Bugfixes:
- Fixed a problem in :func:`.calcPhi` function that raised a name error.
- Fixed a problem in :meth:`.KDTree.getDistances` method that raised a name error when unitcell is provided.
- Fixed a problem in :func:`.buildDistMatrix` and :func:`.calcDistance` functions causing miscalculations when unitcell is given.
- Revised :class:`.KDTree` methods dealing with to handle special cases where unitcell might have some dimensions zero.
Changes:
- :func:`.buildKDTree` method is removed, earlier than planned due to unexpected bugfix releases.
Bugfixes:
- Fixed :mod:`~prody.kdtree` import problem.
New Features:
- :func:`.buildDistMatrix` function that can take periodic boundary conditions is implemented.
Improvements:
- :func:`.calcDistance` function is improved to take periodic boundary conditions into account when provided by the users.
New Features:
- Methods to deal with connected subsets of atoms are implemented, see :meth:`.AtomGroup.iterFragments` and :meth:`.AtomGroup.numFragments`.
- :func:`.pickCentral` method is implemented for picking the atom that is closest to the centroid of a group or subset of atoms.
- ProDy configuration option auto_secondary is implemented to allow for parsing and assigning secondary structure information from PDB file header data automatically. See :func:`.assignSecstr` and :func:`.confProDy` for usage details.
- :program:`prody align` makes use of select when aligning multiple structures. See usage examples: :ref:`prody-align`
- :func:`.printRMSD` function that prints minimum, maximum, and mean RMSD values when comparing multiple coordinate sets is implemented.
- :func:`.findFragments` function that identifies fragments in atom subsets, e.g. :class:`.Selection`, is implemented.
- A new :class:`.KDTree` interface with coherent method names and capability to handle periodic boundary conditions is implemented.
Improvements:
- Performance improvements made in :func:`.saveAtoms` and :func:`.loadAtoms`.
- :func:`.sliceMode`, :func:`.sliceModel`, :func:`.sliceVector`, and :func:`.reduceModel` functions accept :class:`.Selection` instances as well as selection strings. In repeated use of this function, if selections are already made out of the function, considerable speed-ups are achieved when selection is passed instead of selection string.
- Fragment iteration (:meth:`.AtomGroup.iterFragments`) is improved to yield items faster.
Changes:
- There is a change in the behavior of addition operation on instances of :class:`.AtomGroup`. When operands do not have same number of coordinate sets, the result will have one coordinate set that is concatenation of the active coordinate sets of operands.
- :func:`.buildKDTree` function is deprecated for removal, use the new :class:`.KDTree` class instead.
Bugfixes:
- A problem in building hierarchical views when making selections using resindex, chindex, and segindex keywords is fixed.
- A problem in :class:`.Chain` and :class:`.Residue` selection strings that would emerge when a :class:`.HierView` is build using a selection is fixed.
- A problem with copying :class:`.AtomGroup` instances whose coordinates are not set is fixed.
- :class:`.AtomGroup` fragment detection algorithm is rewritten to avoid the problem of reaching maximum recursion depth for large molecules with the old recursive algorithm.
- A problem with picking central atom of :class:`.AtomGroup` instances in :func:`.pickCentral` function is fixed.
- A problem in :class:`.Select` class that caused exceptions when evaluating complex macro definitions is fixed.
- Fixed a problem in handling multiple trajectory files. The problem would emerge when a file was added (:meth:`~.Trajectory.addFile`) to a :class:`.Trajectory` after atoms were set (:meth:`~.Trajectory.setAtoms`). Newly added file would not be associated with the atoms and coordinates parsed from this file would not be set for the :class:`.AtomGroup` instance.
New Features:
- ProDy can be configured to automatically check for updates on a regular basis, see :func:`.checkUpdates` and :func:`.confProDy` functions for details.
- :func:`.alignPDBEnsemble` function is implemented to align PDB files using transformations calculated in ensemble analysis. See usage example in :ref:`pca-blast` example.
- :meth:`.PDBConformation.getTransformation` is implemented to return the transformation that was used to superpose conformation onto reference coordinates. This transformation can be used to superpose the original PDB file onto the reference PDB file.
- Amino acid sequences with regular expressions can be used to make atom selections, e.g.
'sequence "C..C"'. See :ref:`selections` for usage details.- :func:`.calcCrossProjection` function is implemented.
Improvements:
- :class:`.Select` class raises a :class:`.SelectionError` when potential typos are detected in a selection string, e.g.
'chain AB'is a grammatically correct selection string that will return None since no atoms have chain identifier'AB'. In such cases, an exception noting that values exceed maximum number of characters is raised.- :program:`prody align` command accepts percent sequence identity and overlap parameters used when matching chains from given multiple structures.
