>
> hi,
>>
>> I think that it would be much more productive to have discussion on major
>> design changes in IMP meeting and not via emails.
>> It would be preferable to raise issues in an email before the meeting and
>> write an email with conclusions after the meeting.
>>
>
>
> Yes. Also, and perhaps more importantly, now IMP is at a level of maturity
> when it is used by many people in the lab, so changes in it affect others. I
> think …
[View More]that major changes and philosophical view should be discussed previous
> implementation or changed. They "already done" things show a big tendency to
> stay that way even if they could be improved.
>
>
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We need to clean up what happens when multiple molecules are loaded
from a PDB. My current favorite is to
- make the current read_pdb only support loading a single protein
(chain) from the first model of a PDB file and return it as a
Hierarchy with the root being a PROTEIN. It can spit out warnings if
there are other molecules in there.
- add a read_model_from_pdb which loads all molecules from a given
model in the PDB (defaulting to the first) and which returns an array
of …
[View More]Hierarchy decorators each of which has a root of either a PROTEIN
or a MOLECULE (or some other name to specify a molecule that is not a
protein or nucleic acid).
Thoughts?
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- Some support for gather statistics has been added to
Model<file:///flute1/home/drussel/src/IMP/svn/debug/doc/html/classModel.html>(see
Model::set_gather_statistics()). If requested, an API can be provided
so that the individual data points can be returned to programs.
- A class RigidBodyDistancePairScore<file:///flute1/home/drussel/src/IMP/svn/debug/doc/html/classRigidBodyDistancePairScore.html>has
been added which provides accelerated computations for the distance
…
[View More]between two rigid bodies.
- The swig input files were renamed from swig.i to swig.i-in to aid in
dependency tracking.
- rigid bodies now have two sets of particles associated with them in the
various places they are used. One is the RigidBodyMember particles, as was
previously the case. The other is defined through a refiner (and could be
the RigidBodyMember if a
RigidMembersRefiner<file:///flute1/home/drussel/src/IMP/svn/debug/doc/html/classRigidMembersRefiner.html>is
used). The idea is that you sometimes want some particles which are
transformed along with the rigid body, but which are not really part of the
representation of the rigid body. Examples would include marker points or
multiresolution representations of proteins.The RigidMembersRefiner is
generally provided as a default, so the API doesn't change.
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