CANDO: A Compiled Programming Language for Computer-Aided Nanomaterial Design and Optimization

Christian Schafmeister presents CANDO, a compiled programming language built on Common Lisp designed for molecular and nanomaterial design.

ELS 2016, 9th European Lisp Symposium, 9-10 May 2016, Department of Computer Science, AGH University of Science and Technology, Kraków, Poland. Christian E. Schafmeister, Chemistry Department, Temple University, 1901 N. 13th Street Philadelphia, PA. CANDO is a compiled programming language designed for rapid prototyping and design of macromolecules and nano- meter-scale materials. CANDO provides functionality to write programs that assemble atoms and residues into new molecules and construct three-dimensional coordinates for them. CANDO also provides functionality for searching molecules for substructures, automatically assigning atom types, identifying rings, carrying out conformational search- ing, and automatically determining stereochemistry, among other things. CANDO extends the Clasp implementation of the dynamic language Common Lisp. CANDO provides classes for representing atoms, residues, molecules and ag- gregates (collections of molecules) as primitive objects that are implemented in C++ and subject to automatic memory management, like every other object within the language. CANDO inherits all of the capabilities of Clasp, including the easy incorporation of C++ libraries using a C++ tem- plate programming library. This automatically builds wrap- per code to expose the C++ functionality to the CANDO Common Lisp environment and the use of the LLVM li- brary[1] to generate fast native code. A version of CANDO can be built that incorporates the Open Message Passing Interface C++ library[2], which allows CANDO to be run on supercomputers, in order to automatically setup, start, and analyze molecular mechanics simulations on large par- allel computers. CANDO is currently available under the LGPL 2.0 license.