Prody

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**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**: https://github.com/prody/ProDy/compare/v2.4.0...v2.4.1

**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 https://github.com/prody/ProDy/pull/1618
* odcambc made their first contribution in https://github.com/prody/ProDy/pull/1634
* hrnciar made their first contribution in https://github.com/prody/ProDy/pull/1372

**Full Changelog**: https://github.com/prody/ProDy/compare/v2.3.1...v2.4.0

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**Bug Fixes and Improvements**:

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


**Full Changelog**: https://github.com/prody/ProDy/compare/v2.3.0...v2.3.1

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**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**: https://github.com/prody/ProDy/compare/v2.2.0...v2.3.0

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**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**: https://github.com/prody/ProDy/compare/v2.1.2...v2.2.0

What's Changed
* New :function:`.showRMSFlucts` and :function:`.calcRMSFlucts` for root-mean-square fluctuations
* fix to :function:`.showAtomicLines` for overlaying multiple chains

**Full Changelog**: https://github.com/prody/ProDy/compare/v2.1.1...v2.1.2