v2.5.0rc0

v2.5.0 release candidate 0 without copying and manifest.in inclusion of pre-compiled hpb.so

These changes are not merged yet as their impact isn’t fully tested but there is a release candidate 1 at https://github.com/jamesmkrieger/ProDy/releases/tag/v2.5rc1 that includes them to compare

v2.4.1

2.4.1 (Aug 11, 2023)

New Features:

• New function writeBILD to write modes in BILD format for viewing in Chimera/ChimeraX
• New function addMissingAtoms based on PDBFixer or OpenBabel
• Added Seaborn kernel density estimator (KDE) options to showProjection like Kaynak et al., 2022
• Added options to control adjust_text for showProjection
• Added unite_chains option to parseMMCIF to handle splitting over segments
• New function interpolateModel based on SITUS ModeHunter
• New ClustENM app
• New module for analysing water bridges (only for Python 3)
• New option nproc as a number of processors limit for solveEig, ANM, GNM and PCA calcModes

Bug Fixes and Improvements:

• Fixed Trajectory next frame overwriting with atoms linked
• Important fixes to alignBioPairwise
• Update to blastpdb to account for changes to on the NCBI side
• Improvements to apps including writing matrices
• Improved handling of mmCIF files including those from PDB-REDO

Full Changelog: v2.4.0...v2.4.1

v2.4.0

New Features:

• New function alignBioPairwise to address Biopython deprecation
• Added gromos rmsd clustering
• New data_type option for refineEnsemble to use seqid instead of rmsd
• New ignore_ids option for mergeMSA to use different ids for interacting proteins

Bug Fixes and Improvements:

• Fixed error during writeout PQR file
• Proper handling of fragments when bonds are absent
• Setting the atoms for ensemble even if the atoms is a subset
• Allowing setFlags to take scalar values
• Transpose princ axes matrix to get columns
• New flag selpdbter to keep ter lines in selections
• No sorting of strands in writing
• Add cif datafiles to setup
• Select app help fix
• Fixes to mmcif parsing
• Improvements to cutoffs in Dali filtering
• Fix to protein definition
• Set matrix interactive to false and fix to axes3d usage for matplotlib 3.6
• Improved requirements
• Fix to fetchPDB for files with two dots but not gz ending

New Contributors:

• @changephilip made their first contribution in #1618
• @odcambc made their first contribution in #1634
• @hrnciar made their first contribution in #1372

Full Changelog: v2.3.1...v2.4.0

v2.3.1

2.3.1 (Nov 15, 2022)

Bug Fixes and Improvements:

• use of 4-char hybrid36 (residue version) for biomol segnames
• remove pfam tests
• remove python 3.5 support

Full Changelog: v2.3.0...v2.3.1

v2.3.0

2.3.0 (Nov 12, 2022)

New Features:

• new Gamma function class from GOdMD
• added prody energy app based on ClustENM

Bug Fixes and Improvements:

• restored matrix option to dfi and dci
• pfam migrated to pfam-legacy
• fix to apps for broken imp.find_module
• various other fixes including to mmCIF parsing and alignments

Full Changelog: v2.2.0...v2.3.0

v2.2.0

2.2.0 (May 19, 2022)

Bug Fixes and Improvements:

• Updates to :function:`.parseScipionModes`` to use sqlite and xmd metadata files
  and handle eigenvalues

• Actual fix to logging so LOGGER.progress doesn't override logging level

• Updates to the PCA app to better handle number of modes for Scipion

• New arguments sparse, kdtree and turbo for :class:.ClustENM, allowing
  better control of ANM calculations.

• Another bug fix for mmCIF header parsing

• Bug fix for parsing CONECT bond records from PDB files

Full Changelog: v2.1.2...v2.2.0

v2.1.2

What's Changed

• New :function:.showRMSFlucts and :function:.calcRMSFlucts for root-mean-square fluctuations
• fix to :function:.showAtomicLines for overlaying multiple chains

Full Changelog: v2.1.1...v2.1.2

v2.1.1

2.1.1 (April 18, 2022)

Bug Fixes and Improvements:

• :function:.parseScipionModes can handle having a pdb file or not

• fix to mmCIF header parsing for chemicals in blocks not loops

v2.1.0

2.1.0 (April 8, 2022)

New Features:

Integration with Scipion

• New functions :function:.parseScipionModes, :function:.writeScipionModes
  and :function:.calcScipionScore

• New argument --export-scipion (-S) in prody apps

Other

• Added :function:.assignBlocks for assigning blocks for RTB

• Added mmCIF header parsing to create the same header dictionary as PDB header,
  including secstr information and biomolecular assembly building

• New arguments for prody apps, including altloc, zeros, sparse, kdtree and turbo

Bug Fixes and Improvements:

• Improvement to cealign mapping to be faster for protein only alignment

• Bug fix for writing psf files

Full Changelog: v2.0.2...v2.1.0

v2.0.2

2.0.2 (February 17, 2022)

New Features:

• Added :function:.realignModes for comparing sets of modes calculated on unaligned
  structures

• New option by_time in :function:.showProjection, allowing projections onto 1 PC
  and the frames sampled over the time course of a simulation or the conformers in an ensemble.

• Updates to ClustENM(D) to use latest and more efficient OpenMM version, 7.6

• New :function:.parseGromacsModes for parsing NMA and PCA modes calculated in Gromacs,
  allowing the use of all-atom force fields and more efficient handling of large trajectories

Bug Fixes and Improvements:

• Bug fixes to searchPfam and fetchPfamMSA, which no longer worked due to some security change.

• Bug fix to Ensembles and Conformations for weights being indexed twice

• Bug fix to --quiet option of apps that fixes the VMD ProDy interface

• General documentation and error improvements