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 ( 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