PMI2 Transition Progress

Motivation for PMI2:

• Speed. The speedups are mainly possible by using more built-in tools from IMP like Selection and Representation (instead of PMI1's naming system for storing resolutions).
• Modularity. Separate the intimidating PMI1 representation class (which handles all system setup and movers, plus some restraints and constraints) into distinct classes like Topology and DegreesOfFreedom. We also want these classes to produce native IMP hierarchies instead of PMI objects (though we use PMI objects like Molecule for shorter scripts).
• Ease of use. We would like the user to have to write less code that looks better!

Tasks:

• System setup with Topology, DegreesOfFreedom
• Support for IMP.atom.DENSITIES
• Support for ideal helices
• Create nuisance movers from xl restraints (dof.get_nuisances_from_restraint())
• Macro to create PMI2 System: macros.BuildSystem()
• Sampling
• PDB, PSF, and RMF writing
• Replica Exchange Macro (including MC and MD)
• Optimize flexible beads (now in DOF)
• Resume from RMF files - added to tools.set_coordinates_from_rmf()
• Incorporate coloring system for RMFs (add color=? option to molecule.add_representation()) (now works, but still need it to add to BuildSystem macro and TopologyReader. Can't add column without breaking the tutorial though.)
• Stat file parsing (report avg MC acceptance; plot stuff; ...?) (stat files all work great!)
• Convergence test
• Make restraints compatible with PMI2.
• Basic
• Crosslinking
• EM
• EM2D
• Stereochemistry
  • Connectivity
  • Excluded volume
  • Elastic nets
  • Charmm
  • Symmetry
  • Coarse grain backbone restraints: ResidueAngleRestraint,ResidueBondRestraint,ResidueDihedralRestraint, PseudoAtomicRestraint
• Support full analysis pipeline with AnalysisReplicaExchange0
• Clustering
• Model densities
• Precision/RMSF
• accuracy
• XLTable and other plotting tools
• Examples
• multiscale
• atomistic
• crosslink ambiguity
• ideal helices
• coloring system (well, it's in multiscale)
• EM restraint with Gaussian representation
• picking molecules/selection. show the many ways this is possible.
• symmetry
• automatic model building with BuildSystem macro
• analysis: clustering, precision, densities
• Applications
• Re-write imp tutorial (rnapolii)
• Literally every other PMI application
• Reorganization
• Create Restraint base class
• Move DegreesOfFreedom to IMP.pmi.topology module
• Move output into IMP.pmi.io
• Remove macros and incorporate them into individual modules:
  • BuildSystem into IMP.pmi.topology
  • ReplicaExchange into IMP.pmi.Samplers