star8521/chemsharp

Library for processing of chemistry related files (aiming at spectroscopy and structural files)

ChemSharp

.NET Library for processing of chemistry related files. Powers PorphyStruct!

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NuGet Packages

ChemSharp
ChemSharp.Molecules
ChemSharp.Molecules.Blazor
ChemSharp.Spectroscopy
ChemSharp.UnitConversion

^{CI Releases at: GitHub Packages}

Features

• Open and process Molecular files (see Supported Filetypes)
• Sum formula operations and elemental analysis calculation
• Using Elemental Data from https://github.com/JensKrumsieck/periodic-table
• Blazor view for molecules using three.js
• Open and process Spectroscopy related files (see Supported Filetypes)
• Unit Conversion for (Energy, Magnetic Units, Mass)

Basic Usage

Create Molecules

Molecules can be created in a lot of ways. The easiest way is to use MoleculeFactory.Create, which accepts a string path. Depending on the File extension the correct DataProvider is used to load the file.

//Creates a molecule from cif file
const string path = "files/cif.cif";
var mol = MoleculeFactory.Create(path);

It is also possible to create a Molecule by using a specific DataProvider (e.g. if automatic detection fails or you only want to support a selected number of file types)

//You can also create molecules by selecting the provider yourself
const string path = "files/benzene.mol2";
var provider = new Mol2DataProvider(path);
var mol = new Molecule(provider);

You can also add Atoms and Bonds as Lists if you got the data from somewhere else.

//...or by just adding the Atoms & Bonds as Lists
const string path = "files/cif.cif";
var provider = new CIFDataProvider(path);
var mol = new Molecule(provider.Atoms, provider.Bonds);

Create Spectra

Spectra can be created in a lot of ways. The easiest way is to use SpectrumFactory.Create, which accepts a string path. Depending on the File extension the correct DataProvider is used to load the file.

//Creates an UV/Vis Spectrum
const string path = "files/uvvis.dsw";
var uvvis = SpectrumFactory.Create(path);

It is also possible to create a Spectrum by using a specific DataProvider (e.g. if automatic detection fails or you only want to support a selected number of file types)

//You can also create spectra by choosing the provider 
//explicitly. e.g. csv files
//Reads in an CSV Spectrum (first data only)
const string path = "files/uvvis.csv";
var prov = new GenericCSVProvider(path);
var uvvis = new Spectrum(prov);

There is also the MultiCSVProvider which can provide data from multiple XY pairs in a csv file

//To read in all CSV Data stored as (X,Y) pairs use the MultiCSVProvider
//Each Spectrum will be stored as DataPoint[] in MultiXYData
const string file = "files/multicsv.csv";
var provider = new MultiCSVProvider(file);

Supported Filetypes

• Molecule

  • Import (XYZ, CIF (crystallographic information file, CCDC), MOL2 (TRIPOS Mol2), PDB (Protein Data Bank file), CDXML (Single Molecule only))
  • Export (XYZ, MOL2)

• Spectroscopy

  • Import (Varian/Agilient DSW, Bruker EMX SPC/PAR, Bruker TopSpin (fid, (1r/1i processed spectra), JCAMP-DX (acqus, procs, ...)), CSV)
  • Export (CSV)

Used Libraries:

• MathNet.Numerics

Compatibility

• .NET Standard 2.0, .NET Standard 2.1, .NET 5, .NET 6
• Unity (see Wiki )
• Godot Engine (see Wiki for Snippet)
• Blazor (see ChemSharp.Molecules.Blazor)

Used by (Highlights):

• PorphyStruct
• SPCViewer
• CHN-Tool