ProDy 1.1 Series

1.1 (June 1, 2012)

New Features:

• iterFragments() function is added.
• findNeighbors() function is added.
• calcMSF() and calcRMSF() functions are added.
• wrapAtoms() functions is added.
• extendMode() and extendVector() functions are added.
• prody contacts command is added.

Improvements:

• moveAtoms() function is improved to move atoms to a specified location.
• DCDFile and parseDCD() take astype keyword argument for automatic type recasting for coordinate arrays. This option can be used to convert 32-bit coordinate arrays to 64-bit automatically for higher precision calculations.
• Commands prody anm, prody gnm, and prody pca can extend a coarse grained model to backbone or all atoms of the residues. See their documentation pages.

Changes:

• Color scale used by showOverlapTable() is normalized by default.
• tools module is deprecated for removal, use utilities instead.
• array argument in moveAtoms() is replaced with by keyword argument.
• which argument in AtomGroup.copy() method is deprecated for removal in version 1.2.
• DCDFile does not log information for most common type of DCD file, i.e. 32-bit CHARMM format.
• Trajectory.getNextIndex() method is deprecated for removal in v1.2, use nextIndex() instead.

Bugfixes:

• Fixed several problems in iterNeighbors() function and Contacts class that were introduced after transition to new KDTree interface.
• Fixed a problem in setting selection strings of fragments identified using findFragments().
• Fixed a problem in calcCenter() related to weighted center calculation.
• Fixed a problem of in copying AtomMap instances, which would emerge when bond information was present in unusual mappings, such as when atom orders are changed or an atom is present multiple times in the mapping.

Normal Mode Wizard

Improvements:

• Mode scaling options are improved.
• Options added for extending coarse grained NMA models to residue backbone or all atoms.