This is an attempt to build a trans-compiler which can take C like code as input and generates chemical reactions XML file as output supported by CAIN. This XML file can be converted to Visual DSD supported file using CRN2DSD software developed at Gupta Lab. This compiler was developed as a part of my B.Tech project at DA-IICT in 2015.

If you use this work, please cite our paper: Shalin Shah, Manish Gupta. "DNA-based Chemical Compiler." arXiv preprint arXiv:1808.04790 (2018)

The compiler supports following operations :-

• Addition
• Subtraction (non-negative)
• Multiplication
• Identifier declaration

The compiler also supports following operation but is not able to generate code:-

• Division
• Conditional operators
• 'if' branching statement
• 'while' looping statement

The precedence and associativity of operator supported:-

Required Libraries and Tools

• uthash - Required for Hash Map.
• flex - Required to tokenize source code i.e lexical analyzer part.
• bison - Required to parse code as per Context Free Grammar i.e parser.
• gdsl - Required to use data structure like stack, queue, etc.

Steps to build the source code

> bison -y -d parser.y
    
> flex lexer.l
    
> gcc -c y.tab.c lex.yy.c
    
> gcc y.tab.o lex.yy.o symbolTable.c genReaction.c extraModules.c treeParser.c -o ccx -I/usr/local/include/gdsl -L/usr/local/lib -lgdsl

For linking GDSL Lib

export LD_LIBRARY_PATH=/usr/local/include/gdsl:$LD_LIBRARY_PATH

Note: Confirm paths of GDSL flags after installing it in your UNIX system.

Error Handling

The compiler supports following kinds of error reporting:

• Out of memory
• Undeclared variable used
• Incorrect Syntax