README.md

HELMNotationParser

HELMParser is a java-program to parse HELM and HELM2 notation. During the parsing process the validation of HELM2 takes place. The program not only parses but also generates so called notations objects. A file containing in each line a HELM notation is given as the input. It produces an user-defined output, either HELM2 or HELM2 in JSON-format. The created log-file can be found in ./helm2parser.log

The program is called by the following command:

java –jar helm2parser.jar –inputHELM [file] -output [HELM2/JSON]

The program is also able to convert HELM1 to HELM2. To use this additional function call the program with –translate.

java –jar helm2parser.jar –inputHELM [file] -output [HELM2/JSON] -translate

##Example

java -jar helm2parser.jar -inputHELM ./filename.txt -output JSON

##Example for Inputfile PEPTIDE1{A.G.D.A'55'}$$$$V2.0

{
"annotation" : {
"annotation" : ""
},
"listOfPolymers" : [ {
"polymerID" : {
  "id" : "PEPTIDE1"
},
"annotation" : null,
"polymerElements" : {
  "listOfElements" : [ {
    "unit" : "A",
    "annotation" : null,
    "count" : "1"
  }, {
    "unit" : "G",
    "annotation" : null,
    "count" : "1"
  }, {
    "unit" : "D",
    "annotation" : null,
    "count" : "1"
  }, {
    "unit" : "A",
    "annotation" : null,
    "count" : "55"
  } ]
}
} ],
"listOfConnections" : [ ],
"listOfGroupings" : [ ]
}

If you want to use the HELMNotationParser functionality via a GUI and don’t want to compile the code yourself, use the jar file in the release folder. Download and run and it should just work.

You will see a basic user interface you can use to convert HELM1 to HELM2 or JSON with the side-effect of providing a validation tool, since if the input HELM is not valid, it will not be converted.