Scipion-em-prody

Substantial integration and improvements of everything:
1. Improved ensembles and alignments including custom chain matching
2. New ProDyNpzEnsemble object, making everything work more smoothly
3. General improvements including protocol summaries
4. Several new protocols including biomol assemblies, missing atom fixing, RMSD clustering and ClustENM

Whole new working pipelines with tests:
1. GNM analysis and dynamical domain decomposition
2. Ensemble analysis with PCA and projections

28 June 2022
New protocol and viewer for dynamical domain decomposition

New protocol and viewer for Gaussian network model (GNM) analysis

17 May 2022
New viewer for projecting ensembles onto modes

11 May 2022 - more releases with small improvements

13-18 April 2022 - first releases up to v3.0.3
Core pipeline working well with ProDy 2.1.1

8 April 2022
First protocols for ensemble building and principal component analysis
(PCA) added to devel

1 April 2022
Added tests for core pipeline

17 March 2022
Added animate and qualify modes features from continuousflex to new
modes base protocol and used it to add these to the mode editing protocol

25 February 2022
Added protocol for importing modes calculated outside the project.
Can support modes calculated in another Scipion project, ProDy itself,
or Gromacs.

21 February 2022
Added protocol for deformation vector analysis

18 February 2022
Added protocol for editing modes using slice, extend, reduce
and interpolate operations.

9 February 2022
Added protocol for mode comparison

3 February 2022
Added atomic structure manipulation protocols:
1. Selection
2. Superposition

18 January 2022
First working plugin with:
1. installation of ProDy from GitHub
2. protocol for anisotropic network model (ANM)
normal mode analysis (NMA)
3. viewer for normal modes from itself or continuousflex

22 December 2021
Started making scipion-em-prody from template