mmagnus/rna-tools issues and pull requests

#147 - rna_pdb_tools.py -- TypeError when running --edit option

Issue - State: closed - Opened by mjustynaPhD 5 months ago - 2 comments

#146 - `rna_pdb_tools.py --get-ss` causes NameError.

Issue - State: closed - Opened by TakumiOtagaki 6 months ago - 1 comment

#145 - rna_pdb_tools.py with fetch cif files as well

Issue - State: open - Opened by mmagnus 9 months ago
Labels: feature request

#144 - rna_pdb_tools.py with fetch for given residue

Issue - State: open - Opened by mmagnus 9 months ago
Labels: feature request

#143 - --rpr function causes signififant change in the coordinates

Issue - State: closed - Opened by akashbahai 10 months ago - 2 comments

#142 - rna_pdb_tools.py: command not found

Issue - State: closed - Opened by akashbahai 11 months ago - 4 comments

#141 - rna_pdb_inspect.py

Issue - State: open - Opened by mmagnus 11 months ago - 1 comment
Labels: in progress

#140 - rna std add gaps and modified residues to output

Issue - State: open - Opened by mmagnus 12 months ago
Labels: enhancement, feature request

#139 - fix rpr for 1ehz [trna]

Issue - State: closed - Opened by mmagnus 12 months ago - 1 comment

#138 - calc rmsd, target and the rest, without -t ?

Issue - State: open - Opened by mmagnus about 1 year ago
Labels: idea

#137 - calc rmsd: show rmsd without pandas and any other options

Issue - State: open - Opened by mmagnus about 1 year ago
Labels: feature request

#136 - --get-seq should be fasta fasta

Issue - State: open - Opened by mmagnus over 1 year ago
Labels: feature request

#135 - rna_pdb_tools.py --rpr 1ehz.pdb --replace-hetatm KeyError: "C3'"

Issue - State: open - Opened by mmagnus almost 2 years ago - 1 comment

#134 - binaries for Colab

Issue - State: open - Opened by mmagnus almost 2 years ago

#133 - for VARNA vis use varnaapi

Issue - State: open - Opened by mmagnus almost 2 years ago

#132 - rna_calc_inf web view

Issue - State: closed - Opened by mmagnus almost 2 years ago - 2 comments
Labels: rna-tools.online

#131 - clarna_app - NameError: name 'ClaRNA_play_path' is not defined

Issue - State: open - Opened by mmagnus almost 2 years ago

#130 - moderna missing data if installed with pip

Issue - State: closed - Opened by mmagnus about 2 years ago

#129 - Make it possible for RNAStructure to get initialized with a file

Issue - State: open - Opened by valentin994 about 2 years ago - 3 comments

#128 - web: better info when rmsd is not calculated

Issue - State: closed - Opened by mmagnus about 2 years ago
Labels: rna-tools.online

#127 - rna_minimize.py with build in --mdr

Issue - State: open - Opened by mmagnus about 2 years ago
Labels: md

#126 - missing /rna_tools/tools/clarna_play/ClaRNAlib/*

Issue - State: closed - Opened by pengzhangzhi about 2 years ago - 11 comments

#125 - md min, use 10A padding

Issue - State: open - Opened by mmagnus over 2 years ago
Labels: md

#124 - web [for online version]

Issue - State: open - Opened by mmagnus over 2 years ago
Labels: rna-tools.online

#123 - rna-tools --fetch rp12

Issue - State: open - Opened by mmagnus over 2 years ago
Labels: enhancement

#122 - pymol_preview_generator.py: checking the len will not work for pse files

Issue - State: open - Opened by mmagnus over 2 years ago
Labels: bug

#121 - select_fragment.py wil not work with digit chains, e.g. 6

Issue - State: open - Opened by mmagnus over 2 years ago

#120 - fix doc compilation

Issue - State: closed - Opened by mmagnus over 2 years ago
Labels: bug

#119 - mq: upload the final model

Issue - State: open - Opened by mmagnus over 2 years ago
Labels: mq

#118 - mq: review farfar2 wrapper

Issue - State: closed - Opened by mmagnus over 2 years ago

#117 - add --mdr get structures ready for MD

Issue - State: closed - Opened by mmagnus over 2 years ago

#116 - rna_pdb_toolsx.py -> rna_pdb_tools.py

Issue - State: open - Opened by mmagnus over 2 years ago
Labels: enhancement

#115 - Missing rna_clashscore.py

Issue - State: closed - Opened by febos almost 3 years ago - 1 comment

#114 - mqaprnascore.py: progress to ignored + new files (now it's only to new files)

