BioCif.Core 0.9.0

Parses and tokenizes Crystallographic Information File (CIF) files from the Crystallographic Information Framework such as PDBx/mmCIF files used by the protein data bank (PDB). This package contains the core parser, tokenizer and data types used by any CIF file including the crystallographic open database (COD).

For more on the CIF see: https://www.iucr.org/resources/cif

Install-Package BioCif.Core -Version 0.9.0

dotnet add package BioCif.Core --version 0.9.0

<PackageReference Include="BioCif.Core" Version="0.9.0" />

For projects that support PackageReference, copy this XML node into the project file to reference the package.

paket add BioCif.Core --version 0.9.0

The NuGet Team does not provide support for this client. Please contact its maintainers for support.

#r "nuget: BioCif.Core, 0.9.0"

#r directive can be used in F# Interactive, C# scripting and .NET Interactive. Copy this into the interactive tool or source code of the script to reference the package.

// Install BioCif.Core as a Cake Addin
#addin nuget:?package=BioCif.Core&version=0.9.0

// Install BioCif.Core as a Cake Tool
#tool nuget:?package=BioCif.Core&version=0.9.0

The NuGet Team does not provide support for this client. Please contact its maintainers for support.

Readme

The core library for parsing all types of Crystallographic Information File (CIF) such as the PDBx/mmCIF format from the protein data bank (PDB).

Contains the core tokenizer and parser.

Usage

To access the raw stream of tokens:

using BioCif.Core.Tokenization;
using BioCif.Core.Tokens;

using (var fileStream = File.Open(@"C:\path\to\data.cif"))
using (var streamReader = new StreamReader(fileStream))
{
    foreach (Token token in CifTokenizer.Tokenize(streamReader))
    {
        Console.WriteLine(token.TokenType);
    }
}

To access the parsed CIF structure:

using (var fileStream = File.Open(@"C:\path\to\data.cif"))
{
    Cif cif = CifParser.Parse(fileStream);

    DataBlock block = cif.DataBlocks[0];
    Console.WriteLine($"Block name: {block.Name}");

    foreach (IDataBlockMember member in block.Members)
    {
        // ...
    }
}

The core library for parsing all types of Crystallographic Information File (CIF) such as the PDBx/mmCIF format from the protein data bank (PDB).

Contains the core tokenizer and parser.

Usage

To access the raw stream of tokens:

using BioCif.Core.Tokenization;
using BioCif.Core.Tokens;

using (var fileStream = File.Open(@"C:\path\to\data.cif"))
using (var streamReader = new StreamReader(fileStream))
{
    foreach (Token token in CifTokenizer.Tokenize(streamReader))
    {
        Console.WriteLine(token.TokenType);
    }
}

To access the parsed CIF structure:

using (var fileStream = File.Open(@"C:\path\to\data.cif"))
{
    Cif cif = CifParser.Parse(fileStream);

    DataBlock block = cif.DataBlocks[0];
    Console.WriteLine($"Block name: {block.Name}");

    foreach (IDataBlockMember member in block.Members)
    {
        // ...
    }
}