User-defined features and restraint forms

MODELLER provides a variety of pre-defined features and mathematical restraint forms (see Section 5.3.1), but you can add your own by creating new Python classes. For cases where the conventional features and restraints approach is not practical, you can also add new energy function terms which act on all atoms in the system. This can be used to add entirely new kinds of restraint for novel modeling situations.

(Note that Python code is generally substantially slower than compiled C or FORTRAN. If you find yourself relying on a large amount of Python extensions to MODELLER, you may want to recompile the code with Cython, or rewrite your code as C extension modules.)