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 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 ( Cα - Cα )
physical.n_o_distance 10 Distance restraints 2 (N-O)
physical.phi_dihedral 11 Mainchain Φ dihedral restraints
physical.psi_dihedral 12 Mainchain Ψ dihedral restraints
physical.omega_dihedral 13 Mainchain ω dihedral restraints
physical.chi1_dihedral 14 Sidechain χ1 dihedral restraints
physical.chi2_dihedral 15 Sidechain χ2 dihedral restraints
physical.chi3_dihedral 16 Sidechain χ3 dihedral restraints
physical.chi4_dihedral 17 Sidechain χ4 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 χ5 dihedral restraints
physical.phi_psi_dihedral 25 $ (\Phi, \Psi)$ 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

Automatic builds 2017-07-19