251. Isotopic pattern and molecular weight calculator in Python for Linux

UPDATE: I've moved this code to https://sourceforge.net/projects/pyisocalc/

I'm not answering questions about this code -- it's a work in progress (updated every other day) and if you can't figure out how to use it  on your own, you're not the (currently) intended audience. For example, I've only had time to add a small subsection of the elements.

I originally implemented a very different solution -- a very exact and shiny one. The problem is that the number of permutations increases too rapidly, so that anything larger than e.g. B3(NO3)4 would use up 8 GB of RAM or more. 'Easy' molecules like C18 didn't use that much RAM, but still introduced a noticeable delay. Trimming the list of permutations introduces errors (small, hopefully) but speeds things up orders of magnitude.

In other words: this calculator is moderately fast (python), and very accurate (as far as I can tell). As I keep on looking at more and more complex examples for validation I find that I need to introduce various trimming functions to keep the matrices small.

Having said that, it's still kind of neat. Here's RuCl5^2- by my program and Matt Monroe's calculator (which I trust):

Monroe's output:

And plotting on top (scaled Monroe's by 1.08 to compensate for the error in scaling in Monroe's program which gives 108% abundance):

I removed the figures of W6O19^- since the error in the y axis scale in Monroe's program (went to 120%) made it a less good example, and the list of peaks is too long for easy comparison.
Here's another figure:

A hypothetical W6^- molecule

Anyway, here are a couple of syntax examples:

  Usage:
 ./isocalc 'Al2(NO3)3'
 ./isocalc 'Al2(NO3)3' -1
 ./isocalc 'Al2(NO3)3' -1 output.dat
 ./isocalc Al2N3O9 
  ./isocalc Al(NO3)3(OH)1
  ./isocalc Al(NO3)3(OH)
./isocalc Al

See here for the source code:
https://sourceforge.net/projects/pyisocalc/

250. Compiling Kernel 3.6 on Debian Testing/Wheezy

IMPORTANT: a lot of drivers need to be explicitly enabled now, in particular those related to video devices (e.g. saa*, uvcvideo)

Nothing difficult or weird about compiling your own kernel, and 3.6 is no exception. This post is pretty much identical to my previous kernel compile posts, but with 3.6 replacing 3.x.
I've successfully compiled 3.6.0, 3.6.2, 3.6.3 and 3.6.6 this way.

If you're wondering whether it's worth it, you can have a look here:
 http://www.h-online.com/open/features/What-s-new-in-Linux-3-6-1714690.html

If you've never compiled a kernel before you might need to:

sudo apt-get install kernel-package fakeroot build-essential

Then get on with it:

wget http://www.kernel.org/pub/linux/kernel/v3.0/linux-3.6.3.tar.bz2
tar xvf linux-3.6.3.tar.bz2
cd linux-3.6/
cat /boot/config-`uname -r`>.config
make oldconfig

You'll get a whole bunch of questions about what to include. See the end of the post for a list.

Video device drivers
Chances are that you will want to do

make menuconfig

and enable the compilation of various video device drivers e.g. go to Device drivers, Multimedia support, star (*) Cameras/video grabbers support, which enables Video Capture Adapters. Go to Video Capture Adapters and enable e.g. V4L USB devices/USB Video Class (m) to get your webcam working. You may need to enable other things too.

 Next:

make-kpkg clean
time fakeroot make-kpkg -j3 --initrd --revision=3.6.3 --append-to-version=-amd64 kernel_image kernel_headers

Building takes a while -- about 39 minutes on an AMD II X3.

mv ../*3.6.3*.deb .
sudo dpkg -i *.deb

And you're done!

---

---

What's new:

