- meld.system.builders.build_elastic_network_restraints.create_elastic_network_restraints(system, chain_indices, cutoff=Quantity(value=1.0, unit=nanometer), restrained_atom='CA', residue_separation=3, k=Quantity(value=2500, unit=kilojoule / nanometer**2 * mole), only_inter=False, scaler=None, write_file=None)
Create elastic network restraints between specified backbone atoms within a single chain
Args: system: system object that is used for indexing
- chain_indices: provide a single int or list of integer ids that you want restraints built between
if you only want intra chain restraints (i.e. only restraints within a chain) only specify a single index and just re-use the function for as many chains as you want intra chain restraints. if you want restraints between chains (e.g. restraints to keep a complex together), provide a list of indices
cutoff: distance cutoff. Any restrained_atoms below the cutoff will have elastic network restraints created between them restrained_atom: atom name that restraints between residues will use. Currently only a single atom name is supported residue_separation: minimum sequence separation between restraints. k: force constant only_inter: only build restraints between chains. do not build restraints within a chain. useful if elastic network restraints
have come from somewhere else (e.g. martinize for martini builder)
- scaler: Optional specify a Scaler to vary the force constant with alpha.
None, then a constant 1.0 scaler will be used.
- write_file: Optional parameter to output restraints to a text file.
Useful for comparing restraints generated by different functions