Tyler Reddy edited this page May 5, 2015 · 2 revisions

Major Changes

  • Amber support (PRMTOP topology file reader and TRJ trajectory file reader...netcdf4 format NOT yet included)
  • PQR file reading support (Issue 54)


  • new analysis.contacts.ContactAnalysis1 class that supports a native contact analysis between arbitrary groups
  • new analysis.density module for the creation and analysis of volume data (uses the GridDataFormats package)
  • new examples (e.g. peptide helix clustering in a membrane)
  • fixed Issue 58 (align.rms_fit_trj; fix reported by Joshua Adelman)
  • fast RMSD aligner based on Douglas Theobald's QCP method for calculating the minimum RMSD between two structures and determining the optimal least-squares rotation matrix; replaces the slower previous code (implemented by Joshua Adelman from his pyqcprot package)
  • deprecated core.rms_fitting.rms_rotation_matrix() and scheduled for removal in 0.8 (the QCP rotationmatrix calculation is much faster)
  • uses cython instead of pyrex


denniej0, orbeckst, jandom,, Joshua Adelman

Project Information

GNU GPL v2 code license
Labels: python, molecular dynamics, analysis, DCD, CHARMM, LAMMPS, NAMD, Gromacs, computer simulation, atoms, coordinates, trajectory, XTC, Library, object-oriented
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