Expose hardware/virtual IRQ mapping via debugfs (IRQ_DOMAIN_DEBUG) [N/y/?] (NEW) *
Memory Resource Controller for Control Groups (MEMCG) [N/y/?] (NEW)
HugeTLB Resource Controller for Control Groups (CGROUP_HUGETLB) [N/y/?] (NEW)
Virtual (secure) IP: tunneling (NET_IPVTI) [N/m/?] (NEW)
NFQUEUE integration with Connection Tracking (NETFILTER_NETLINK_QUEUE_CT) [N/y/?] (NEW)
CAN Identifier (NET_EMATCH_CANID) [N/m/?] (NEW)     IPset (NET_EMATCH_IPSET) [N/m/?] (NEW)
Three-wire UART (H5) protocol support (BT_HCIUART_3WIRE) [N/y/?] (NEW)
Trace all mac80211 debug messages (MAC80211_MESSAGE_TRACING) [N/y/?] (NEW)   *
Driver for Broadcom BCM8706 and BCM8727 PHYs (BCM87XX_PHY) [N/m/?] (NEW) 
rt2800pci - Include support for rt3290 devices (EXPERIMENTAL) (RT2800PCI_RT3290) [Y/n/?] (NEW) 
MELFAS MMS114 touchscreen (TOUCHSCREEN_MMS114) [N/m/?] (NEW) 
EDT FocalTech FT5x06 I2C Touchscreen support (TOUCHSCREEN_EDT_FT5X06) [N/m/?] (NEW) 
Analog Devices AD-FMCOMMS1-EBZ SPI-I2C-bridge driver (SPI_XCOMM) [N/m/?] (NEW) 
BT8XX GPIO abuser (GPIO_BT8XX) [N/m/y/?] (NEW)   
AMD 8111 GPIO driver (GPIO_AMD8111) [N/m/y/?] (NEW)  
4096-Bit Addressable 1-Wire EEPROM with PIO (DS28E04-100) (W1_SLAVE_DS28E04) [N/m/?] (NEW)
Adaptive Voltage Scaling class support (POWER_AVS) [N/y/?] (NEW) *
Honeywell Humidicon HIH-6130 humidity/temperature sensor (SENSORS_HIH6130) [N/m/?] (NEW) 
BCMA Broadcom GBIT MAC COMMON core driver (BCMA_DRIVER_GMAC_CMN) [N/y/?] (NEW)
Support Wolfson Microelectronics Arizona platform with I2C (MFD_ARIZONA_I2C) [N/m/?] (NEW)
Support Wolfson Microelectronics Arizona platform with SPI (MFD_ARIZONA_SPI) [N/m/y/?] (NEW)
Cameras/video grabbers support (MEDIA_CAMERA_SUPPORT) [N/y/?] (NEW)  
Analog TV support (MEDIA_ANALOG_TV_SUPPORT) [N/y/?] (NEW) 
Digital TV support (MEDIA_DIGITAL_TV_SUPPORT) [N/y/?] (NEW)  
AM/FM radio receivers/transmitters support (MEDIA_RADIO_SUPPORT) [N/y/?] (NEW) 
Remote Controller support (MEDIA_RC_SUPPORT) [N/y/?] (NEW) 
Enable framebuffer console under vmwgfx by default (DRM_VMWGFX_FBCON) [N/y/?] (NEW)  
User-space I/O driver support for HID subsystem (UHID) [N/m/?] (NEW)  
Lenovo ThinkPad USB Keyboard with TrackPoint (HID_LENOVO_TPKBD) [N/m/?] (NEW) 
LED support for LM3556 Chip (LEDS_LM3556) [N/m/?] (NEW)  
LED support for the BlinkM I2C RGB LED (LEDS_BLINKM) [N/m/?] (NEW) 
LED One-shot Trigger (LEDS_TRIGGER_ONESHOT) [N/m/y/?] (NEW) 
EDAC legacy sysfs (EDAC_LEGACY_SYSFS) [Y/n/?] (NEW)  
VFIO Non-Privileged userspace driver framework (VFIO) [N/m/y/?] (NEW) *
Xen platform mcelog (XEN_MCE_LOG) [N/y/?] (NEW) *
Comedi misc drivers (COMEDI_MISC_DRIVERS) [N/y/?] (NEW) *
Comedi PCI drivers (COMEDI_PCI_DRIVERS) [N/y/?] (NEW) *
Comedi PCMCIA drivers (COMEDI_PCMCIA_DRIVERS) [N/y/?] (NEW) *
Comedi USB drivers (COMEDI_USB_DRIVERS) [N/y/?] (NEW) *
CSR wireless driver (CSR_WIFI) [N/m/?] (NEW) *
Pulse-Width Modulation (PWM) Support (PWM) [N/y/?] (NEW) *
Log kernel console messages (PSTORE_CONSOLE) [N/y/?] (NEW)   
Provide swap over NFS support (NFS_SWAP) [N/y/?] (NEW) 
Notifier error injection (NOTIFIER_ERROR_INJECTION) [N/m/y/?] (NEW)
Set upper limit of TLB entries to flush one-by-one (DEBUG_TLBFLUSH) [N/y/?] (NEW)
Serpent cipher algorithm (x86_64/AVX) (CRYPTO_SERPENT_AVX_X86_64) [N/m/y/?] (NEW) 
Twofish cipher algorithm (x86_64/AVX) (CRYPTO_TWOFISH_AVX_X86_64) [N/m/y/?] (NEW)   *
TCM_VHOST fabric module (EXPERIMENTAL) (TCM_VHOST) [N/m/?] (NEW) #

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Links to this post:
http://forumubuntusoftware.info/viewtopic.php?f=117&t=8832
http://linux.org.ru/forum/linux-hardware/8339795
http://www.taringa.net/comunidades/ubuntuparataringeros/6513772/_ayuda_compilar-kernel-3_6-en-crunchbang.html
http://kenan.abdullahoglu.com/index.php/bilisim
http://crunchbang.org/forums/viewtopic.php?id=24484
http://forum.teneon.de/index.php?yshout&file=home&history&n=1000

249. Quick but precise isotopic pattern (isotope envelope) calculator in Octave

UPDATE: Below is an accurate calculator,  but it is impractically slow for large molecules. A practical AND accurate calculator is found here:http://verahill.blogspot.com.au/2012/10/isotopic-pattern-caculator-in-python.html

Use the post below to learn about the fundamental theory, but then look at the other post to understand how to implement it.

