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Pass to restrain_atoms a list of atom indices

See original GitHub issue

I came across a case where creating a DSL selection string for the atoms I need to restrain is quite a pain. I’m thinking of making forcefactories.restrain_atoms() a little more flexible by changing its signature from

def restrain_atoms(..., topology, atoms_dsl,...):


def restrain_atoms(..., restrained_atoms, ...):

where restrained_atoms is a simple list of atom indices. Any objections to this?

Issue Analytics

  • State:closed
  • Created 6 years ago
  • Comments:7 (7 by maintainers)

github_iconTop GitHub Comments

Lnadencommented, Sep 8, 2017

Better. I really think having both functionalities, or at bare minimum a DSL processing is much better from a user standpoint than just atom indices.

andrrizzicommented, Sep 8, 2017

I like that better (I hate not having proper overloading in Python)! Although, I’d do only 2 methods

def restrain_atoms_by_dsl(..., topology, atoms_dsl, ...):
    restrained_atoms =
    return restrain_atoms(...,restrained_atoms,...)

def restrain_atoms(..., atom_indices, ...):
    # Stuff
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