Atompaint: development notes and source code

This archive contains a record of the development of Atompaint, which is a computational method for designing protein/non-protein binding interfaces. Specifically, this record contains (i) notes about the many different ideas and directions that were pursued, (ii) slides and documents used to describe the method to various audiences, and (iii) source code for all of the computational experiments that were performed.Not all of the source code associated with this project is contained in this archive. Much is also organized into general-purpose libraries published on GitHub. Refer to the publication for links to this software.To keep the size of the archive manageable, some large files have been excluded from the archive. These exclusions include datasets, post-training model weights, and caches used for various analysis scripts. A separate archive containing the most important datasets and model weights has been uploaded; refer to the publication for the link to this archive.