Skip to content
Switch branches/tags

Latest commit


Git stats


Failed to load latest commit information.
Latest commit message
Commit time


A simple type-safe Domain Specific Language (DSL) for chemistry and biology.


usage: [-h] -i INPUT [-d] [-wd WORKING_DIRECTORY] [-o OUTPUT]
       [-t {m,i,p,inkwell,l,llvm,ir,mfsim,puddle}] [-cfg] [-inline]
       [-stats] [-lu] [-sim {False,True}] [-id {0,1,2,32,4,8,16}]
       [-nf] [-smarts SMARTS] [-tcl {none,warn,error}] [-tc]
       [-tcu {complex,simple,s,c}] [-epa EPA_DEFS] [-abs ABS_INT]
       [--dbname DBNAME] [--dbuser DBUSER] [--dbpass DBPASS]
       [--dbaddr DBADDR] [--dbdriver {odbc,mysql}] [-lib LIBRARY]
       [-flow {passive,p,a,active}] [--cdb CDB] [--schema SCHEMA]

Optional Arguments:

Short Long Flag Purpose
-h --help show this help message and exit
-i --input path/to/ Location of input file
-d --debug Enable debugging.
-t --target {i,inkwell,p,puddle,m,mfsim,l,llvm, ir,} What platform do you wish to target?
-o --output path/to/output/dir Enable writing output. Must be set to write anything
-wd --working-directory path/to/directory Directory from where you wish to work
-cfg --write-cfg Write the CFG to a dot file
-inline --inline Inline all non-recursive functions
-lu --loopunroll Unroll all un-rollable loops
-stats --stats Print the stats to std out
-cfg --write-cfg Write the programs control flow graph to disk


Chemistry specific arguments

Short Long Flag Purpose
-sim --simulate {True, False} Simulate chemistry?
-id --identify {0,1,2,32,4,8,16} Chemical identification level
-nf --no-filters Disable smart filter creation
-smarts --smarts 0-255 Length of smarts file to use


Typing specific arguments

Short Long Flag Purpose
-tcl --typechecklevel {error, warn, none} What interactions elicit notifications
-tc --typecheck Enable type checking of input program
-tcu --typesused {s, simple, c, complex} What types to use to typecheck a program, s = {mat, nat, real}, c = {all types in chemtype}
-epa --epa-defs Path/to/epa_defs.json Location of the EPA definition file (default: ./resources/epa.json)
-abs --abs-int path/to/abs-int.txt Location of the abstract interaction file (default: ./resources/abstract-interaction.txt)


Database specific arguments

Flag Argument Purpose
--dbname str Name of database.
--dbuser str Database user.
--dbpass str Database password for user.
--dbaddr {IP, Host} Address of database.
--dbdriver {mysql,odbc} Database driver.


Inkwell specific (-t inkwell) flags

Short Long Flag Purpose
-lib --library path/to/json/component/lib The path to the component library
-flow --flow {p, a, passive, active} Which type of flow-based device are you targeting
-cdb database Name of component database (not supported)
--schema Path to schema.json The ParchMint schema file
--validate Validate a netlist against the ParchMint schema


You'll need Python3 (apt-get install python3), and GraphViz installed (apt-get install graphviz)

If on macOS, install brew, then brew install python3 and brew install graphviz.

BioScript's grammar is attached as a submodule. Hence, if cloning this repo, make sure to include the --recursive tag:

git clone --recursive

Also, if BioScriptGrammar (or any other submodule) is updated, you'll need to run git submodule foreach git pull origin master if your version of git does not do this automatically for you.

Install required python modules: pip install -r requirements.txt

Try running the example usage (below). It's possible that a C-style comment /* ... */ is present in some of the grammar files generated by Antlr. Open any offending files and use proper pythong comments # to mitigate this issue.

Some modules may have not installed properly even using the recursive pip install method above.

Continue trying the example usage (below), and pip install any missing modules.

Note: you may need to use pip3 install if python3/pip3 is not your default python/pip alias.

Example Usages:

Enable debug (-d), compile a file (-i ...), target BioScript's IR (-t ...), and place the output files in the specified location:

python -d -i tests/test_cases/mix/ -t ir -o ./output -cfg

Your output folder should includ the following files:,,

You can either use graphviz to create a .png of the generated dag (dot -Tpng -o dag.png), or use and paste the contents of the .dot or .dag file for visualization.


The BioScript compiler, ChemStor storage, and Application Binder.



No releases published


No packages published