Ben Webb
Ben Webb
`IMP::atom::get_volume_from_residue_type` currently returns no useful value for RNA or DNA. This causes a warning when using PMI to build models containing nucleic acids. We should add appropriate volumes.
It would be useful to add a two-way interface to [NAMD](https://www.ks.uiuc.edu/Research/namd/) so that 1. IMP `ScoringFunction`s can be added to the NAMD forcefield so that we can use NAMD's integrator....
e.g. CHARMM sterochemistry, anything that uses a list of pairs/triples of particles should all be trivially parallelizable with OpenMP.
Release builds still include a lot of `USAGE` checks in performance-critical parts of the code that make the builds substantially slower than fast builds (with no checks at all). Many...
`IMP::cgal` makes use of CGAL functionality from `CGAL/Convex_hull_d.h` and `CGAL/Regular_complex_d.h`. This functionality is deprecated in newer versions of CGAL. Use the [Triangulation package](http://doc.cgal.org/latest/Triangulation) instead.
IMP currently takes as input files in a variety of formats, but doesn't care where those files originate. This becomes a problem when we come to publish a modeling study...
`IMP.pmi` currently supports mmCIF output, but it is strongly tied to PMI1's representation. We would also like to be able to output files in mmCIF format using PMI2, or even...
RMF trajectories are slow to read in Chimera, and RMF support is unlikely to be added to ChimeraX unless we really really push for it. We can't reasonably use mmCIF...
`core::TransformationSymmetry` and `core::TransformationAndReflectionSymmetry` make sure that a particle P' is kept with its coordinates derived from a reference particle P (by transformation and optionally also reflection). However, any forces on...
CMake provides a macro `generate_export_header` that generates a header file with the necessary `#define`s to export symbols. See, for example, salilab/mdt@e329212ce36c. May make sense to use that rather than our...