Issue - State: closed - Opened by mmagnus almost 3 years ago
Labels: bug

#113 - mq: farna problem with csv headers

Issue - State: closed - Opened by mmagnus almost 3 years ago

#110 - rna_calc_inf.do_job in Jupyter Notebook: NameError: name 'args' is not defined

Issue - State: closed - Opened by mariagviegas about 3 years ago - 1 comment

#109 - fix bug at ipknot

Pull Request - State: closed - Opened by edge2992 almost 4 years ago - 1 comment

#108 - build(deps-dev): bump node-sass from 3.3.3 to 4.14.1 in /docs

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies

#106 - where is --get_simrna_ready ?

Issue - State: closed - Opened by filipsPL about 4 years ago - 4 comments

#104 - rna_pdb_toolsx.py --get-seq should warn that it does not work for proteins

Issue - State: closed - Opened by mmagnus over 4 years ago - 1 comment
Labels: enhancement

#103 - question on additional constraints

Issue - State: closed - Opened by ahorvath over 4 years ago - 5 comments

#102 - rna_calc_inf.py: must use stacking otherwise there is an error in inf_all

Issue - State: closed - Opened by mmagnus over 4 years ago

#101 - rna_calc_rmsd.py: sort the csv file according to rmsd

Issue - State: closed - Opened by mmagnus over 4 years ago
Labels: feature request

#100 - a new format for rna_pdb_toolsx.py --get-seq

Issue - State: closed - Opened by mmagnus over 4 years ago - 1 comment

#99 - Py3

Pull Request - State: closed - Opened by mmagnus almost 5 years ago - 1 comment

#98 - --un-nmr should start from 1 ;-)

Issue - State: closed - Opened by mmagnus almost 5 years ago

#97 - Clanstix: no multiprocessing, empty scores

Issue - State: closed - Opened by mmagnus about 5 years ago

#95 - code with new Feature for parallel processing and pvalue matrix

Issue - State: closed - Opened by iswaryapj about 5 years ago

#94 - Fix all underscores into dashes in arguments

Issue - State: closed - Opened by mmagnus about 5 years ago

#93 - Python3 for everything!

Issue - State: closed - Opened by mmagnus about 5 years ago - 1 comment
Labels: !!!!!!!!!!

#92 - run clanstixs in multi processor

Issue - State: closed - Opened by iswaryapj about 5 years ago - 2 comments
Labels: feature request

#91 - Clanstixs problem with group and coloring

Issue - State: closed - Opened by iswaryapj about 5 years ago - 2 comments
Labels: bug

#90 - Update rna_clanstix.py

Pull Request - State: closed - Opened by iswaryapj about 5 years ago

#89 - Update README.md

Pull Request - State: closed - Opened by m54x49 about 5 years ago

#88 - dot2ct():

Issue - State: closed - Opened by mmagnus about 5 years ago
Labels: feature request, easy-fix

#86 - UNK should be ? or something, not k

Issue - State: open - Opened by mmagnus about 5 years ago
Labels: enhancement

#85 - Merge RNAseq with RNAseq from the alignment module

Issue - State: open - Opened by mmagnus about 5 years ago
Labels: enhancement

#84 - --rpr fix TER and atom numbering

Issue - State: closed - Opened by mmagnus about 5 years ago - 1 comment

#83 - Pre release

Pull Request - State: closed - Opened by mmagnus about 5 years ago - 1 comment

#82 - Pre release

Pull Request - State: closed - Opened by mmagnus about 5 years ago - 1 comment

#81 - Documentation does not compile for rna-tools

Issue - State: closed - Opened by mmagnus about 5 years ago

#80 - Add --rename-chain

Pull Request - State: closed - Opened by mmagnus about 5 years ago

#79 - Pre release

Pull Request - State: closed - Opened by mmagnus about 5 years ago

#78 - Cannot install

Issue - State: closed - Opened by marrrcin about 5 years ago - 1 comment
Labels: feature request, !!!!!!!!!!

#77 - `--compact` is missing (?)

