New Features:
- Membership, equality, and non-equality test operation are defined for all :mod:`~prody.atomic` classes. See :ref:`selection-operations`.
- Two functions are implemented for dealing with anisotropic temperature factors: :func:`.calcADPAxes` and :func:`.buildADPMatrix`.
- :meth:`.NMA.setEigens` and :meth:`.NMA.addEigenpair` methods are implemented to assist analysis of normal modes calculated using external software.
- :func:`.parseNMD` is implemented for parsing NMD files.
- :func:`.parseModes` is implemented for parsing normal mode data.
- :func:`.parseArray` is implementing for reading numeric data, particularly normal mode data calculated using other software for analysis using ProDy.
- The method in [BH02]_ to calculate overlap between covariance matrices is implemented as :func:`.calcCovOverlap` function.
- :func:`.trimEnsemble` to trim :class:`.Ensemble` instances is implemented.
- :func:`.checkUpdates` to check for ProDy updates is implemented.
Changes:
- Change in default behavior of :func:`.parsePDB` function. When alternate locations exist, those indicated by A are parsed. For parsing all alternate locations user needs to pass
altloc=Trueargument.- :func:`getSumOfWeights` is renamed as :func:`.calcSumOfWeights`.
- :func:`mapAtomsToChain` is renamed as :func:`.mapOntoChain`.
- :func:`ProDyStartLogFile` is renamed as :func:`.startLogfile`.
- :func:`ProDyCloseLogFile` is renamed as :func:`.closeLogfile`.
- :func:`ProDySetVerbosity` is renamed as :func:`.changeVerbosity`.
Improvements:
- A few bugs in ensemble and dynamics classes are fixed.
- Improvements in :class:`RCSB_PDBFetcher` allow it not to miss a PDB file if it exists in the target folder.
- :func:`.writeNMD` is fixed to output B-factors (Thanks to Dan Holloway for pointing it out).
Bug Fixes:
- An important fix in :func:`.sampleModes` function was made (Thanks to Alberto Perez for finding the bug and suggesting a solution).
Improvements:
- Improvements in :meth:`.ANM.calcModes`, :meth:`.GNM.calcModes`, and :meth:`.PCA.calcModes` methods prevent Numpy/Scipy throwing an exception when more than available modes are requested by the user.
- Improvements in :func:`.blastPDB` enable ProDy throw an exception when no internet connection is found, and warn user when downloads fail due to restriction in network regulations (Thanks to Serkan Apaydin for helping identify these improvements).
- New example :ref:`writepdb`.
Changes in dependencies:
- Scipy (linear algebra module) is not required package anymore. When available it replaces Numpy (linear algebra module) for greater flexibility and efficiency. A warning message is printed when Scipy is not found.
- Biopython KDTree module is not required for ENM calculations (specifically for building Hessian (ANM) or Kirchoff (GNM) matrices). When available it is used to increase the performance. A warning message is printed when KDTree is not found.
New Features:
- :class:`.AtomPointer` base class for classes pointing to atoms in an :class:`.AtomGroup`.
- :class:`.AtomPointer` instances (Selection, Residue, etc.) can be added. See :ref:`selection-operations` for examples.
- :meth:`.Select.getIndices` and :meth:`.Select.getBoolArray` methods to expand the usage of :class:`.Select`.
- :func:`.sliceVector` and :func:`.sliceMode` functions.
- :func:`.saveModel` and :func:`.loadModel` functions for saving and loading NMA data.
- :func:`.parsePDBStream` can now parse specific chains or alternate locations from a PDB file.
- :func:`.alignCoordsets` is implemented to superimpose coordinate sets of an :class:`.AtomGroup` instance.
Bug Fixes:
- A bug in :func:`.parsePDBStream` that caused unidentified errors when a model in a multiple model file did not have the same number of atoms is fixed.
Changes:
- Iterating over a :class:`.Chain` instance yields :class:`.Residue` instances.
- :class:`.Vector` instantiation requires an array only. name is an optional argument.
- Functions starting with
getand performing a calculations are renamed to start withcalc, e.g. :func:`getRMSD` is now :func:`.calcRMSD`.