highlights

Compared to the old trajectory infrastructure, the new one performs better in the following aspects

  • tracking virtual sites (pseudo atoms)
  • handling triclinic systems and orthorhombic systems whose primitive cell vectors do not align with the axes
  • unwrapping coordinates around periodic boundary condition (automatically or manually)

It is also made more robust and faster.

module changes

The following modules are deprecated 

schrodinger.trajectory
schrodinger.infra.desmond
schrodinger.application.desmond.destro
schrodinger.application.desmond.periodicfix
schrodinger.application.desmond.framesettools
schrodinger.application.desmond.generictrajectory

And the replacements are 

schrodinger.application.desmond.packages.topo
schrodinger.application.desmond.packages.traj
schrodinger.application.desmond.packages.traj_util
schrodinger.application.desmond.packages.analysis
schrodinger.application.desmond.packages.destro
schrodinger.application.desmond.packages.staf

  • topo: Cms object manipulation, GID tracking/conversion
  • traj and traj_util: definition of the new Frame object, trajectory read/write
  • analysis: definition of various trajectory analyzers (see below)
  • destro: the maeff class enables low-level mae file IO (try to avoid using it if you can, it bypasses all python-level and swig-level APIs)
  • staf: abstract base classes for trajectory analyzers

analyzers in the new trajectory infrastructure

  • basic geometric operations
    • Angle
    • Distance
    • PlanarAngle
    • Torsion
    • Vector
  • CenterOf
    • Centroid
    • CoC: center of charge
    • Com: center of mass
  • Dipole
  • Gyradius: radius of gyration
  • HydrogenBondFinder
  • MassAvgVel: mass-averaged velocity
  • MolecularSurfaceArea
  • MomentOfInertia
  • OrderParameter
    • the following analyzers are inputs to OrderParameter
      • AxisDirector
      • DipoleDirector
      • LipidDirector
        • sn1
        • sn2
        • all
      • MomentOfInertiaDirector
      • SmartsDirector
      • SystemDipoleDirector
  • PolarSurfaceArea
  • PosAlign: align positions
    • RMSD: Root mean square deviation
      • LigandRMSD: further includes symmetry consideration
    • RMSF: Root mean square fluctuation
      • ProteinRMSF
    • CovarianceMatrix
  • PosTrack: track positions of selected atoms in a trajectory
  • ProtLigInter: Protein-ligand interactions
    • HydrophobicInter, `_HydrophobicInter
    • MetalInter
    • ProtLigHbondInter
    • ProtLigPiInter
    • ProtLigPolarInter, _ProtLigPolarInter
    • WaterBridges
    • WatLigFragDistance, _WatLigFragDistance
  • ProtProtInter: Protein-protein interactions
    • ProtProtHbondInter
    • ProtProtPiInter
    • ProtProtSaltBridges
  • Rdf: Radial distribution function
  • Ramachandran
  • SecondaryStructure
  • SaltBridgeFinder
  • SolventAccessibleSurfaceArea
  • SolventAccessibleSurfaceAreaByResidue
  • VolumeMapper

In case you want to write customerized analyzer, I can share another document with you.