Major Changes

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

Changes

• 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

Authors

denniej0, orbeckst, jandom, tyler.je.reddy, Joshua Adelman