,'Lr':262,'Rf':261,'Db':262,'Sg':266,
'Bh':264,'Hs':277,'Mt':268,'Ds':271,'Rg':272, 'Uus':0
}
#######################################
#Computes the MW of an atom-number pair
#######################################
def getMass(x):
atom=re.findall('[A-Z][a-z]*',x)
number=re.findall('[0-9]+', x)
if len(number) == 0:
multiplier = 1
else:
multiplier = float(number[0])
atomic_mass=TableofElements[atom[0]]
return (atomic_mass*multiplier)
################################################################
#Segments formula into atom-number sections (i.e. 'H3' or 'N10')
################################################################
def parseFormula(fragment):
segments=re.findall('[A-Z][a-z]*[0-9]*',fragment)
return (segments)
##################################################################################
#Computes total mass of both parenthetical and nonparenthetical formula components
##################################################################################
def molmass(formula):
parenMass=0
nonparenMass=0
while (len(formula)>0):
#First computes the molecular weight of all parenthetical formulas from left to right
while (len(re.findall('\(\w*\)[0-9]+', formula))!=0):
parenthetical=re.findall('\(\w*\)[0-9]+',formula)
for i in range(0,len(parenthetical)):
parenMult1 = re.findall('\)[0-9]+', parenthetical[i])
parenMult2 = re.findall('[0-9]+', parenMult1[0])
segments =parseFormula(parenthetical[i])
for i in range(0, len(segments)):
parenMass= parenMass + ((getMass(segments[i]))*(float(parenMult2[0])))
formula=re.sub('\(\w*\)[0-9]+', '', formula)
#Sums nonparenthetical molecular weights when all parenthetical molecular weights have been summed
segments = parseFormula(formula)
for i in range(0, len(segments)):
nonparenMass=nonparenMass + getMass(segments[i])
formula=re.sub(formula, '', formula)
Mass=parenMass+nonparenMass
return Mass
if __name__ == '__main__':
test=test.split(',')
for element in test:
print ('The mass of %(substance)s is %(Mass)f.' % {'substance': \
element, 'Mass': molmass(element)})
The best molecular weight calculator which I've encountered is Matthew Monroe's Molecular Weight Calculator, which can be found at http://ncrr.pnnl.gov/software/
It does everything. Molecular weights. Isotopic patterns. And so, so, so much more.
It has one major drawback though - it's written for Windows. Luckily, it sort of works under Wine after you've done a bit of wine-trick-ery.
As great as the calculator is, sometimes you only need to calculate the molecular weight of something, and nothing else. Searching the debian repos I can' t find a single dedicated molecular weight calculator. In particular, a command-line driven calculator would be nice.
Seriously - it's a crying shame that the distribution with the largest repos, i.e. Debian, does not have a single passable molecular weight calculator. It is even more surprising given the number of chemistry-related packages which are present.
So, here's what I did:
a quick google on "python molecular weight calculator" brought me to http://pygments.org
A little bit of editing gave the code below, which was saved as molcalc, copied to /usr/bin, followed by sudo chmod +x /usr/bin/molcalc. It can now be called using
molcalc "(Co(CO)5)2"
and returns
The mass of (Co(CO)5)2 is 257.916890.
Here's the code, which is 99.9% the original and 0.1% my modification. All credit thus due to Lee, Freitas and Tucker.
NOTE: it doesn't handle layered parentheses. (Al(NO3)3)2 gets interpreted as Al2(NO3)3.
