Open source/ open data concept¶
All MMMx functions and definitions are open source. Almost all module output is provided or can be requested in the file formats that can be read by non-proprietary software. The single exception are rigid-body assemblies generated by the Rigi module, which are output in the form of a Matlab file.
Branched pipeline concept¶
In general, MMMx modules read and write conformer structures from and into minimal PDB files. Raw ensembles are sets of such PDB files. Refined and contracted (representative) ensembles are specified by a list of conformer PDB files with associated populations (ensemble list). This allows for replacing any module of MMMx by third-party software that can fulfil the same task and to feed MMMx output at any point of a modeling pipeline into other software.