Next: energy_data() create Up: MODELLER command reference Previous: environ.make_pssmdb() Create Contents Index

The `energy_data` class: objective function parameters

The energy_data class is used to configure the objective function, selecting which types of dynamic restraints (see Section 5.3.1) to calculate (e.g., soft-sphere, Coulomb), and how to calculate them (e.g., distance cutoffs).

Subsections

energy_data() -- create a new set of objective function parameters
energy_data.contact_shell -- nonbond distance cutoff
energy_data.update_dynamic -- nonbond recalculation threshold
energy_data.sphere_stdv -- soft-sphere standard deviation
energy_data.dynamic_sphere -- calculate soft-sphere overlap restraints
energy_data.dynamic_lennard -- calculate Lennard-Jones restraints
energy_data.dynamic_coulomb -- calculate Coulomb restraints
energy_data.dynamic_modeller -- calculate non-bonded spline restraints
energy_data.excl_local -- exclude certain local pairs of atoms
energy_data.radii_factor -- scale atomic radii
energy_data.lennard_jones_switch -- Lennard-Jones switching parameters
energy_data.coulomb_switch -- Coulomb switching parameters
energy_data.relative_dielectric -- relative dielectric
energy_data.covalent_cys -- use disulfide bridges in residue distance
energy_data.nonbonded_sel_atoms -- control interaction with picked atoms
energy_data.nlogn_use -- select non-bond list generation algorithm
energy_data.energy_terms -- user-defined global energy terms

Automatic builds 2013-06-11

The energy_data class: objective function parameters

The `energy_data` class: objective function parameters