20. Is there no molecular weight calculator in the Debian repos?

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)})