#!/usr/bin/python2.6
#########################################################################
# Author: Toni Lee with the help of Guilherme Freitas and Becky Tucker. Minor changes by Lindqvist
# Copyright: This module has been placed in the public domain
#########################################################################
#Import regular expressions
import re
import sys
try:
test=sys.argv[1]
except:
quit()
#Create the dictionary (From Becky with a value of 0 inserted for Uus(mass not measurable))
TableofElements ={ 'H':1.00794,'He':4.002602,'Li':6.941,'Be':9.012182,
'B':10.811,'C':12.0107,'N':14.0067,'O':15.9994,'F':18.9984032,'Ne':20.1797,
'Na':22.98976928,'Mg':24.3050,'Al':26.9815386,'Si':28.0855,
'P':30.973762,'S':32.065,'Cl':35.453,'Ar':39.948,'K':39.0983,'Ca':40.078,
'Sc':44.955912,'Ti':47.867,'V':50.9415,'Cr':51.9961,'Mn':54.938045,
'Fe':55.845,'Ni':58.6934,'Co':58.933195,'Cu':63.546,'Zn':65.38,'Ga':69.723,
'Ge':72.64,'As':74.92160,'Se':78.96,'Br':79.904,'Kr':83.798,'Rb':85.4678,
'Sr':87.62,'Y':88.90585,'Zr':91.224,'Nb':92.90638,'Mo':95.96,'Tc':98,
'Ru':101.07,'Rh':102.90550,'Pd':106.42,'Ag':107.8682,'Cd':112.411,
'In':114.818,'Sn':118.710,'Sb':121.760,'Te':127.60,'I':126.90447,
'Xe':131.293,'Cs':132.9054519,'Ba':137.327,'La':138.90547,'Ce':140.116,
'Pr':140.90765,'Nd':144.242,'Pm':145,'Sm':150.36,'Eu':151.964,'Gd':157.25,
'Tb':158.92535,'Dy':162.500,'Ho':164.93032,'Er':167.259,'Tm':168.93421,
'Yb':173.054,'Lu':174.9668,'Hf':178.49,'Ta':180.94788,'W':183.84,
'Re':186.207,'Os':190.23,'Ir':192.217,'Pt':195.084,'Au':196.966569,
'Hg':200.59,'Tl':204.3833,'Pb':207.2,'Bi':208.98040,'Po':210,'At':210,
'Rn':220,'Fr':223,'Ra':226,'Ac':227,'Th':232.03806,'Pa':231.03588,
'U':238.02891,'Np':237,'Pu':244,'Am':243,'Cm':247,'Bk':247,'Cf':251,
'Es':252,'Fm':257,'Md':258,'No':259,'Lr':262,'Rf':261,'Db':262,'Sg':266,
'Bh':264,'Hs':277,'Mt':268,'Ds':271,'Rg':272, 'Uus':0
}
#######################################
#Computes the MW of an atom-number pair
#######################################
def getMass(x):
atom=re.findall('[A-Z][a-z]*',x)
number=re.findall('[0-9]+', x)
if len(number) == 0:
multiplier = 1
else:
multiplier = float(number[0])
atomic_mass=TableofElements[atom[0]]
return (atomic_mass*multiplier)
################################################################
#Segments formula into atom-number sections (i.e. 'H3' or 'N10')
################################################################
def parseFormula(fragment):
segments=re.findall('[A-Z][a-z]*[0-9]*',fragment)
return (segments)
##################################################################################
#Computes total mass of both parenthetical and nonparenthetical formula components
##################################################################################
def molmass(formula):
parenMass=0
nonparenMass=0
while (len(formula)>0):
#First computes the molecular weight of all parenthetical formulas from left to right
while (len(re.findall('\(\w*\)[0-9]+', formula))!=0):
parenthetical=re.findall('\(\w*\)[0-9]+',formula)
for i in range(0,len(parenthetical)):
parenMult1 = re.findall('\)[0-9]+', parenthetical[i])
parenMult2 = re.findall('[0-9]+', parenMult1[0])
segments =parseFormula(parenthetical[i])
for i in range(0, len(segments)):
parenMass= parenMass + ((getMass(segments[i]))*(float(parenMult2[0])))
formula=re.sub('\(\w*\)[0-9]+', '', formula)
#Sums nonparenthetical molecular weights when all parenthetical molecular weights have been summed
segments = parseFormula(formula)
for i in range(0, len(segments)):
nonparenMass=nonparenMass + getMass(segments[i])
formula=re.sub(formula, '', formula)
Mass=parenMass+nonparenMass
return Mass
if __name__ == '__main__':
test=test.split(',')
for element in test:
print ('The mass of %(substance)s is %(Mass)f.' % {'substance': \
element, 'Mass': molmass(element)})
This is dummy text. It is not meant to be read. Accordingly, it is difficult to figure out when to end it. But then, this is dummy text. It is not meant to be read. Period.
ConversionConversion EmoticonEmoticon