Prody

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**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

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**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**: https://github.com/prody/ProDy/compare/v2.0.2...v2.1.0

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**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

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**New Features**:

* Added :function:`.calcRWSIP` for comparing sets of modes

* New methods to convert :class:`.Atom`, :class:`.Atomic` and :class:`.EMDMAP`
to TEMPy objects, allowing calculations such as cross-correlation coefficient (CCC)
to EM maps.

* Added :func:`.calcDynamicFlexibilityIndex` and :func:`.calcDynamicCouplingIndex`
for further interpretation of PRS results.

* Reinstated the option of using forces in PRS as in ProDy v1.8 (`turbo=**False**`)

* Added GitHub Actions Continuous Integration in place of Travis.

**Bug Fixes and Improvements**:

* Compatibility and bug fixes for various functions, including pyparsing for selections.

* Extended :class:`.AdaptiveANM` to work with other models including explicit membrane
ANM, :class:`.exANM`.

* Improved capabilities for fetching and parsing mmCIF and EMD files.

* Improved handling of residue and serial numbers including hexadecimal and hybrid36 formats.

* Consistency fixes.

* More non-standard amino acids (MEN, CSB, CME).

**Full Changelog**: https://github.com/prody/ProDy/compare/v2.0...v2.0.1

Major version released to PyPI on Feb 7th, 2021.