Protein Manipulation Domain Specific

LanguageLu Sun

Shuo Wu

OutlineBackground

Development Environment

Goals of DSL

Grammar model

Grammar

Editor

Code generation

Future work and Conclusion

BackgroundDSL

General-purpose programming languageC, Java or Python

Domain specific languageSQL, HTML, YACC

XtextDefine grammar

XtendLanguage execution

Development EnvironmentOperating System: Windows 7

Eclipse Integrated with Xtext

JDK 1.7

Goals of DSLThe PDB(Protein Data Bank) file is used to describe

protein structures.

An example of PDB files:

Only desceibe the name of the atoms as well as their coordinates.

ATOM 1 N GLN A 1 12.606 0.298 -13.791ATOM 2 CA GLN A 1 13.611 1.223 -13.286ATOM 3 C GLN A 1 14.099 0.753 -11.915ATOM 4 O GLN A 1 15.229 1.025 -11.507ATOM 5 CB GLN A 1 13.013 2.631 -13.203ATOM 6 CG GLN A 1 13.956 3.685 -12.648ATOM 7 CD GLN A 1 13.321 5.064 -12.624

Goals of DSLOur DSL is designed to simplify management and

manipulation of the protein description file.

expected functionality: import and export protein conformations into or

from the DSL program. implement insert and link operations on the protein

objects.

Grammer - semantic model

Grammer

Grammer//Declaration of protein

protein p

//import a protein conformation from an external file

import 'input.pdb' into p

//export a protein conformation into an external file

dump 'output.pdb' from p

Grammer//link two proteins

combine p1 p2 into p

//insert a segment into a protein

insert p1(12,33) into p2(124,145)

Grammer

declaration

operation

*The operations can be in any orders

Editor

Eclipse and Xtext automatically generate an editor with code completion and error checking.

Editor

Code Generation

Code Generation

Code Generation

Future Work and Conclusion

Grammer EvolutionAdd iteration to handle the batch taskOptimize the structure of the grammer

Functionality EvolutionComplete the functionalities

Manipulate protein structure in other waysCompare a pair of protein’s structure

ConclusionNatual language like Easy to use