NMRPyStar 0.0.7

## NMRPyStar ##

A library for parsing data in NMR-Star format, used by the BMRB for NMR (Nuclear Magnetic Resonance) data archival.

Why is this project necessary? After all, many people have already written working NMR-Star parsers.

However, not all parsers – even of the same format – are identical. Here are some of the important characteristics that determine how nice, easy, etc. it is to use a parser:

• what language the parser actually accepts. Some NMR-Star parsers accept malformed files, or fail on perfectly acceptable NMR-Star files.

  This project aims to: 1) accurately parse all valid NMR-Star input, and 2) accurately recognize and report all invalid NMR-Star input.

  This is done using a grammar to define the syntax, from which a parser is generated. Although the grammar is believed to be correct, it’s always possible that there are mistakes – feel free to contact me if you find one, I will be happy to make any corrections.

• what the parse result is. What access does the user have to the parsed result? What, if any, information is missing from the result?

  The output of this parser is a parse tree representing the structure of the input, including data blocks, save frames, loops, and key-value pairs. The parse tree is composed of Python objects, against which queries can be easily written to extract the required data.

• how, when, and with what debugging information errors are reported

  Accurately reporting where and why input is malformed is a key aspect of a parser that’s nice to use. Arguably, error reporting should be part of a format specification – this parser does its best to report errors, but it’s not always clear how an error should be reported. Suggestions welcome!

• how the parser is used – is it a stand-alone tool? Can it be imported as a library?

  This parser is designed to be used as a library – simply import it, hand it your NMR-Star input, and set it loose!

• modularity and flexibility – can the parser operate on stdin and stdout? Can it parse content pulled from a web page? Can it parse multiple files at once?

  This parser doesn’t know anything about files, urls, or I/O streams – any way you use to read in your data and hand it to the parser is fine. This means that it’s easy to parse files from the BMRB’s web interface – just use the urllib2 library to grab a web page, and hand the contents to the parser!

• licensing, cost, restrictions.

  This project is 100% open-source under the MIT license. This means that you may use it in any way you wish, including reading, modifying, and sharing the code.

### General project organization ###

• parser combinators. General set of building blocks for constructing parsers

• full NMR-Star:

  • grammar

  • tokenizer

• simplified NMR-Star: reduces rule duplication and removes need for lookahead and backtracking. Allows better error reporting and easier unparsing

  • grammar

  • tokenizer

  • unparser

• NMR-Star data model

• NMR-Star hierarchical parser input: tokens output: error or instance of NMR-Star data model

• unit tests

### Contact information ###

Found a bug? Need help figuring something out? Want a new feature? Feel free to report anything using the github issue tracker, or email me directly at mfenwick100 at gmail dot com