Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/zanpeeters/interference_calculator
Calculate mass interference based on the composition of a sample and a target.
https://github.com/zanpeeters/interference_calculator
mass-spectrometry science sims
Last synced: 1 day ago
JSON representation
Calculate mass interference based on the composition of a sample and a target.
- Host: GitHub
- URL: https://github.com/zanpeeters/interference_calculator
- Owner: zanpeeters
- License: bsd-3-clause-clear
- Created: 2017-12-27T23:42:11.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2022-09-27T02:21:45.000Z (about 2 years ago)
- Last Synced: 2024-11-22T15:27:18.131Z (30 days ago)
- Topics: mass-spectrometry, science, sims
- Language: Python
- Size: 1.16 MB
- Stars: 2
- Watchers: 2
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.rst
- License: LICENSE.rst
Awesome Lists containing this project
README
.. image:: interference_calculator/icon.svg
:width: 128px
:height: 128px
:align: right
:alt: icon.svg
***********************
Interference calculator
***********************
Interference calculator calculates all molecules that can be formed (the interferences) from a combination of a list of atoms (sample composition), given a target mass and range. The calculation considers all isotopes of the sample atoms and build molecules up to a given size. The results are displayed in both a table and a mass spectrum.
.. image:: screenshot_1.png
:align: center
:alt: screenshot-1
The program can also display the standard ratios of the isotopes for any given element. The results include the natural abundance, standard ratio, inverse ratio, and the standard material in which the isotopic ratios where measured.
.. image:: screenshot_2.png
:align: center
:alt: screenshot-2
Installation
============
To use interference_calculator, first you need to have Python installed. Download Python `here `_. Once Python is installed, open a terminal window (command window on Windows) and type:
.. code-block:: bash
$ pip install interference_calculator
on the command line to install interference calculator.
Running
=======
To start the program, simply run the ui.py script.
.. code-block:: bash
$ python interference_calculator/ui.py
Use in IPython
==============
Interference_calculator can also be used from an interactive interpreter or in another Python script. For example, to calculate the mass interference around iron (Fe, mass 56), given a sample that consists of Si, Ca, O, and H, use it like this. ::
>>> import interference_calculator as ic
>>> ic.interference(['Ca', 'O', 'H', 'Si'], 'Fe')
molecule charge mass/charge mass/charge diff MRP \
0 O Ca - 1 55.958054 0.023118 2419.529988
1 Si2 - 1 55.954402 0.019466 2873.520086
2 18O3 D - 1 56.012129 0.077193 724.609657
3 18O3 H2 - 1 56.013677 0.078741 710.361726
4 17O 18O2 H D - 1 56.019926 0.084990 658.132608
5 D4 48Ca - 1 56.009478 0.074542 750.376520
6 O 18O2 D2 - 1 56.021986 0.087050 642.561143
7 17O2 18O D2 - 1 56.026175 0.091239 613.057735
8 Fe - 1 55.934936 0.000000 inf
probability target
0 9.671034e-01 False
1 8.506314e-01 False
2 7.556442e-15 False
3 3.999731e-06 False
4 1.103164e-13 False
5 1.100126e-18 False
6 3.721482e-09 False
7 1.103556e-16 False
8 9.175400e-01 True
>>> ic.standard_ratio(['Ca', 'O'])
isotope mass abundance ratio inverse ratio standard
13 16O 15.994915 0.997621 1.000000 1.000000 VSMOW
14 17O 16.999132 0.000379 0.000380 2632.244327 VSMOW
15 18O 17.999160 0.002000 0.002005 498.710558 VSMOW
41 40Ca 39.962591 0.969410 1.000000 1.000000 NIST SRM 915
42 42Ca 41.958618 0.006470 0.006674 149.831530 NIST SRM 915
43 43Ca 42.958766 0.001350 0.001393 718.081481 NIST SRM 915
44 44Ca 43.955482 0.020860 0.021518 46.472196 NIST SRM 915
45 46Ca 45.953690 0.000040 0.000041 24235.250000 NIST SRM 915
46 48Ca 47.952523 0.001870 0.001929 518.401070 NIST SRM 915
There is also a class ``Molecule``, that can parse strings with molecular formulas. After parsing, it holds information about the molecule, such as mass, elements, isotopes, and relative abundance. ``Molecule.formula()`` can be used to typeset the molecular formula in various ways.::
>>> m = ic.Molecule('C2 15N O3 2+')
>>> m.elements
['N', 'C', 'O']
>>> m.isotopes
['15N', '12C', '16O']
>>> m.masses
[15.000108899, 12.0, 15.99491462]
>>> m.mass
86.985949918818
>>> m.abundances
[0.003663, 0.988922, 0.9976206]
>>> m.abundance
1.317443808955884e-05
>>> m.formula(style='latex')
'$\\mathrm{{}^{15}{N}{C}_{2}{O}_{3}{}^{2-}}$'
See the docstrings for detailed help and options.