https://github.com/jmwoll/goccs

goccs is an ion mobility collision cross section prediction software with binaries for all major platforms. CCS values are calculated in a few simple steps. No installation is required!
https://github.com/jmwoll/goccs

chemistry ion-mobility mass-spectrometry spectroscopy

Last synced: 13 days ago
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goccs is an ion mobility collision cross section prediction software with binaries for all major platforms. CCS values are calculated in a few simple steps. No installation is required!

• Host: GitHub
• URL: https://github.com/jmwoll/goccs
• Owner: jmwoll
• License: gpl-3.0
• Created: 2017-08-27T11:35:49.000Z (over 7 years ago)
• Default Branch: master
• Last Pushed: 2018-06-07T16:21:43.000Z (almost 7 years ago)
• Last Synced: 2024-06-20T01:59:12.544Z (10 months ago)
• Topics: chemistry, ion-mobility, mass-spectrometry, spectroscopy
• Language: Go
• Homepage:
• Size: 9.05 MB
• Stars: 4
• Watchers: 1
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        


## About

goccs is a parallel cross platform CCS prediction software implemented in go.

CCS values can be easily computed in a few steps:

![CCS calculation in simple steps.](https://github.com/jmwoll/goccs/blob/master/doc/animation_usage.gif)

## Overview

Running the command

```

goccs_windows_386.exe -xyzfile example.xyz -approximation PA -parameters mobcal

```

gives out the CCS value in angstrom^2, where approximation is either 'PA' or 'EHS'.

Note that the name of the executable varies depending on the platform used. Custom parameters can be

specified in the JSON format:

```

goccs_windows_386.exe -xyzfile example.xyz -approximation PA -parameters '{"H": 1.23, "C": 2.34, "N": 3.45, "O": 4.56}'

```

Binaries for several platforms (Linux, OSX, Windows) can be found under ```bin/``` .

The number of processes are controlled via the ```-processes``` flag (defaults to 10).

For example, the command

```

goccs_windows_386.exe -xyzfile example.xyz -approximation PA -parameters mobcal -processes 100

```

uses 100 processes in parallel.

Citations for the parameters can be found below:

Mobcal parameters:

```

SM. F. Mesleh, J. M. Hunter, A. A. Shvartsburg, G. C. Schatz, M. F. Jarrold, Structural Information from Ion Mobility Measurements:  Effects of the Long-Range Potential, J. Phys. Chem. 1996, 100, 16082-16086.

J. Phys. Chem. A 1997, 101, 968.

A. A.Shvartsburg, M. F. Jarrold, An exact hard-spheres scattering model for the mobilities of polyatomic ions, Chem. Phys. Lett. 1996, 261, 86-91.

```

Default parameters:

```

C.-K. Siu, Y. Guo, I. S. Saminathan, A. C. Hopkinson, K. M. Siu, Optimization of ion-mobility calculation for conformational analyses, J. Phys. Chem. B, 2010, 114, 1204-1212.

```

## Benchmark

Here a Projection Approximation (PA) benchmark against the established Mobcal software:

![PA Benchmark.](https://github.com/jmwoll/goccs/blob/master/benchmark/benchmark_pa.png)

The PA CCS values exhibit excellent agreement with the literature values. For the

exact hard sphere (EHS) method, we observe slight implementation-dependent

differences to the Mobcal implementation. Generally, values predicted by goccs tend

to lie nearer to the Trajectory Method (TM) values than the Mobcal calculation.

Here an Exact Hard Sphere Scattering (EHS) benchmark against the established Mobcal software:

![PA Benchmark.](https://github.com/jmwoll/goccs/blob/master/benchmark/benchmark_ehs.png)