Rna-tools

Fixed:

rna_tools_lib.py (RNAStructure) for remove_hydrogen, correct atom name position now
rna_pdb_tools.py --get-seq works with protein fix 104
spotifer.py - fix alignments, and lots of other improvements

Added:

rna_pdb_tools.py:
- add --fetch-chain to first fetch a structure and extract chain in one step

mqapRNA: py3 wrappers and include them in RT
- RASP
- Dfire
- RNA3DCNN
- QRNA
- FARNA
- AnalyzeGeometry and ClashScore (add rna_clashscore.py app)
- eSCORE (barnaba)
- 3dRNAscore
- RNAkb (!!!!)
- libs

mq: add mq to RNAStructure and a simple Jupyter notebook to test it

rna_tools_lib.py (RNAStructure):
- add .name attribute with filename (only filename, e.g. "1XJR.pdb")
- --bases-only and --no-backbone

rna_tools_lib.py: add load_rnas to load structural files (via glob)

rna_calc_rmsd_all_vs_all.py: add rmsd calc based on pymol
Add PyMOL plugin to do that in pymol: PyMOL4RNA.py: rmsdx (get all vs all rmsd matrix)

plotting: add rna_plot_heatmap.py

simrna_trajectory: calc rmsd to another frame

Changed:

rna_tools_lib.py (RNAStructure) when rpr loads structure with biopython the error is not suppressed

Fixed:

rna_secondary_structure_prediction.py: fixes

Added:

PyMOL4RNA.py: mutate, rpr, diff, move rnapuzzle coloring code to own file

Fixed:

rna_pdb_tools.py: --rpr fix correct resi for remarks
rna_pdb_tools.py: --rpr with --keep-hetatm ! [fixed issue with 71]

Added:

rna_pdb_tools.py: --set-chain, set chain for all ATOM lines and TER (quite brutal function)
rna_pdb_tools.py: add --triple-mode,--column-name
rna_pdb_tools.py: add --backbone-only
rna_pdb_tools.py: --rpr no also fixes missing OP1 and OP2 in backbone
rna_pdb_tools.py: refactor, path code executed once
rna_pdb_tools.py: add --inspect

rna_tools_lib.py (RNAStructure) - add get_res_text() & get_remarks_text()
rna_tools_lib.py (RNAStructure) - add reload()
rna_tools_lib.py (RNAStructure) - change write() now saves by default to self.fn

rna_calc_rmsd_biopython.py: --triple-mode works (final test!) 201118
rna_calc_rmsd_biopython.py: introduce way to save models after rmsd calc
rna_calc_rmsd_biopython.py: add --triple-mode,--column-name

PyMOL4RNA: add inspect function for rna_pdb_tools.py: --inspect

Bug fixes and small improvements.

https://github.com/mmagnus/rna-tools/issues/71

- add digitifier.py
- rna_clanstix.py: deal with colors using shapes (type)
- spotifier.py:
- clean spotifier.py, -m -> <map>
- spotifier.py: add logging, process reporters plates, add dont-anntate

- spotifier.py:
- deal better with fonts
- add to setup.py spotifier program

- spotifier.py:
- "--map" should be required=True
- trim -> dont-align, works on PSD, clean