ProDy 1.0 Series

1.0.4 (May 2, 2012)

Bugfixes:

  • Fixed a problem in calcPhi() function that raised a name error.
  • Fixed a problem in KDTree.getDistances() method that raised a name error when unitcell is provided.
  • Fixed a problem in buildDistMatrix() and calcDistance() functions causing miscalculations when unitcell is given.
  • Revised KDTree methods dealing with to handle special cases where unitcell might have some dimensions zero.

Changes:

  • buildKDTree() method is removed, earlier than planned due to unexpected bugfix releases.

1.0.3 (May 1, 2012)

Bugfixes:

  • Fixed kdtree import problem.

New Features:

  • buildDistMatrix() function that can take periodic boundary conditions is implemented.

Improvements:

  • calcDistance() function is improved to take periodic boundary conditions into account when provided by the users.

1.0.2 (May 1, 2012)

New Features:

  • Methods to deal with connected subsets of atoms are implemented, see AtomGroup.iterFragments() and AtomGroup.numFragments().
  • 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 assignSecstr() and confProDy() for usage details.
  • prody align makes use of --select when aligning multiple structures. See usage examples: prody align
  • printRMSD() function that prints minimum, maximum, and mean RMSD values when comparing multiple coordinate sets is implemented.
  • findFragments() function that identifies fragments in atom subsets, e.g. Selection, is implemented.
  • A new KDTree interface with coherent method names and capability to handle periodic boundary conditions is implemented.

Improvements:

Changes:

  • There is a change in the behavior of addition operation on instances of 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.
  • buildKDTree() function is deprecated for removal, use the new KDTree class instead.

Bugfixes:

  • A problem in building hierarchical views when making selections using resindex, chindex, and segindex keywords is fixed.
  • A problem in Chain and Residue selection strings that would emerge when a HierView is build using a selection is fixed.
  • A problem with copying AtomGroup instances whose coordinates are not set is fixed.
  • 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 AtomGroup instances in pickCentral() function is fixed.
  • A problem in 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 (addFile()) to a Trajectory after atoms were set (setAtoms()). Newly added file would not be associated with the atoms and coordinates parsed from this file would not be set for the AtomGroup instance.

1.0.1 (Apr 6, 2012)

New Features:

  • ProDy can be configured to automatically check for updates on a regular basis, see checkUpdates() and confProDy() functions for details.
  • alignPDBEnsemble() function is implemented to align PDB files using transformations calculated in ensemble analysis. See usage example in Homologous Proteins example.
  • 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 Atom Selections for usage details.
  • calcCrossProjection() function is implemented.

Improvements:

  • Select class raises a 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.
  • prody align command accepts percent sequence identity and overlap parameters used when matching chains from given multiple structures.
  • When using prody align command to align multiple structure, all models in NMR structures are aligned onto the reference structure.
  • prody catdcd command accepts --align SELSTR argument that can be used to align frames when concatenating files.
  • showProjection() and showCrossProjection() functions are improved to evaluate list of markers, color, labels, and texts. See usage example in Plotting.
  • Trajectory instances can be used for calculating and plotting projections using calcProjection(), showProjection(), calcCrossProjection(), and 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 Atom Selections for definitions of protein and acidic keywords.
  • Hit dictionaries from PDBBlastRecord will use percent_overlap instead of percent_coverage. Older key will be removed in v1.1.
  • Transformation.get4x4Matrix() method is deprecated for removal in v1.1, use Transformation.getMatrix() method instead.

Bugfixes:

  • A bug in some ProDy Applications 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.

1.0 (Mar 7, 2012)

Improvements:

  • 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 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.
  • prody script is updated. Importing Prody and Numpy libraries are avoided. Script responses to help queries faster. See ProDy Applications for script usage details.
  • Added bonded to ... selection method that expands a selection to immediately bound atoms. See Atom Selections for its description.
  • fetchPDBLigand() parses bond data from the XML file.
  • fetchPDBLigand() can optionally save compressed XML files into ProDy package folder so that frequent access to same files will be more rapid. See confProDy() function for setting this option.
  • 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 prody blast command.

Changes:

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 prody blast so that when a path for downloading files are given files are not save to local PDB folder.