dope_loopmodel reference

The dope_loopmodel class is derived from loopmodel, and is very similar in operation, except that a newer DOPE-based loop modeling protocol is used (see selection.assess_dope()). The main differences are:

• DOPE (see selection.assess_dope()) potential used in combination with GB/SA implicit solvent interaction (see Section 6.14).

• Lennard-Jones potential used rather than soft-sphere.

• Improved handling of ligand-loop interactions.

To use, simply use 'dope_loopmodel' rather than 'loopmodel' in your Python scripts (see Section 2.3 for examples). Note that it will be significantly slower than the regular loop modeling procedure, primarily due to the GB/SA interaction.