UPDATE 02/02/2012:
It seems like whatever the problem was, it's gone now. An up-to-date testing system with ibus runs smoothly.
26/11/2011
For some reason, after updating today I'm having a hard time entering input in various gnome applications, whereas non-gnome applications work fine.
E.g. I can't type certain letters, and in general it's difficult to provide any inpurt, in gnome-terminal and gnome-session-properties. lxterm and guake work completely normal though.
No sure what is causing this, but it's happening on my Thinkpad SL410 as well as on my Optiplex 910. The only thing they have in common is the operating system (up-to-date debian testing 64 bit).
Don't know enough about it to file a bug report.
Edit: the problem is present in Evolution as well. Still present as of 28/11/2011. Problem exists on a home-built six-core AMD with 1 GB graphics card.
Edit 2: It sounds a bit like this, which was reported in June (!).
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=631116
It seems to be related to iBus/SCIM
Edit 3: Evolution is also affected, as is gEdit. Turning off iBus 'solves' the problem. Now, why does it affect the standard gnome applications, but not other packages?
At any rate, this bug has given me the incentive to leave gnome-terminal for guake, and to give alpine and thunderbird a try instead of evolution.
I tried
sudo apt-get install ibus-gtk3
sudo apt-get autoremove ibus-gtk
iBus still works. But unfortunately evolution is still way too slow to be useful.
Lindqvist - a blog about Linux and Science. Mostly.
25 November 2011
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)})
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)})
22 November 2011
19. Gnome3/gnome-shell -- 11 days later
So, I stuck it out. The new gnome-shell is fairly functional for me, finally.
The lack of system indicator applets was solved by using conky to overlay information on the desktop.
Frippery's gnome-shell extensions also make the experience less frustrating.
However, it still feels like everything I've done have been finding /work-arounds/ rather than /customisation/. In the end the whole idea of an application-centric desktop is unsuitable for me -- I would expect this to be true for the majority of established linux users.
Edit (25/11/2011):The screengrab shows what my heavily modified desktop looks like.
The lack of system indicator applets was solved by using conky to overlay information on the desktop.
Frippery's gnome-shell extensions also make the experience less frustrating.
However, it still feels like everything I've done have been finding /work-arounds/ rather than /customisation/. In the end the whole idea of an application-centric desktop is unsuitable for me -- I would expect this to be true for the majority of established linux users.
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