Re: [IMP-dev] Proposed modification of how code accepts rigid bodies
To: List for IMP development <>
Subject: Re: [IMP-dev] Proposed modification of how code accepts rigid bodies
From: Daniel Russel <>
Date: Fri, 8 Oct 2010 13:58:55 -0700
Reply-to: List for IMP development <>
On Oct 7, 2010, at 2:04 PM, Ben Webb wrote:
> On 10/6/10 11:16 AM, Daniel Russel wrote:
>> I propose a new standard type of interface, namely, simply taking all
>> the XYZR particles of interest, whether or not they happen to be part
>> of a rigid body. That is, if you have some rigid proteins and some
>> non-rigid proteins and are representing everything with all atoms,
>> you simply pass all the atoms.
>
> Sounds reasonable and less confusing for users to me. My only concern
> is: what happens in the above case if the user passes a list that
> contains only some atoms from a given rigid body? (e.g. protein A is
> rigid, protein B is non-rigid, and the user passes in just a few of the
> atoms from protein A) Any code that currently makes the assumption that
> an entire rigid body is involved (e.g. I suspect FitRestraint) would
> have to do the right thing (or maybe throw an exception and require that
> all members of a rigid body go in).
Any code that currently makes such an assumption is currently broken (since a single rigid body can include multiple representations of the same structure, as the ones created by the IMP::atom::create_rigid_body do).