Old post:
Getting fast and accurate isotopic patterns can be tricky using tools available online, for download or which form part of commercial packages. A particular problem is that different tools give slightly different values -- so which one to trust?

The answer: the tool for which you know that the algorithm is sound.

The extreme conclusion of that way of thinking is to write your own calculator.
Below is the conceptual process of calculating the isotopic pattern of a molecule using GNU Octave.

You need the linear algebra package:
sudo apt-get install octave octave-linear-algebra

b is the isotopic distribution for an element, and bb are the masses of those isotopes.

Once you've got a computational engine it's not too difficult to expand it for more general cases, account for charge, and instrument resolution.

---

Molecule: Cl₄

b=[0.7578,0.2422];
bb=[34.96885,36.96885];
e=prod(cartprod(b,b,b,b),2);
ee=sum(cartprod(bb,bb,bb,bb),2);
n=4;
g=histc([ee e],linspace(min(ee),max(ee),n*(max(ee)-min(ee)+1)),2);
h=linspace(min(ee),max(ee),n*(max(ee)-min(ee)+1));
distr=e'*g;
plot(h,100.*distr/max(distr))
[h' (100.*distr/max(distr))']

Here's the output for n=1:

   139.87540    78.22048
   140.87540     0.00000
   141.87540   100.00000
   142.87540     0.00000
   143.87540    47.94141
   144.87540     0.00000
   145.87540    10.21502
   146.87540     0.00000
   147.87540     0.81620

And here's the output from Matt Monroe's calculator:

Isotopic Abundances for Cl4
  Mass/Charge Fraction  Intensity
   139.87541 0.3297755   78.22
   140.87541 0.0000000    0.00
   141.87541 0.4215974  100.00
   142.87541 0.0000000    0.00
   143.87541 0.2021197   47.94
   144.87541 0.0000000    0.00
   145.87541 0.0430662   10.22
   146.87541 0.0000000    0.00
   147.87541 0.0034411    0.82

---

Another molecule: Li2Cl2

Here's the code:

a=[0.0759,0.9241];
aa=[6.01512,7.01512];
b=[0.7578,0.2422];
bb=[34.96885,36.96885];
e=prod(cartprod(a,a,b,b),2);
ee=sum(cartprod(aa,aa,bb,bb),2);
n=1;
g=histc([ee e],linspace(min(ee),max(ee),n*(max(ee)-min(ee)+1)),2);
h=linspace(min(ee),max(ee),n*(max(ee)-min(ee)+1));
distr=e'*g;
plot(h,100.*distr/max(distr))
[h' (100.*distr/max(distr))']

ans =

    81.96794     0.67170
    82.96794    16.35626
    83.96794   100.00000
    84.96794    10.45523
    85.96794    63.71604
    86.96794     1.67079
    87.96794    10.17116

vs Matt Monroe's calculator:

Isotopic Abundances for Li2Cl2
  Mass/Charge Fraction  Intensity
    81.96795 0.0033082    0.67
    82.96795 0.0805564   16.36
    83.96795 0.4925109  100.00
    84.96795 0.0514932   10.46
    85.96795 0.3138084   63.72
    86.96795 0.0082288    1.67
    87.96795 0.0500941   10.17

---

We can then expand the code to allow for plotting

a=[0.0759,0.9241];
aa=[6.01512,7.01512];
b=[0.7578,0.2422];
bb=[34.96885,36.96885];
e=prod(cartprod(a,a,b,b),2);
ee=sum(cartprod(aa,aa,bb,bb),2);
n=1;

g=histc([ee e],linspace(min(ee),max(ee),n*(max(ee)-min(ee)+1)),2);
h=linspace(min(ee),max(ee),n*(max(ee)-min(ee)+1));
distr=e'*g;
gauss= @(x,c,r,s) r.*1./(s.*sqrt(2*pi)).*exp(-0.5*((x-c)./s).^2);
k=100.*distr/max(distr);

npts=1000;
resolution=0.25;

x=linspace(min(ee)-1,max(ee)+1,npts);
l=cumsum(gauss(x,h',k',resolution));
l=100*l./max(l(rows(l),:));
plot(x,l(rows(l),:))

which gives:

Compare with Matt Monroe's calculator: