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Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

See https://github.com/mmagnus/rna-tools/releases for more details for 3.7.x

3.7

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

3.6.2

Fixed:

    rna_secondary_structure_prediction.py: fixes

Added:

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

3.6 201122

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.

#71

3.5.4 200710

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

3.5.3 200703

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

3.5.2 200702

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

3.5.1 200629

  • Fix scrutinizer and small fixes

3.5 200629

  • rna_calc_inf.py:

    • --renumber-residues
    • clean sel pdb files, and --dont-remove-sel-files
    • force to run ClaRNA even if .outCR file is there, for will be auto True when selection defined
    • rna_calc_inf.py: up readme
    • rna_calc_inf.py: with model_selection and target_selection
    • Fix problems with rna_calc_inf.py, re-write tests, add docs

  • rna_pdb_tools.py:

    • add --no-progress-bar
    • add --color-seq
    • add --rpr for --mutate

  • diffpdb.py: fix --names-and-resi

Update update_readme.py and update readme (Used in papers)

Bug fixes and small improvements.

3.4 200626

200626

3.2

  • 200330 read the docs py3 now https://readthedocs.org/projects/rna-tools/builds/

  • 190821

    • Add rna_alignment/rna_align_foldability.py
    • Seq.py now you can set .name
    • Seq.py mc-fold:
      • Add: explore option
      • Change: verbose now also shows full output of the program
      • Add: comment field for some extra information from the program

  • 190820 Add: rna_align_distance_to_seq.py

  • 190815 Add: Seq.py: load_fasta_ss_into_RNAseqs()

  • 190813 Add: copied and edited from rna_pdb_merge_into_one.py to:

    rna_pdb_tools.py --nmr-dir . 'cwc15_u5_fragments*.pdb' > ~/Desktop/cwc15-u5.pdb

  • 190810 Add: ENTRNA wrapper for foldability

Added

  • rna_dot2ct.py
  • rna_pdb_tools.py --swap-chains SWAP_CHAINS [190530]
  • Clanstix: with smart group name picking [190500]
  • rna_pdb_tools.py --split-alt-locations
  • rna_pdb_tools.py --delete-anisou
  • copied and edited from rna_pdb_merge_into_one.py to rna_pdb_tools.py --nmr-dir . 'cwc15_u5_fragments*.pdb' > ~/Desktop/cwc15-u5.pdb [190813 ]

Changed

  • Rename rna_ss_pred.py to rna_secondary_structure_prediction.py
  • Changed all underscores into dashes in arguments, .e.g --get_seq to --get-seq #94 [190529]
  • PyMOL4RNA: scale down shapes for inorganic, to 0.25

Fixed

  • Clanstix problem with group and coloring bug #91

History

170814 Python3 everywhere (at least it should be)

170608 Add --get_ss (secondary structure) using x3dna.

170518 Edit in place [experimental, only for get_rnapuzzle_ready] rna_pdb_tools.py --rpr 7_Das_7_rpr.pdb --inplace. (2) get a structure in org-mode format <sick!>

170517 Fix #37 mis-align atom names after rpr-ing bug

170515 Fix fixing missing O2'

170404 rna_simrna_extract.py -t template.pdb -f *05.trafl -c -n 1 # extract only the first model

170331 rna-pdb-tools meets Emacs!

170325 Seq: secondary structure prediction with constraints

>>> seq = Seq("CCCCUUUUGGGG")
>>> seq.name = 'RNA03'
>>> print(seq.predict_ss("RNAfold", constraints="((((....))))"))
>RNA03
CCCCUUUUGGGG
((((....)))) ( -6.40)

170324 Starting converting to Python3, fetch_align by Pietro

170320 rna_cartoon in PyMOL

170319 Add clanstix (move it from its own GitHub repository).

170315 SimRNA_trajectory:

  • get len of frame, and trajectory
  • warn about broken frame
  • only_first_frame to get only the first frame

170311 Get seq (v2) gets segments of chains with correct numbering

> 6_solution_0 A:1-19 26-113 117-172
GGCGGCAGGUGCUCCCGACGUCGGGAGUUAAAAGGGA

170308 Add fixing missing atoms of bases, and O2'

... many things! :-)

~2011 Prelimiary version as rnastruc, yapdb_parser etc.