This is a development branch that breaks many features. To install
the the previous release, use the 1.1 release, the main branch, or
pip install -U alhambra.
Alhambra, formerly tilesetdesigner, is a package for designing DNA tile systems.
This is the 2.0 prerelease, which is being built to support both SST and DX tiles, and the ability to extensibly add other motifs.
For DX tiles, it uses stickydesign to create sticky end sequences, and peppercompiler with spuriousSSM to create core sequences. For SSTs, it will use DSD. It uses an extensible system for tileset design, and can flexibly take inputs of YAML or similar formats.
Alhambra is designed to be installed as a Python package.
To install the prerelease version, use
pip install -U --pre alhambra
To install the latest git version (which may be broken), use
pip install -U 'alhambra @ git+https://github.com/DNA-and-Natural-Algorithms-Group/alhambra@v2'
Alhambra 2 is designed to work with Python 3.9 or later.
To install development versions, you can check out this github
repository, and use pip -e or some other method for installing Python
packages. Multiple versions can be handled through virtualenv.
All Alhambra requirements should be handled through setuptools dependencies, but note that xgrow and peppercompiler both rely on C code being compiled, which may fail.
Documentation is available online on readthedocs.io. In particular, see the tutorial. It is also available in the docs/ folder.
Most user-facing functions are on the TileSet class.
Please send any questions to Constantine Evans, at cevans@evanslabs.org or cge@dna.caltech.edu.