ProDy 0.5 Series

0.5.3 (Feb 11, 2011)

New Features:

• Membership, equality, and non-equality test operation are defined for all atomic classes. See Operations on Selections.
• Two functions are implemented for dealing with anisotropic temperature factors: calcADPAxes() and buildADPMatrix().
• NMA.setEigens() and NMA.addEigenpair() methods are implemented to assist analysis of normal modes calculated using external software.
• parseNMD() is implemented for parsing NMD files.
• parseModes() is implemented for parsing normal mode data.
• 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 calcCovOverlap() function.
• trimEnsemble() to trim Ensemble instances is implemented.
• checkUpdates() to check for ProDy updates is implemented.

Changes:

• Change in default behavior of parsePDB() function. When alternate locations exist, those indicated by A are parsed. For parsing all alternate locations user needs to pass altloc=True argument.
• getSumOfWeights() is renamed as calcSumOfWeights().
• mapAtomsToChain() is renamed as mapOntoChain().
• ProDyStartLogFile() is renamed as startLogfile().
• ProDyCloseLogFile() is renamed as closeLogfile().
• ProDySetVerbosity() is renamed as changeVerbosity().

Improvements:

• A few bugs in ensemble and dynamics classes are fixed.
• Improvements in RCSB_PDBFetcher allow it not to miss a PDB file if it exists in the target folder.
• writeNMD() is fixed to output B-factors (Thanks to Dan Holloway for pointing it out).

0.5.2 (Jan 12, 2011)

Bug Fixes:

• An important fix in sampleModes() function was made (Thanks to Alberto Perez for finding the bug and suggesting a solution).

Improvements:

• Improvements in ANM.calcModes(), GNM.calcModes(), and PCA.calcModes() methods prevent Numpy/Scipy throwing an exception when more than available modes are requested by the user.
• Improvements in 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 Write PDB file.

0.5.1 (Dec 31, 2010)

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.

0.5 (Dec 21, 2010)

New Features:

• AtomPointer base class for classes pointing to atoms in an AtomGroup.
• AtomPointer instances (Selection, Residue, etc.) can be added. See Operations on Selections for examples.
• Select.getIndices() and Select.getBoolArray() methods to expand the usage of Select.
• sliceVector() and sliceMode() functions.
• saveModel() and loadModel() functions for saving and loading NMA data.
• parsePDBStream() can now parse specific chains or alternate locations from a PDB file.
• alignCoordsets() is implemented to superimpose coordinate sets of an AtomGroup instance.

Bug Fixes:

• A bug in 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 Chain instance yields Residue instances.
• Vector instantiation requires an array only. name is an optional argument.
• Functions starting with get and performing a calculations are renamed to start with calc, e.g. getRMSD() is now calcRMSD().