New Features:
- :func:`.iterFragments` function is added.
- :func:`.findNeighbors` function is added.
- :func:`.calcMSF` and :func:`.calcRMSF` functions are added.
- :func:`.wrapAtoms` functions is added.
- :func:`.extendMode` and :func:`.extendVector` functions are added.
- :ref:`prody-contacts` command is added.
Improvements:
- :func:`.moveAtoms` function is improved to move atoms to a specified location.
- :class:`.DCDFile` and :func:`.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 :ref:`prody-anm`, :ref:`prody-gnm`, and :ref:`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 :func:`.showOverlapTable` is normalized by default.
- :mod:`.tools` module is depracated for removal, use :mod:`.utilities` instead.
- array argument in :func:`.moveAtoms` is replaced with by keyword argument.
- which argument in :meth:`.AtomGroup.copy` method is deprecated for removal in version 1.2.
- :class:`.DCDFile` does not log information for most common type of DCD file, i.e. 32-bit CHARMM format.
- :meth:`.Trajectory.getNextIndex` method is deprecated for removal in v1.2, use :meth:`~.Trajectory.nextIndex` instead.
Bugfixes:
- Fixed several problems in :func:`.iterNeighbors` function and :class:`.Contacts` class that were introduced after transition to new :class:`.KDTree` interface.
- Fixed a problem in setting selection strings of fragments identified using :func:`.findFragments`.
- Fixed a problem in :func:`.calcCenter` related to weighted center calculation.
- Fixed a problem of in copying :class:`.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.
Improvements:
- Mode scaling options are improved.
- Options added for extending coarse grained NMA models to residue backbone or all atoms.