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## physical.values() -- create a new set of physical values

`values(default=1.0, **keys)`

> This creates a new empty `values` object. This is very similar to a Python dictionary; valid keys are `'default'` or any of the objects from Table 6.1. For example, if `'v'` is a new object, you can set the value for the bond angle contribution to `'0.5'` with `'v[physical.angle] = 0.5'`. If you try to read a physical type from `'v'` which is not set, you'll get `v['default']`. As a convenience, you can set initial values for the default and/or physical types by passing them as parameters to the `'physical.values()'` constructor, without the `'physical.'` prefix. For example `'physical.values(default=1.0, h_bond=0.1, coulomb=0.1)'` would scale all types by 1.0 except for the H bond and Coulomb terms.

Example: See selection.debug_function() command.

Table 6.1: List of ``physical'' restraint types.
Python object | Index | `Group`
`physical.bond` | 1 | Bond length potential
`physical.angle` | 2 | Bond angle potential
`physical.dihedral` | 3 | Stereochemical cosine dihedral potential
`physical.improper` | 4 | Stereochemical improper dihedral potential
`physical.soft_sphere` | 5 | soft-sphere overlap restraints
`physical.lennard_jones` | 6 | Lennard-Jones 6-12 potential
`physical.coulomb` | 7 | Coulomb point-point electrostatic potential
`physical.h_bond` | 8 | H-bonding potential
`physical.ca_distance` | 9 | Distance restraints 1 ( - )
`physical.n_o_distance` | 10 | Distance restraints 2 (N-O)
`physical.phi_dihedral` | 11 | Mainchain dihedral restraints
`physical.psi_dihedral` | 12 | Mainchain dihedral restraints
`physical.omega_dihedral` | 13 | Mainchain dihedral restraints
`physical.chi1_dihedral` | 14 | Sidechain dihedral restraints
`physical.chi2_dihedral` | 15 | Sidechain dihedral restraints
`physical.chi3_dihedral` | 16 | Sidechain dihedral restraints
`physical.chi4_dihedral` | 17 | Sidechain dihedral restraints
`physical.disulfide_distance` | 18 | Disulfide distance restraints
`physical.disulfide_angle` | 19 | Disulfide angle restraints
`physical.disulfide_dihedral` | 20 | Disulfide dihedral angle restraints
`physical.lower_distance` | 21 | X lower bound distance restraints
`physical.upper_distance` | 22 | X upper bound distance restraints
`physical.sd_mn_distance` | 23 | Distance restraints 3 (SDCH-MNCH)
`physical.chi5_dihedral` | 24 | Sidechain dihedral restraints
`physical.phi_psi_dihedral` | 25 | binomial dihedral restraints
`physical.sd_sd_distance` | 26 | Distance restraints 4 (SDCH-SDCH)
`physical.xy_distance` | 27 | Distance restraints 5 (X-Y)
`physical.nmr_distance` | 28 | NMR distance restraints 6 (X-Y)
`physical.nmr_distance2` | 29 | NMR distance restraints 7 (X-Y)
`physical.min_distance` | 30 | Minimal distance restraints
`physical.nonbond_spline` | 31 | Non-bonded spline restraints
`physical.accessibility` | 32 | Atomic accessibility restraints
`physical.density` | 33 | Atom density restraints
`physical.absposition` | 34 | Absolute position restraints
`physical.dihedral_diff` | 35 | Dihedral angle difference restraints
`physical.gbsa` | 36 | GBSA implicit solvent potential
`physical.em_density` | 37 | EM density fitting potential
`physical.saxs` | 38 | SAXS restraints
`physical.symmetry` | 39 | Symmetry restraints

Next: The optimizers module: optimization Up: The physical module: contributions Previous: The physical module: contributions Contents Index