Issue - State: closed - Opened by mmagnus about 5 years ago

#76 - Pre release

Pull Request - State: closed - Opened by mmagnus about 5 years ago

#75 - Pre release

Pull Request - State: closed - Opened by mmagnus about 5 years ago

#73 - --split-alt-locations

Issue - State: open - Opened by mmagnus over 5 years ago
Labels: feature request

#72 - clanstix with smart group name picking

Issue - State: closed - Opened by mmagnus over 5 years ago - 1 comment

#71 - Handle input/K.pdb

Issue - State: closed - Opened by mmagnus over 5 years ago - 1 comment
Labels: bug

#70 - minor issue with progressbar

Issue - State: closed - Opened by kekexin714 over 5 years ago - 1 comment

#69 - Clean up various systems of tests in the package

Issue - State: open - Opened by mmagnus over 5 years ago
Labels: enhancement

#68 - mcfold with constraints in the console

Issue - State: closed - Opened by mmagnus over 5 years ago

#67 - remove_gaps() is not removing every gap present

Issue - State: closed - Opened by thedjofsis almost 6 years ago - 2 comments

#66 - Unable to parse a stockholm format file using rna-pdb-tools, but can do so using biopython

Issue - State: closed - Opened by thedjofsis almost 6 years ago - 1 comment

#65 - PyMOL4RNA: ss_all: name file as PyMOL name

Issue - State: closed - Opened by mmagnus about 6 years ago

#64 - Vienna RNA: use as a library not like os.system

Issue - State: open - Opened by mmagnus over 6 years ago
Labels: enhancement

#63 - If there is chain A already, rename chains will not work

Issue - State: closed - Opened by mmagnus over 6 years ago - 1 comment

#62 - GC SS_cons2 is not correctly parsed

Issue - State: open - Opened by mmagnus over 6 years ago - 1 comment
Labels: easy-fix

#61 - PDB files are getting truncated

Issue - State: closed - Opened by filipsPL over 6 years ago - 2 comments
Labels: bug

#60 - rna_compare.py: calc RMSD and INF in one script to one csv file

Issue - State: open - Opened by mmagnus over 6 years ago
Labels: feature request, easy-fix

#59 - rna_calc_inf.py: WC (AU, GC) canonical change annotation, make it more clear

Issue - State: open - Opened by mmagnus over 6 years ago
Labels: feature request

#58 - rename chains, use syntax A>B

Issue - State: open - Opened by mmagnus over 6 years ago - 1 comment
Labels: feature request

#57 - find_seq should give back a list of hits

Issue - State: open - Opened by mmagnus over 6 years ago
Labels: feature request, easy-fix

#56 - FIX this commit rna_pdb_tools_lib.py - TER 24 G A 37 -> TER for now

Issue - State: closed - Opened by mmagnus almost 7 years ago
Labels: bug, !!!!!!!!!!

#55 - rna pdb toolsx (py3, fix imports)

Pull Request - State: closed - Opened by mmagnus almost 7 years ago

#54 - Rnanarchix

Pull Request - State: closed - Opened by mmagnus almost 7 years ago

#53 - --get_rnapuzzle_ready made nanotube from rybosime

Issue - State: closed - Opened by Aazyla about 7 years ago - 3 comments

#52 - Fix Useless Use of ls * in the docs

Issue - State: closed - Opened by mmagnus about 7 years ago
Labels: easy-fix

#51 - --get_rnapuzzle_ready and --renumber_residues don't like each other

Issue - State: closed - Opened by Aazyla about 7 years ago

#50 - Delete Nt "yg" after -get_rnapuzle_ready

Issue - State: closed - Opened by Aazyla about 7 years ago

#49 - Seq.py - report an error if no correct method is chosen

Issue - State: closed - Opened by mmagnus about 7 years ago

#48 - Generated PDB files have incompatible HEADER line

Issue - State: closed - Opened by tzok about 7 years ago - 2 comments

#47 - Work on files

Pull Request - State: closed - Opened by mmagnus about 7 years ago

#46 - PR test to myself

Pull Request - State: closed - Opened by mmagnus about 7 years ago - 1 comment

#45 - work on a list of files: rna_pdb_tools.py --delete B:67-75 --inplace *.pdb

Issue - State: closed - Opened by mmagnus about 7 years ago

#44 - in RNApuzzle ready, add an option `--dont_rename_chains`

Issue - State: closed - Opened by mmagnus about 7 years ago

#43 - get_seq: chains are not in the order as in the file

Issue - State: closed - Opened by mmagnus about 7 years ago

#42 - test.sh -- logging is triggered?

Issue - State: closed - Opened by mmagnus about 7 years ago - 1 comment

#41 - rnastruc_inspect_pdb.py 3b4c_1.pdb

Issue - State: open - Opened by mmagnus about 7 years ago
Labels: feature request

GitHub / mmagnus/rna-tools issues and pull requests