- When using :program:`prody align` command to align multiple structure, all models in NMR structures are aligned onto the reference structure.
- :program:`prody catdcd` command accepts
--align SELSTRargument that can be used to align frames when concatenating files.- :func:`.showProjection` and :func:`.showCrossProjection` functions are improved to evaluate list of markers, color, labels, and texts. See usage example in :ref:`pca-xray-plotting`.
- :class:`.Trajectory` instances can be used for calculating and plotting projections using :func:`.calcProjection`, :func:`.showProjection`, :func:`.calcCrossProjection`, and :func:`.showCrossProjection` functions.
Changes:
- Phosphorylated amino acids, phosphothreonine (TPO), O-phosphotyrosine (PTR), and phosphoserine (SEP), are recognized as acidic protein residues. This prevents having breaks in protein chains which contains phosphorylated residues. See :ref:`selections` for definitions of protein and acidic keywords.
- Hit dictionaries from :class:`.PDBBlastRecord` will use percent_overlap instead of percent_coverage. Older key will be removed in v1.1.
- :meth:`.Transformation.get4x4Matrix` method is deprecated for removal in v1.1, use :meth:`.Transformation.getMatrix` method instead.
Bugfixes:
- A bug in some :ref:`prody-apps` is fixed. The bug would emerge when invalid arguments were passed to effected commands and throw an unrelated exception hiding the error message related to the arguments.
- A bug in
'bonded to ...'is fixed that emerged when'...'selected nothing.- A bug in
'not'selections using.operator is fixed.
Improvements:
- :meth:`.ANM.buildHessian` method is not using a KDTree by default, since with some code optimization the version not using KDTree is running faster. Same optimization has gone into :meth:`.GNM.buildKirchhoff` too, but for Kirchoff matrix, version using KDTree is faster and is the default. Both methods have kdtree argument to choose whether to use it or not.
- :program:`prody` script is updated. Importing Prody and Numpy libraries are avoided. Script responses to help queries faster. See :ref:`prody-apps` for script usage details.
- Added
bonded to ...selection method that expands a selection to immediately bound atoms. See :ref:`selections` for its description.- :func:`.fetchPDBLigand` parses bond data from the XML file.
- :func:`.fetchPDBLigand` can optionally save compressed XML files into ProDy package folder so that frequent access to same files will be more rapid. See :func:`.confProDy` function for setting this option.
- :class:`.Select` class is revised. All exceptions are handled delicately to increase the stability of the class.
- Distance based atom selection is 10 to 15% faster for atom groups with more than 5K atoms.
- Added uncompressed file saving option to :ref:`prody-blast` command.
Changes:
- All deprecated method and functions scheduled for removal are removed.
- :meth:`~.Mode.getEigenvector` and :meth:`~.Mode.getEigenvalue` methods are deprecated for removal in v1.1, use :meth:`.Mode.getEigvec` and :meth:`.Mode.getEigval` instead.
- :meth:`~.NMA.getEigenvectors` and :meth:`~.NMA.getEigenvalues` methods are deprecated for removal in v1.1, use :meth:`.NMA.getEigvecs` and :meth:`.NMA.getEigvals` instead.
- :meth:`.Mode.getCovariance` and :meth:`.ModeSet.getCovariance` methods are deprecated for removal in v1.1, use :func:`.calcCovariance` method instead.
- :meth:`Mode.getCollectivity` method is removed, use :func:`.calcCollectivity` function instead.
- :meth:`Mode.getFractOfVariance` method is removed, use the new :func:`.calcFractVariance` function instead.
- :meth:`Mode.getSqFlucts` method is removed, use :func:`.calcSqFlucts` function instead.
- Renamed :func:`showFractOfVar` function as :func:`.showFractVars` function instead.
- Removed :func:`calcCumOverlapArray`, use :func:`.calcCumulOverlap` with
array=Trueargument instead.- Renamed :func:`extrapolateModel` as :func:`.extendModel`.
- The relation between :class:`.AtomGroup`, :class:`.Trajectory`, and :class:`.Frame` instances have changed. See :ref:`trajectory2` and :ref:`outputtraj`, and :ref:`frame` usage examples.
- :class:`.AtomGroup` cannot be deformed by direct addition with a vector instance.
- Unmapped atoms in :class:`.AtomMap` instances are called dummies. :meth:`.AtomMap.numUnmapped` method, for example, is renamed as :meth:`.AtomMap.numDummies`.
- :func:`.fetchPDBLigand` accepts only filename (instead of save and folder) argument to save an XML file.
Bugfixes:
- A problem in distance based atom selection which would could cause problems when a distance based selection is made from a selection is fixed.
- Changed :ref:`prody-blast` so that when a path for downloading files are given files are not save to local PDB folder.